M3i

Keith G, Heitzler J, el Adlouni C, Glasser A L, Fix C, Desgres J, Dirheimer G

The primary structure of cytoplasmic initiator tRNA(Met) from Schizosaccharomyces pombe Article de journal

Dans: Nucleic Acids Res, vol. 21, no. 12, p. 2949, 1993, ISBN: 8332511, (0305-1048 Journal Article).

Liens | BibTeX | Étiquettes: Base Sequence Molecular Sequence Data RNA, Fungal/*chemistry RNA, Met/*chemistry Schizosaccharomyces/*genetics, Transfer, Unité ARN

Jaeger L, Westhof E, Michel F

Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3' terminal intron components Article de journal

Dans: J Mol Biol, vol. 234, no. 2, p. 331-346, 1993, ISBN: 8230218, (0022-2836 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Bacteriophage T4/*genetics Base Sequence Enzyme Activation Enzyme Stability Introns/*physiology Models, Catalytic/drug effects/*metabolism/radiation effects RNA, Molecular Molecular Sequence Data Nucleic Acid Denaturation/physiology RNA, Non-U.S. Gov't Thermodynamics Ultraviolet Rays, Unité ARN, Viral/drug effects/*metabolism/radiation effects Support

@article{,

title = {Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3' terminal intron components},

author = {L Jaeger and E Westhof and F Michel},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8230218},

isbn = {8230218},

year  = {1993},

date = {1993-01-01},

journal = {J Mol Biol},

volume = {234},

number = {2},

pages = {331-346},

abstract = {We have studied the mechanism by which the 3' terminal domain of the sunY intron of bacteriophage T4 activates the group I ribozyme core of this intron, from which it is separated by some 800 nucleotides. As shown by monitoring either UV absorbance or self-splicing reaction kinetics as a function of temperature, intron transcripts undergo highly cooperative unfolding/inactivation upon heating: the two methods yield similar estimates of the thermodynamic parameters associated with this process. Such cooperativity makes it possible in turn to assess the energetic contribution of specific interactions to the overall structure, by comparing the sensitivity to heat inactivation of molecules carrying various nucleotide substitutions. By combining this approach with chemical modification, we have probed several proven or putative interactions between the core and 3' terminal domain of the intron and conclude that the role of the 3' terminal domain is to stabilize the active form of the ribozyme. Interestingly, the P9.0 interaction, which brings 3' terminal nucleotides next to the core site that binds the guanosine cofactor of the self-splicing reaction, is now shown to be composed in fact of two distinct pairings. An isolated base-pair (P9.0a), involving a residue located only six nucleotides upstream of the 3' splice site, participates in the stabilization of the ribozyme and appears to persist during the second stage of self-splicing (exon ligation). In contrast, formation of the previously demonstrated P9.0b pairing, which involves the two penultimate intron nucleotides, contributes no additional stability and results in no detectable rearrangement of the core structure. Implications for the concept of a static ribozyme are discussed in the light of a slightly revised three-dimensional model of the sunY intron.},

note = {0022-2836 

Journal Article},

keywords = {Bacteriophage T4/*genetics  Base Sequence  Enzyme Activation  Enzyme Stability  Introns/*physiology  Models, Catalytic/drug effects/*metabolism/radiation effects  RNA, Molecular  Molecular Sequence Data  Nucleic Acid Denaturation/physiology  RNA, Non-U.S. Gov't  Thermodynamics  Ultraviolet Rays, Unité ARN, Viral/drug effects/*metabolism/radiation effects  Support},

pubstate = {published},

tppubtype = {article}

}

Fermer

Isel C, Marquet R, Keith G, Ehresmann C, Ehresmann B

Modified nucleotides of tRNA(3Lys) modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription Article de journal

Dans: J Biol Chem, vol. 268, no. 34, p. 25269-25272, 1993, ISBN: 7503978, (0021-9258 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Anticodon/genetics/metabolism Base Sequence Binding Sites Comparative Study DNA Primers HIV-1/genetics/*metabolism HIV-1 Reverse Transcriptase HIV-2/genetics/metabolism Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Genetic *Transcription, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/*biosynthesis RNA-Directed DNA Polymerase/*metabolism SIV/genetics/metabolism Support

@article{,

title = {Modified nucleotides of tRNA(3Lys) modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription},

author = {C Isel and R Marquet and G Keith and C Ehresmann and B Ehresmann},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7503978},

isbn = {7503978},

year  = {1993},

date = {1993-01-01},

journal = {J Biol Chem},

volume = {268},

number = {34},

pages = {25269-25272},

abstract = {In all retroviruses, reverse transcription is primed by a tRNA whose 3' end 18 nucleotides are complementary to the so called viral primer binding site. Previous work showed that reverse transcription of HIV-1 RNA is initiated by tRNA(3Lys). Using a variety of chemical and enzymatic structural probes, we investigated the interactions between HIV-1 RNA and its natural primer tRNA(3Lys). In addition to the predictable contacts between the viral primer binding site and the 3' end of tRNA(3Lys), a specific interaction takes place between an A-rich loop located upstream of the primer binding site region and the anticodon loop of tRNA(3Lys). This AAAA/Umcm5s2UUU loop-loop interaction is not observed when the natural primer is replaced by an in vitro synthesized tRNA(3Lys) transcript. Furthermore, dethiolation of the modified nucleotide mcm5s2U at position 34 of tRNA(3Lys) strongly destabilizes this interaction. Sequence and structure comparisons indicate that the primer/template loop-loop interaction is conserved in all HIV-1 isolates, and possibly also in HIV-2 and SIV.},

note = {0021-9258 

Journal Article},

keywords = {Anticodon/genetics/metabolism  Base Sequence  Binding Sites  Comparative Study  DNA Primers  HIV-1/genetics/*metabolism  HIV-1 Reverse Transcriptase  HIV-2/genetics/metabolism  Molecular Sequence Data  Nucleic Acid Conformation  RNA, Genetic, Genetic  *Transcription, Lys/*metabolism  RNA, MARQUET, Non-U.S. Gov't  Templates, Transfer, Unité ARN, Viral/*biosynthesis  RNA-Directed DNA Polymerase/*metabolism  SIV/genetics/metabolism  Support},

pubstate = {published},

tppubtype = {article}

}

Fermer

Hou Y M, Westhof E, Giege R

An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA Article de journal

Dans: Proc Natl Acad Sci U S A, vol. 90, no. 14, p. 6776-6780, 1993, ISBN: 8341698, (0027-8424 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Amino Acyl-tRNA Ligases/*metabolism Base Sequence Escherichia coli/*chemistry/genetics/metabolism Hydrogen Bonding Models, Cys/*chemistry/genetics/metabolism Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN

@article{,

title = {An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA},

author = {Y M Hou and E Westhof and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8341698},

isbn = {8341698},

year  = {1993},

date = {1993-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {90},

number = {14},

pages = {6776-6780},

abstract = {The nucleotides in a tRNA that specifically interact with the cognate aminoacyl-tRNA synthetase have been found largely located in the helical stems, the anticodon, or the discriminator base, where they vary from one tRNA to another. The conserved and semiconserved nucleotides that are responsible for the tRNA tertiary structure have been shown to have little role in synthetase recognition. Here we report that aminoacylation of Escherichia coli tRNA(Cys) depends on the anticodon, the discriminator base, and a tertiary interaction between the semiconserved nucleotides at positions 15 and 48. While all other tRNAs contain a purine at position 15 and a complementary pyrimidine at position 48 that establish the tertiary interaction known as the Levitt pair, E. coli tRNA(Cys) has guanosine -15 and -48. Replacement of guanosine -15 or -48 with cytidine virtually eliminates aminoacylation. Structural analyses with chemical probes suggest that guanosine -15 and -48 interact through hydrogen bonds between the exocyclic N-2 and ring N-3 to stabilize the joining of the two long helical stems of the tRNA. This tertiary interaction is different from the traditional base pairing scheme in the Levitt pair, where hydrogen bonds would form between N-1 and O-6. Our results provide evidence for a role of RNA tertiary structure in synthetase recognition.},

note = {0027-8424 

Journal Article},

keywords = {Amino Acyl-tRNA Ligases/*metabolism  Base Sequence  Escherichia coli/*chemistry/genetics/metabolism  Hydrogen Bonding  Models, Cys/*chemistry/genetics/metabolism  Support, Molecular  Molecular Sequence Data  *Nucleic Acid Conformation  RNA, Non-U.S. Gov't, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Gilmer D, Allmang C, Ehresmann C, Guilley H, Richards K, Jonard G, Ehresmann B

The secondary structure of the 5'-noncoding region of beet necrotic yellow vein virus RNA 3: evidence for a role in viral RNA replication Article de journal

Dans: Nucleic Acids Res, vol. 21, no. 6, p. 1389-1395, 1993, ISBN: 8464729, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence Gene Expression Hydrogen Bonding Molecular Sequence Data Mutagenesis, Messenger/genetics RNA, Site-Directed Nucleic Acid Conformation Plant Viruses/*genetics/ultrastructure Promoter Regions (Genetics) RNA Viruses/*genetics/ultrastructure RNA, Unité ARN, Viral/chemistry/*genetics/ultrastructure Vegetables *Virus Replication

@article{,

title = {The secondary structure of the 5'-noncoding region of beet necrotic yellow vein virus RNA 3: evidence for a role in viral RNA replication},

author = {D Gilmer and C Allmang and C Ehresmann and H Guilley and K Richards and G Jonard and B Ehresmann},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8464729},

isbn = {8464729},

year  = {1993},

date = {1993-01-01},

journal = {Nucleic Acids Res},

volume = {21},

number = {6},

pages = {1389-1395},

abstract = {Secondary structure-sensitive chemical and enzymatic probes have been used to produce a model for the folding of the first 312 residues of the long 5'-noncoding region of beet necrotic yellow vein virus RNA 3. The structure consists of two major domains, one of which includes long distance base-pairing interactions between two short sequence elements (Box I and Box II) situated between positions 237 and 292 and complementary elements (Box I' and II') near the 5'-terminus. Previous studies have shown that base pairing between these sequence elements (in either the plus-strand or minus-strand RNA) is important for RNA 3 accumulation during infection. RNA 3 transcripts were produced containing mutations which preferentially disrupted Box II-II' base pairing in either the plus- or minus-strand. In infection experiments, transcripts with mutations which disrupted the Box II-II' interaction in the plus-strand structure replicated less efficiently than mutants in which the Box II-II' interaction was disrupted in the minus-strand. These findings indicate that the complex 5'-proximal plus-strand structure to which the Box II-II' interaction contributes comprises at least part of the promoter for plus-strand RNA synthesis.},

note = {0305-1048 

Journal Article},

keywords = {Base Sequence  Gene Expression  Hydrogen Bonding  Molecular Sequence Data  Mutagenesis, Messenger/genetics  RNA, Site-Directed  Nucleic Acid Conformation  Plant Viruses/*genetics/ultrastructure  Promoter Regions (Genetics)  RNA Viruses/*genetics/ultrastructure  RNA, Unité ARN, Viral/chemistry/*genetics/ultrastructure  Vegetables  *Virus Replication},

pubstate = {published},

tppubtype = {article}

}

Fermer

Giege R, Puglisi J D, Florentz C

tRNA structure and aminoacylation efficiency Article de journal

Dans: Prog Nucleic Acid Res Mol Biol, vol. 45, p. 129-206, 1993, ISBN: 8341800, (0079-6603 Journal Article Review Review, Academic).

Liens | BibTeX | Étiquettes: Acylation Amino Acids/metabolism Amino Acyl-tRNA Ligases/metabolism Animals Base Sequence Dna Human Molecular Sequence Data *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't, Transfer/*chemistry/metabolism Support, Unité ARN

Giege R, Florentz C, Dreher T W

The TYMV tRNA-like structure Article de journal

Dans: Biochimie, vol. 75, no. 7, p. 569-582, 1993, ISBN: 8268257, (0300-9084 Journal Article Review Review, Tutorial).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence Molecular Sequence Data *Nucleic Acid Conformation RNA, FLORENTZ, Transfer/*chemistry/metabolism RNA, Unité ARN, Viral/*chemistry/metabolism Tymovirus/*genetics

Frugier M, Florentz C, Schimmel P, Giege R

Triple aminoacylation specificity of a chimerized transfer RNA Article de journal

Dans: Biochemistry, vol. 32, no. 50, p. 14053-14061, 1993, ISBN: 8268184, (0006-2960 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Acylation Alanine/metabolism Base Sequence Chimera Escherichia coli/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation Phenylalanine/metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/genetics Support, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Support, P.H.S. Valine/metabolism, Transfer, U.S. Gov't, Unité ARN

Fritsch V, Ravishanker G, Beveridge D L, Westhof E

Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations Article de journal

Dans: Biopolymers, vol. 33, no. 10, p. 1537-1552, 1993, ISBN: 8218922, (0006-3525 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence Chemistry, Physical Comparative Study Computer Simulation Molecular Sequence Data Poly dA-dT/*chemistry Solvents Thermodynamics, Unité ARN

@article{,

title = {Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations},

author = {V Fritsch and G Ravishanker and D L Beveridge and E Westhof},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8218922},

isbn = {8218922},

year  = {1993},

date = {1993-01-01},

journal = {Biopolymers},

volume = {33},

number = {10},

pages = {1537-1552},

abstract = {The program AMBER 3.0 has been used to generate molecular dynamics trajectories of a poly(dA).poly(dT) decamer. The simulations were performed using different methods to treat solvent effects. Results of a simulation including 18 counterions NH4+ and 4109 water molecules under (N, P, T) conditions were compared to simulation runs with implicit solvent representation in which solvent screening effects were represented by the use of a sigmoidal distance-dependent dielectric function. In the latter case, the system was simulated under microcanonical (N, V, E) and canonical (N, V, T) conditions. For the fully hydrated system simulation, a preequilibration protocol was developed since it was observed that long and progressive periods of heating and equilibration on the overall system were necessary in order to avoid energetic collisions between the solute and the solvent molecules, leading to severe irreversible deformation of the solute. A detailed analysis of DNA conformations, sugar puckers, and stability of the hydrogen bonds, Watson-Crick and three-center H bonds, is reported. The results show that DNA remains essentially in the B conformer with a tendency in the hydrated model to adopt a slightly distorted, unwound, and stretched conformation in comparison to standard B-DNA. Concerning sugar puckers, the mean pseudorotation phases of the adenine residues are systematically higher than those of the thymine residues, except in the case of the hydrated model for which a articular behavior is observed for the adenine strand. In this case, the terminal bases oscillate between C2'-endo and O4'-endo and the central ones stay in the C3'-endo domain. The mean lifetimes of the internal Watson-Crick H-bond (A) HN6.O4(T) are also dependent on the base pairs included in the calculation, excepted for the implicit solvent simulation at constant temperature. The three-center H bonds have very small mean lifetimes in all three cases of MD simulation. In the minor groove of the hydrated model, a spine of hydration is found as observed by x-ray crystallography and other theoretical simulations. On the basis of the rms deviations, it appears that the fully hydrated simulation has not reached a plateau at the end of the run, while the implicit simulation at constant energy seems to have converged. At constant temperature, very large oscillations in rms deviations are observed.},

note = {0006-3525 

Journal Article},

keywords = {Base Sequence  Chemistry, Physical  Comparative Study  Computer Simulation  Molecular Sequence Data  Poly dA-dT/*chemistry  Solvents  Thermodynamics, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

The program AMBER 3.0 has been used to generate molecular dynamics trajectories of a poly(dA).poly(dT) decamer. The simulations were performed using different methods to treat solvent effects. Results of a simulation including 18 counterions NH4+ and 4109 water molecules under (N, P, T) conditions were compared to simulation runs with implicit solvent representation in which solvent screening effects were represented by the use of a sigmoidal distance-dependent dielectric function. In the latter case, the system was simulated under microcanonical (N, V, E) and canonical (N, V, T) conditions. For the fully hydrated system simulation, a preequilibration protocol was developed since it was observed that long and progressive periods of heating and equilibration on the overall system were necessary in order to avoid energetic collisions between the solute and the solvent molecules, leading to severe irreversible deformation of the solute. A detailed analysis of DNA conformations, sugar puckers, and stability of the hydrogen bonds, Watson-Crick and three-center H bonds, is reported. The results show that DNA remains essentially in the B conformer with a tendency in the hydrated model to adopt a slightly distorted, unwound, and stretched conformation in comparison to standard B-DNA. Concerning sugar puckers, the mean pseudorotation phases of the adenine residues are systematically higher than those of the thymine residues, except in the case of the hydrated model for which a articular behavior is observed for the adenine strand. In this case, the terminal bases oscillate between C2'-endo and O4'-endo and the central ones stay in the C3'-endo domain. The mean lifetimes of the internal Watson-Crick H-bond (A) HN6.O4(T) are also dependent on the base pairs included in the calculation, excepted for the implicit solvent simulation at constant temperature. The three-center H bonds have very small mean lifetimes in all three cases of MD simulation. In the minor groove of the hydrated model, a spine of hydration is found as observed by x-ray crystallography and other theoretical simulations. On the basis of the rms deviations, it appears that the fully hydrated simulation has not reached a plateau at the end of the run, while the implicit simulation at constant energy seems to have converged. At constant temperature, very large oscillations in rms deviations are observed.

Fermer

Felden B, Florentz C, Westhof E, Giege R

Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA Article de journal

Dans: Biochimie, vol. 75, no. 12, p. 1143-1157, 1993, ISBN: 8199250, (0300-9084 Journal Article Review Review, Tutorial).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence Bromovirus/*genetics Computer Simulation Genome, FLORENTZ, Molecular Molecular Sequence Data Mutation/genetics Nucleic Acid Conformation Promoter Regions (Genetics) RNA, Non-U.S. Gov't Tyrosine-tRNA Ligase/chemistry/*metabolism, Transfer/*chemistry/genetics/metabolism RNA, Unité ARN, Viral Models, Viral/*chemistry/genetics/metabolism Structure-Activity Relationship Support

@article{,

title = {Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA},

author = {B Felden and C Florentz and E Westhof and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8199250},

isbn = {8199250},

year  = {1993},

date = {1993-01-01},

journal = {Biochimie},

volume = {75},

number = {12},

pages = {1143-1157},

abstract = {A 3-D model of the tyrosylable tRNA-like domain of the genomic brome mosaic virus RNAs was built by computer modelling based on solution probing of the molecule with different chemical and enzymatic reagents. This model encompasses four major structural domains, including two peculiar substructures oriented perpendicularly and mimicking a tRNA structure, and a fifth domain which makes the connection with the rest of the viral RNA. After recalling the different steps that led to the present structural knowledge of the BMV tRNA-like domain, we review its novel structural features revealed by the modelling and that did not appear in older versions of 3-D models of this structure. These features comprise additional base-pairs, hairpin loops, new tertiary long-range interactions, and a second pseudoknot. The main goal of this paper is to strengthen the validity of the model by establishing correlations between the putative 3-D conformation and the functional properties of the domain. For that, we show how the present structural model rationalises mutagenic and footprinting data that have established the importance of specific regions of the RNA for its recognition and aminoacylation by yeast tyrosyl-tRNA synthetase. We discuss further how the model corroborates mutational analyses performed to understand recognition of this RNA domain by the (ATP,CTP):tRNA nucleotidyl-transferase and by the viral replicase. The published mutants of the BMV tRNA-like domain fall into two classes. In one class, the mutants leave unchanged the overall architecture of the molecule, thereby affecting functions directly. In the second class, the overall architecture of the mutants is perturbed, and thus functions are affected indirectly.},

note = {0300-9084 

Journal Article 

Review 

Review, Tutorial},

keywords = {Base Sequence  Bromovirus/*genetics  Computer Simulation  Genome, FLORENTZ, Molecular  Molecular Sequence Data  Mutation/genetics  Nucleic Acid Conformation  Promoter Regions (Genetics)  RNA, Non-U.S. Gov't  Tyrosine-tRNA Ligase/chemistry/*metabolism, Transfer/*chemistry/genetics/metabolism  RNA, Unité ARN, Viral  Models, Viral/*chemistry/genetics/metabolism  Structure-Activity Relationship  Support},

pubstate = {published},

tppubtype = {article}

}

Fermer

Eriani G, Cavarelli J, Martin F, Dirheimer G, Moras D, Gangloff J

Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline Article de journal

Dans: Proc Natl Acad Sci U S A, vol. 90, no. 22, p. 10816-10820, 1993, ISBN: 8248175, (0027-8424 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Asp/metabolism Saccharomyces cerevisiae/chemistry Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*chemistry Fungal Proteins/chemistry Kinetics Macromolecular Systems Models, ERIANI, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Proline/chemistry Protein Binding Protein Conformation RNA, Transfer, Unité ARN

@article{,

title = {Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline},

author = {G Eriani and J Cavarelli and F Martin and G Dirheimer and D Moras and J Gangloff},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8248175},

isbn = {8248175},

year  = {1993},

date = {1993-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {90},

number = {22},

pages = {10816-10820},

abstract = {Cytoplasmic aspartyl-tRNA synthetase (AspRS; EC 6.1.1.12) from yeast is, as are most class II synthetases, an alpha 2 dimer. The only invariant amino acid in signature motif 1 of this class is Pro-273; this residue is located at the dimer interface. To understand the role of Pro-273 in the conserved dimeric configuration, we tested the effect of a Pro-273-->Gly (P273G) substitution on the catalytic properties of homo- and heterodimeric AspRS. Heterodimers of AspRS were produced in vivo by overexpression of their respective subunit variants from plasmid-encoded genes and purified to homogeneity in one HPLC step. The homodimer containing the P273G shows an 80% inactivation of the enzyme and an affinity decrease for its cognate tRNA(Asp) of one order of magnitude. The P273G-mutated subunit recovered wild-type enzymatic properties when associated with a native subunit or a monomer otherwise inactivated having an intact dimeric interface domain. These results, which can be explained by the crystal structure of the native enzyme complexed with its substrates, confirm the structural importance of Pro-273 for dimerization and clearly establish the functional interdependence of the AspRS subunits. More generally, the dimeric conformation may be a structural prerequisite for the activity of mononucleotide binding sites constructed from antiparallel beta strands.},

note = {0027-8424 

Journal Article},

keywords = {Asp/metabolism  Saccharomyces cerevisiae/chemistry  Structure-Activity Relationship  Support, Aspartate-tRNA Ligase/*chemistry  Fungal Proteins/chemistry  Kinetics  Macromolecular Systems  Models, ERIANI, Molecular  Mutagenesis, Non-U.S. Gov't, Site-Directed  Proline/chemistry  Protein Binding  Protein Conformation  RNA, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

el Adlouni C, Keith G, Dirheimer G, Szarkowski J W, Przykorska A

Rye nuclease I as a tool for structural studies of tRNAs with large variable arms Article de journal

Dans: Nucleic Acids Res, vol. 21, no. 4, p. 941-947, 1993, ISBN: 8383845, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Animals Anticodon Base Sequence Cattle Molecular Sequence Data Nucleic Acid Conformation *Nucleotidases RNA, Leu/chemistry RNA, Non-U.S. Gov't, Ser/chemistry Saccharomyces cerevisiae Secale cereale/*enzymology Support, Transfer, Transfer/*chemistry RNA, Unité ARN

@article{,

title = {Rye nuclease I as a tool for structural studies of tRNAs with large variable arms},

author = {C el Adlouni and G Keith and G Dirheimer and J W Szarkowski and A Przykorska},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8383845},

isbn = {8383845},

year  = {1993},

date = {1993-01-01},

journal = {Nucleic Acids Res},

volume = {21},

number = {4},

pages = {941-947},

abstract = {A single-strand-specific nuclease from rye germ (Rn nuclease I) was used for secondary and tertiary structure investigations of tRNAs with large variable arms (class II tRNAs). We have studied the structure in solution of two recently sequenced tRNA(Leu): yeast tRNA(Leu)(ncm5UmAA) and bovine tRNA(Leu)(XmAA) as well as yeast tRNA(Leu)(UAG), tRNA(Leu)(m5CAA) and tRNA(Ser)(IGA). The latter is the only tRNA with a long variable arm for which the secondary and tertiary structure has already been studied by use of chemical probes and computer modelling. The data obtained in this work showed that the general model of class II tRNAs proposed by others for tRNA(Ser) can be extended to tRNAs(Leu) as well. However interesting differences in the structure of tRNAs(Leu) versus tRNA(Ser)(IGA) were also noticed. The main difference was observed in the accessibility of the variable loops to nucleolytic attack of Rn nuclease I: variable loops of all studied tRNA(Leu) species were cut by Rn nuclease I, while that of yeast tRNA(Ser)(IGA) was not. This could be due to differences in stability of the variable arms and the lengths of their loops which are 3 and 4 nucleotides in tRNA(Ser)(IGA) and tRNAs(Leu) respectively.},

note = {0305-1048 

Journal Article},

keywords = {Animals  Anticodon  Base Sequence  Cattle  Molecular Sequence Data  Nucleic Acid Conformation  *Nucleotidases  RNA, Leu/chemistry  RNA, Non-U.S. Gov't, Ser/chemistry  Saccharomyces cerevisiae  Secale cereale/*enzymology  Support, Transfer, Transfer/*chemistry  RNA, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Brunel C, Romby P, Moine H, Caillet J, Grunberg-Manago M, Springer M, Ehresmann B, Ehresmann C

Translational regulation of the Escherichia coli threonyl-tRNA synthetase gene: structural and functional importance of the thrS operator domains Article de journal

Dans: Biochimie, vol. 75, no. 12, p. 1167-1179, 1993, ISBN: 8199252, (0300-9084 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Bacterial/*genetics Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) Point Mutation Protein Structure, Base Sequence Escherichia coli/*enzymology/genetics Gene Deletion Gene Expression Regulation, Genetic, Messenger/chemistry/metabolism RNA, Met/chemistry/metabolism Ribosomes/metabolism Structure-Activity Relationship Support, Non-U.S. Gov't Threonine-tRNA Ligase/chemistry/*genetics/metabolism Translation, ROMBY, Secondary RNA, Transfer, Unité ARN

@article{,

title = {Translational regulation of the Escherichia coli threonyl-tRNA synthetase gene: structural and functional importance of the thrS operator domains},

author = {C Brunel and P Romby and H Moine and J Caillet and M Grunberg-Manago and M Springer and B Ehresmann and C Ehresmann},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8199252},

isbn = {8199252},

year  = {1993},

date = {1993-01-01},

journal = {Biochimie},

volume = {75},

number = {12},

pages = {1167-1179},

abstract = {Previous work showed that E coli threonyl-tRNA synthetase (ThrRS) binds to the leader region of its own mRNA and represses its translation by blocking ribosome binding. The operator consists of four distinct domains, one of them (domain 2) sharing structural analogies with the anticodon arm of the E coli tRNA(Thr). The regulation specificity can be switched by using tRNA identity rules, suggesting that the operator could be recognized by ThrRS as a tRNA-like structure. In the present paper, we investigated the relative contribution of the four domains to the regulation process by using deletions and point mutations. This was achieved by testing the effects of the mutations on RNA conformation (by probing experiments), on ThrRS recognition (by footprinting experiments and measure of the competition with tRNA(Thr) for aminoacylation), on ribosome binding and ribosome/ThrRS competition (by toeprinting experiments). It turns out that: i) the four domains are structurally and functionally independent; ii) domain 2 is essential for regulation and contains the major structural determinants for ThrRS binding; iii) domain 4 is involved in control and ThrRS recognition, but to a lesser degree than domain 2. However, the previously described analogies with the acceptor-like stem are not functionally significant. How it is recognized by ThrRS remains to be resolved; iv) domain 1, which contains the ribosome loading site, is not involved in ThrRS recognition. The binding of ThrRS probably masks the ribosome binding site by steric hindrance and not by direct contacts. This is only achieved when ThrRS interacts with both domains 2 and 4; and v) the unpaired domain 3, which connects domains 2 and 4, is not directly involved in ThrRS recognition. It should serve as an articulation to provide an appropriate spacing between domains 2 and 4. Furthermore, it is possibly involved in ribosome binding.},

note = {0300-9084 

Journal Article},

keywords = {Bacterial/*genetics  Molecular Sequence Data  Mutation  Nucleic Acid Conformation  *Operator Regions (Genetics)  Point Mutation  Protein Structure, Base Sequence  Escherichia coli/*enzymology/genetics  Gene Deletion  Gene Expression Regulation, Genetic, Messenger/chemistry/metabolism  RNA, Met/chemistry/metabolism  Ribosomes/metabolism  Structure-Activity Relationship  Support, Non-U.S. Gov't  Threonine-tRNA Ligase/chemistry/*genetics/metabolism  Translation, ROMBY, Secondary  RNA, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Baudin F, Marquet R, Isel C, Darlix J L, Ehresmann B, Ehresmann C

Functional sites in the 5' region of human immunodeficiency virus type 1 RNA form defined structural domains Article de journal

Dans: J Mol Biol, vol. 229, no. 2, p. 382-397, 1993, ISBN: 8429553, (0022-2836 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Electrophoresis, Genetic, MARQUET, Non-U.S. Gov't Translation, Polyacrylamide Gel HIV-1/*genetics Molecular Sequence Data Nucleic Acid Conformation RNA, Unité ARN, Viral/*chemistry/metabolism Rabbits Support

@article{,

title = {Functional sites in the 5' region of human immunodeficiency virus type 1 RNA form defined structural domains},

author = {F Baudin and R Marquet and C Isel and J L Darlix and B Ehresmann and C Ehresmann},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8429553},

isbn = {8429553},

year  = {1993},

date = {1993-01-01},

journal = {J Mol Biol},

volume = {229},

number = {2},

pages = {382-397},

abstract = {The 5' region of HIV-1 RNA contains functional elements involved in key steps of the retroviral cycle, such as genomic RNA transcription, splicing, translation, dimerization or initiation of reverse transcription. In the present work, we investigated the conformation of the first 500 nucleotides covering the RNA leader and the 5' gag coding sequences of HIV-MAL, using chemical probing. We provide detailed information on almost each nucleotide at one of their Watson-Crick positions and on position N-7 of purines. Experiments were conducted on two in vitro transcribed RNA fragments (1 to 707 and 1 to 311). A secondary structure model was derived by combining the experimental data, computer predictions and sequence comparison. Under conditions favoring dimerization (high salt concentration), HIV-1 RNA folds into independent structural domains that can be related to defined functional regions. The first domain corresponds to TAR forming a stable stem-loop. Intrinsic structural features are found to stabilize the TAR hairpin loop. The second domain (nucleotides 56 to 299) contains the PBS sequence, which is located in a stable subdomain constrained by a four stem junction (nucleotides 139 to 218). Although the MAL isolate has an insertion near the PBS, probably resulting from the duplication of a 23-nucleotide sequence, the structural organization of this subdomain is conserved in all other HIV-1 isolates. The third domain (nucleotides 300 to 404) contains the splice donor site, packaging and dimerization elements and the AUG initiation codon of gag. A major result is the structural versatility of this region. Two mutually exclusive structures, both equally in agreement with probing data, could modulate the different functions involving this domain. The reduced accessibility of the gag translational initiation site possibly accounts for the low efficiency of the in vitro translation of the dimer. Finally, the 5' gag coding sequences form a metastable domain.},

note = {0022-2836 

Journal Article},

keywords = {Animals  Base Sequence  Electrophoresis, Genetic, MARQUET, Non-U.S. Gov't  Translation, Polyacrylamide Gel  HIV-1/*genetics  Molecular Sequence Data  Nucleic Acid Conformation  RNA, Unité ARN, Viral/*chemistry/metabolism  Rabbits  Support},

pubstate = {published},

tppubtype = {article}

}

Fermer

Baron C, Westhof E, Bock A, Giege R

Solution structure of selenocysteine-inserting tRNA(Sec) from Escherichia coli. Comparison with canonical tRNA(Ser) Article de journal

Dans: J Mol Biol, vol. 231, no. 2, p. 274-292, 1993, ISBN: 8510147, (0022-2836 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Adenine/chemistry Aspergillus Nuclease S1/pharmacology Base Sequence Comparative Study Escherichia coli/*chemistry Guanine/chemistry Lead/pharmacology Models, Amino Acid-Specific/*chemistry/drug effects RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Ser/*chemistry/drug effects Selenocysteine/*metabolism Sequence Homology, Transfer, Unité ARN

@article{,

title = {Solution structure of selenocysteine-inserting tRNA(Sec) from Escherichia coli. Comparison with canonical tRNA(Ser)},

author = {C Baron and E Westhof and A Bock and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8510147},

isbn = {8510147},

year  = {1993},

date = {1993-01-01},

journal = {J Mol Biol},

volume = {231},

number = {2},

pages = {274-292},

abstract = {Selenocysteine-inserting tRNAs (or tRNA(Sec)) are structurally untypical tRNAs that are charged by seryl-tRNA synthetase before being recognized by the selenocysteine synthase that converts serine into selenocysteine. tRNA(Sec) from Escherichia coli contains 95 nucleotides and is the longest tRNA known to date, in contrast to canonical tRNA(Ser), 88 nucleotides-long. We have studied its solution conformation by chemical and enzymatic probing. Global structural features were obtained by cobra venom and S1 nuclease mapping, as well as by probing with Pb2+. Accessibilities of phosphate groups were measured by ethylnitrosourea probing. Information about positions in bases involved in Watson-Crick pairing, in stacking or in tertiary interactions were obtained by chemical probing with dimethylsulfate, diethylpyrocarbonate, kethoxal and carbodiimide. On the basis of these chemical data, a three-dimensional model was constructed by computer modeling and compared to that of canonical tRNA(Ser). tRNA(Sec) resembles tRNA(Ser) at the level of its T-arm and anticodon-arm conformations, as well as at the joining of the D- and T-loops by a tertiary Watson-Crick G19-C56 interaction. Its extra-long variable arm is a double-stranded structure closed by a four nucleotide loop that is linked to the body of the tRNA in a way different from that found in tRNA(Ser). As anticipated from the peculiar features of the sequence in the D-loop and at the junction of amino acid and D-arms, tRNA(Sec) possesses a novel but restricted set of tertiary interactions in the core of its three-dimensional structure: a G8-A21-U14 triple pair and a novel interaction between C16 of the D-loop and C59 of the T-loop. A third triple interaction involving C15-G20a-G48 is suggested but some experimental evidence for it is still lacking. It is furthermore concluded that the D-arm has six base-pairs instead of three, as in canonical class II tRNA(Ser), with the D-loop containing only four nucleotides. Finally, the amino acid accepting arm forms a stack of eight Watson-Crick base-pairs (instead of 7 in other tRNAs). The biological relevance of this model with regard to interaction with seryl-tRNA synthetase and enzymes from the selenocysteine metabolism is discussed.},

note = {0022-2836 

Journal Article},

keywords = {Adenine/chemistry  Aspergillus Nuclease S1/pharmacology  Base Sequence  Comparative Study  Escherichia coli/*chemistry  Guanine/chemistry  Lead/pharmacology  Models, Amino Acid-Specific/*chemistry/drug effects  RNA, Molecular  Molecular Sequence Data  Nucleic Acid Conformation  RNA, Non-U.S. Gov't, Nucleic Acid  Support, Ser/*chemistry/drug effects  Selenocysteine/*metabolism  Sequence Homology, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Selenocysteine-inserting tRNAs (or tRNA(Sec)) are structurally untypical tRNAs that are charged by seryl-tRNA synthetase before being recognized by the selenocysteine synthase that converts serine into selenocysteine. tRNA(Sec) from Escherichia coli contains 95 nucleotides and is the longest tRNA known to date, in contrast to canonical tRNA(Ser), 88 nucleotides-long. We have studied its solution conformation by chemical and enzymatic probing. Global structural features were obtained by cobra venom and S1 nuclease mapping, as well as by probing with Pb2+. Accessibilities of phosphate groups were measured by ethylnitrosourea probing. Information about positions in bases involved in Watson-Crick pairing, in stacking or in tertiary interactions were obtained by chemical probing with dimethylsulfate, diethylpyrocarbonate, kethoxal and carbodiimide. On the basis of these chemical data, a three-dimensional model was constructed by computer modeling and compared to that of canonical tRNA(Ser). tRNA(Sec) resembles tRNA(Ser) at the level of its T-arm and anticodon-arm conformations, as well as at the joining of the D- and T-loops by a tertiary Watson-Crick G19-C56 interaction. Its extra-long variable arm is a double-stranded structure closed by a four nucleotide loop that is linked to the body of the tRNA in a way different from that found in tRNA(Ser). As anticipated from the peculiar features of the sequence in the D-loop and at the junction of amino acid and D-arms, tRNA(Sec) possesses a novel but restricted set of tertiary interactions in the core of its three-dimensional structure: a G8-A21-U14 triple pair and a novel interaction between C16 of the D-loop and C59 of the T-loop. A third triple interaction involving C15-G20a-G48 is suggested but some experimental evidence for it is still lacking. It is furthermore concluded that the D-arm has six base-pairs instead of three, as in canonical class II tRNA(Ser), with the D-loop containing only four nucleotides. Finally, the amino acid accepting arm forms a stack of eight Watson-Crick base-pairs (instead of 7 in other tRNAs). The biological relevance of this model with regard to interaction with seryl-tRNA synthetase and enzymes from the selenocysteine metabolism is discussed.

Fermer

Baranowski W, Tomaszewski J, Keith G

[Methylation of DNA in tissue of ovarian malignant tumors in women] Article de journal

Dans: Ginekol Pol, vol. 64, no. 4, p. 169-173, 1993, ISBN: 8282237, (0017-0011 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Adult Carcinoma/genetics DNA, Neoplasm/*metabolism English Abstract Female Human Methylation Middle Aged Ovarian Neoplasms/*genetics Sertoli Cell Tumor/genetics, Unité ARN

Baranowski W, Tomaszewski J, Keith G

Unusual deficiency of the modified purine base queuine in transfer ribonucleic acid from the human placenta as tested by enzymatic assay Article de journal

Dans: Am J Obstet Gynecol, vol. 169, no. 3, p. 581-582, 1993, ISBN: 8372867, (0002-9378 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Female Guanine/*analogs & derivatives/chemistry Human Placenta/*chemistry Pregnancy RNA, Transfer/*chemistry, Unité ARN

Pfeiffer P, Jung J L, Heitzler J, Keith G

Unusual structure of the double-stranded RNA associated with the '447' cytoplasmic male sterility in Vicia faba Article de journal

Dans: J Gen Virol, vol. 74, no. Pt 6, p. 1167-1173, 1993, ISBN: 7685375, (0022-1317 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence Cytoplasm Extrachromosomal Inheritance/*genetics Fabaceae/*genetics Inclusion Bodies, Genetic, Medicinal Pollen/genetics RNA/*genetics/isolation & purification RNA Replicase/metabolism Transcription, Unité ARN, Viral Infertility/genetics Molecular Sequence Data *Plants

@article{,

title = {Unusual structure of the double-stranded RNA associated with the '447' cytoplasmic male sterility in Vicia faba},

author = {P Pfeiffer and J L Jung and J Heitzler and G Keith},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7685375},

isbn = {7685375},

year  = {1993},

date = {1993-01-01},

journal = {J Gen Virol},

volume = {74},

number = {Pt 6},

pages = {1167-1173},

abstract = {The 16.7 kbp dsRNA specific to the '447' cytoplasmic male sterility (CMS) line of Vicia faba was labelled in vitro with [alpha-32P]ATP and poly(A) polymerase, and by T4 RNA ligase-mediated addition of [32P]pCp. Analysis of the reaction products under denaturing conditions revealed in both cases extensive labelling of a 4.5 kb ssRNA, already detected in previous experiments in which the RNA-dependent RNA polymerase associated with the dsRNA was allowed to pursue RNA synthesis on preinitiated complexes. Mobility shift analysis of total pCp-labelled dsRNA revealed not two but three different 3' termini. The most prominent sequencing pattern corresponded to the 4.5 kb ssRNA, indicating that this RNA species has a preferentially accessible, free 3' OH extremity. Northern blot analysis of the denatured dsRNA confirmed that the 4.5 kb ssRNA is a subgenomic mRNA and detected its counterpart of about 12 kb. Nearly all 16.7 kbp dsRNA molecules featured an interrupted positive-sense strand, indicating a marked prevalence of transcription over replication complexes. This unusual strategy of transcription by a strand displacement mechanism, following initiation at an internal discontinuity, is compared with that of other dsRNA viruses or defective viruses, and is discussed in relation to the expression of the CMS trait.},

note = {0022-1317 

Journal Article},

keywords = {Base Sequence  Cytoplasm  Extrachromosomal Inheritance/*genetics  Fabaceae/*genetics  Inclusion Bodies, Genetic, Medicinal  Pollen/genetics  RNA/*genetics/isolation & purification  RNA Replicase/metabolism  Transcription, Unité ARN, Viral  Infertility/genetics  Molecular Sequence Data  *Plants},

pubstate = {published},

tppubtype = {article}

}

Fermer

Wilhelm M L, Keith G, Fix C, Wilhelm F X

Pleiotropic effect of a point mutation in the yeast SUP4-o tRNA gene: in vivo pre-tRNA processing in S. cerevisiae Article de journal

Dans: Nucleic Acids Res, vol. 20, no. 4, p. 791-796, 1992, ISBN: 1542574, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence Blotting, Fungal/*genetics Genes, Fungal/genetics/metabolism RNA, Northern Genes, Suppressor/*genetics Introns/genetics Molecular Sequence Data Mutation/genetics RNA Precursors/*metabolism RNA, Transfer, Tyr/*genetics/metabolism Saccharomyces cerevisiae/*genetics/metabolism, Unité ARN

@article{,

title = {Pleiotropic effect of a point mutation in the yeast SUP4-o tRNA gene: in vivo pre-tRNA processing in S. cerevisiae},

author = {M L Wilhelm and G Keith and C Fix and F X Wilhelm},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1542574},

isbn = {1542574},

year  = {1992},

date = {1992-01-01},

journal = {Nucleic Acids Res},

volume = {20},

number = {4},

pages = {791-796},

abstract = {The expression of mutant tyrosine-inserting ochre suppressor SUP4-o tRNA genes in vivo in S. cerevisiae was examined as a basis for further studies of tRNA transcription and processing. In vivo yeast precursor tRNAs have been identified by filter hybridization and primer extension analysis. We have previously shown that a mutant SUP4-o tRNA gene with a C52----A52 transversion at positive 52 (C52----A52(+IVS) allele) was transcribed but that the primary transcript was not processed correctly. We show here that 5' and 3' end processing as well as splicing are defective for this mutant but that the 5' end processing is restored when the intron is removed from the gene by oligonucleotide directed mutagenesis (C52----A52(-IVS) allele). Our results imply that the C52----A52 transversion by itself cannot account for the lack of susceptibility to RNase P cleavage but that the overall tertiary structure of the mutant tRNA precursor is destabilized by the intron/anticodon stem. A second consequence of the C52----A52 transversion is to prevent complete maturation of the tRNA precursor at its 3' end since intermediates containing incompletely processed 3' trailers accumulate in the yeast cells transformed with the C52----A52(-IVS) allele. A correct structure of the T stem might therefore define a structural feature required for the recognition of the 3' processing activity.},

note = {0305-1048 

Journal Article},

keywords = {Base Sequence  Blotting, Fungal/*genetics  Genes, Fungal/genetics/metabolism  RNA, Northern  Genes, Suppressor/*genetics  Introns/genetics  Molecular Sequence Data  Mutation/genetics  RNA Precursors/*metabolism  RNA, Transfer, Tyr/*genetics/metabolism  Saccharomyces cerevisiae/*genetics/metabolism, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Wilhelm M L, Baranowski W, Keith G, Wilhelm F X

Rapid transfer of small RNAs from a polyacrylamide gel onto a nylon membrane using a gel dryer Article de journal

Dans: Nucleic Acids Res, vol. 20, no. 15, p. 4106, 1992, ISBN: 1508703, (0305-1048 Journal Article).

Liens | BibTeX | Étiquettes: 5S/*isolation & purification RNA, Acrylic Resins Human Nylons RNA, Ribosomal, Small Nuclear/*isolation & purification RNA, Transfer/*isolation & purification Yeasts/genetics, Unité ARN

Westhof E, Michel F

Some tertiary motifs of RNA foldings Chapitre d'ouvrage

Dans: Lilley, D M J; Heumann, H; Suck, D (Ed.): Structural Tools for the Analysis of Protein-Nucleic Acid Complexes (Advances in Life Sciences), p. 255-267, Birkhauser Verlag, Basel, 1992.

Liens | BibTeX | Étiquettes: Unité ARN

Westhof E, Jaeger L

RNA pseudoknots Article de journal

Dans: Curr Opin Struct Biol, vol. 2, no. 3, p. 327-333, 1992.

Résumé | Liens | BibTeX | Étiquettes: Unité ARN

Westhof E

Westhof's rule Article de journal

Dans: Nature, vol. 358, no. 6386, p. 459-460, 1992, ISBN: 1641036, (0028-0836 Letter).

Liens | BibTeX | Étiquettes: *Hydrogen Bonding *Nucleic Acid Conformation, Unité ARN, WESTHOF

Tounekti N, Mougel M, Roy C, Marquet R, Darlix J L, Paoletti J, Ehresmann B, Ehresmann C

Effect of dimerization on the conformation of the encapsidation Psi domain of Moloney murine leukemia virus RNA Article de journal

Dans: J Mol Biol, vol. 223, no. 1, p. 205-220, 1992, ISBN: 1731069, (0022-2836 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence Comparative Study Hydrogen Bonding Macromolecular Systems Molecular Sequence Data Molecular Structure Moloney murine leukemia virus/*ultrastructure Nucleic Acid Conformation Phylogeny RNA, MARQUET, Non-U.S. Gov't, Unité ARN, Viral/chemistry/*ultrastructure Sequence Alignment Support

@article{,

title = {Effect of dimerization on the conformation of the encapsidation Psi domain of Moloney murine leukemia virus RNA},

author = {N Tounekti and M Mougel and C Roy and R Marquet 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=1731069},

isbn = {1731069},

year  = {1992},

date = {1992-01-01},

journal = {J Mol Biol},

volume = {223},

number = {1},

pages = {205-220},

abstract = {In Moloney murine leukemia virus, the encapsidation Psi element was shown to be necessary and sufficient to promote packaging of viral RNA, and to be required for dimerization. The conformation of the Psi domain (nucleotides 215 to 565) was investigated in solution by chemical probing. The four bases were monitored at one of their Watson-Crick positions with dimethylsulfate at cytosine N3 and adenosine N1, and with a carbodiimide derivative at guanosine N1 and uridine N3. Position N7 of adenine residues was probed with diethylpyrocarbonate. The analyses were conducted on in vitro transcribed fragments corresponding either to the isolated Psi domain or to the 5'-terminal 725 nucleotides. The RNA fragments were analyzed in their monomeric and dimeric forms. A secondary structure model was derived from probing data, computer prediction and sequence analysis of related murine retroviruses. One major result is that Psi forms an independent and highly structured domain. Dimerization induces an extensive reduction of reactivity in region 278 to 309 that can be interpreted as the result of intermolecular interactions and/or intramolecular conformational rearrangements. A second region (around position 215) was shown to display discrete reactivity changes upon dimerization. These two regions represent likely elements of dimerization. More unexpectedly, reactivity changes (essentially enhancement of reactivity) were also detected in another part of Psi (around position 480) not believed to contain elements of dimerization. These reactivity changes could be interpreted as dimerization-induced allosteric transitions.},

note = {0022-2836 

Journal Article},

keywords = {Base Sequence  Comparative Study  Hydrogen Bonding  Macromolecular Systems  Molecular Sequence Data  Molecular Structure  Moloney murine leukemia virus/*ultrastructure  Nucleic Acid Conformation  Phylogeny  RNA, MARQUET, Non-U.S. Gov't, Unité ARN, Viral/chemistry/*ultrastructure  Sequence Alignment  Support},

pubstate = {published},

tppubtype = {article}

}

Fermer

Sturchler C, Carbon P, Krol A

An additional long-range interaction in human U1 snRNA Article de journal

Dans: Nucleic Acids Res, vol. 20, no. 6, p. 1215-1221, 1992, ISBN: 1532853, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites Hela Cells Human Molecular Sequence Data Mutagenesis, Site-Directed Nucleic Acid Conformation RNA, Small Nuclear, Small Nuclear/*chemistry/metabolism Ribonucleases/metabolism Ribonucleoproteins/metabolism Ribonucleoproteins, Unité ARN

Skouri M, Munch J P, Lorber B, Giege R, Candau S

Interaction between lysozyme molecules under precrystallization conditions studied by light scattering. Article de journal

Dans: J Crystal Growth, vol. 122, no. 1-4, p. 14-20, 1992, ISBN: 10.1016/0022-0248(92)90221-4.

Résumé | Liens | BibTeX | Étiquettes: Unité ARN

Senger B, Despons L, Walter P, Fasiolo F

The anticodon triplet is not sufficient to confer methionine acceptance to a transfer RNA Article de journal

Dans: Proc Natl Acad Sci U S A, vol. 89, no. 22, p. 10768-10771, 1992, ISBN: 1438273, (0027-8424 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Anticodon/genetics/*metabolism Base Sequence Kinetics Methionine/*metabolism Models, Genetic, Met/genetics/*metabolism Saccharomyces cerevisiae/*genetics Support, Non-U.S. Gov't Transcription, Structural Molecular Sequence Data Nucleic Acid Conformation RNA, Transfer, Unité ARN

Rudinger J, Puglisi J D, Putz J, Schatz D, Eckstein F, Florentz C, Giege R

Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase Article de journal

Dans: Proc Natl Acad Sci U S A, vol. 89, no. 13, p. 5882-5886, 1992, ISBN: 1631068, (0027-8424 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/*metabolism Saccharomyces cerevisiae/enzymology Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*metabolism Base Sequence Binding Sites DNA Mutational Analysis Fungal Proteins/metabolism Molecular Sequence Data Protein Binding RNA, FLORENTZ, Fungal/chemistry/metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN

@article{,

title = {Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase},

author = {J Rudinger and J D Puglisi and J Putz and D Schatz and F Eckstein and C Florentz and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1631068},

isbn = {1631068},

year  = {1992},

date = {1992-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {89},

number = {13},

pages = {5882-5886},

abstract = {The interaction of wild-type and mutant yeast tRNA(Asp) transcripts with yeast aspartyl-tRNA synthetase (AspRS; EC 6.1.1.12) has been probed by using iodine cleavage of phosphorothioate-substituted transcripts. AspRS protects phosphates in the anticodon (G34, U35), D-stem (U25), and acceptor end (G73) that correspond to determinant nucleotides for aspartylation. This protection, as well as that in anticodon stem (C29, U40, G41) and D-stem (U11 to U13), is consistent with direct interaction of AspRS at these phosphates. Other protection, in the variable loop (G45), D-loop (G18, G19), and T-stem and loop (G53, U54, U55), as well as enhanced reactivity at G37, may result from conformational changes of the transcript upon binding to AspRS. Transcripts mutated at determinant positions showed a loss of phosphate protection in the region of the mutation while maintaining the global protection pattern. The ensemble of results suggests that aspartylation specificity arises from both protein-base and protein-phosphate contacts and that different regions of tRNA(Asp) interact independently with AspRS. A mutant transcript of yeast tRNA(Phe) that contains the set of identity nucleotides for specific aspartylation gave a phosphate protection pattern strikingly similar to that of wild-type tRNA(Asp). This confirms that a small number of nucleotides within a different tRNA sequence context can direct specific interaction with synthetase.},

note = {0027-8424 

Journal Article},

keywords = {Asp/chemistry/*metabolism  Saccharomyces cerevisiae/enzymology  Structure-Activity Relationship  Support, Aspartate-tRNA Ligase/*metabolism  Base Sequence  Binding Sites  DNA Mutational Analysis  Fungal Proteins/metabolism  Molecular Sequence Data  Protein Binding  RNA, FLORENTZ, Fungal/chemistry/metabolism  RNA, Non-U.S. Gov't, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Rudinger J, Florentz C, Dreher T, Giege R

Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA Article de journal

Dans: Nucleic Acids Res, vol. 20, no. 8, p. 1865-1870, 1992, ISBN: 1579487, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence Codon/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data Mosaic Viruses/enzymology/genetics/*metabolism Mutation/genetics Nucleic Acid Conformation RNA, FLORENTZ, His/*metabolism RNA, Non-P.H.S. Yeasts/enzymology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN, Viral/*metabolism Support

@article{,

title = {Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA},

author = {J Rudinger and C Florentz and T Dreher and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1579487},

isbn = {1579487},

year  = {1992},

date = {1992-01-01},

journal = {Nucleic Acids Res},

volume = {20},

number = {8},

pages = {1865-1870},

abstract = {Mischarging of the valine specific tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA has been tested in the presence of purified arginyl-, aspartyl-, histidinyl-, and phenylalanyl-tRNA synthetases from bakers' yeast. Important mischarging of a 264 nucleotide-long transcript was found with histidinyl-tRNA synthetase which can acylate this fragment up to a level of 25% with a loss of specificity (expressed as Vmax/KM ratios) of only 100 fold as compared to a yeast tRNA(His) transcript. Experiments on transcripts of various lengths indicate that the minimal valylatable fragment (n = 88) is the most efficient substrate for histidinyl-tRNA synthetase, with kinetic characteristics similar to those found for the control tRNA(His) transcript. Mutations in the anticodon or adjacent to the 3' CCA that severely affect the valylation capacity of the 264 nucleotide long TYMV fragment are without negative effect on its mischarging, and for some cases even improve its efficiency. A short fragment (n = 42) of the viral RNA containing the pseudoknot and corresponding to the amino acid accepting branch of the molecule is an efficient histidine acceptor.},

note = {0305-1048 

Journal Article},

keywords = {Base Sequence  Codon/genetics  Histidine-tRNA Ligase/*metabolism  Kinetics  Molecular Sequence Data  Mosaic Viruses/enzymology/genetics/*metabolism  Mutation/genetics  Nucleic Acid Conformation  RNA, FLORENTZ, His/*metabolism  RNA, Non-P.H.S.  Yeasts/enzymology, Non-U.S. Gov't  Support, Transfer, U.S. Gov't, Unité ARN, Viral/*metabolism  Support},

pubstate = {published},

tppubtype = {article}

}

Fermer

Romby P, Brunel C, Caillet J, Springer M, Grunberg-Manago M, Westhof E, Ehresmann C, Ehresmann B

Molecular mimicry in translational control of E. coli threonyl-tRNA synthetase gene. Competitive inhibition in tRNA aminoacylation and operator-repressor recognition switch using tRNA identity rules Article de journal

Dans: Nucleic Acids Res, vol. 20, no. 21, p. 5633-5640, 1992, ISBN: 1280807, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Acylation Anticodon Base Sequence Binding, Bacterial Methionine-tRNA Ligase/metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/metabolism RNA, Competitive Escherichia coli/enzymology/*genetics *Gene Expression Regulation, Genetic, Met/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/antagonists & inhibitors/*genetics/metabolism Translation, ROMBY, Thr/metabolism Repressor Proteins/*metabolism Ribosomes/metabolism Support, Transfer, Transfer/*metabolism RNA, Unité ARN

@article{,

title = {Molecular mimicry in translational control of E. coli threonyl-tRNA synthetase gene. Competitive inhibition in tRNA aminoacylation and operator-repressor recognition switch using tRNA identity rules},

author = {P Romby and C Brunel and J Caillet and M Springer and M Grunberg-Manago and E Westhof and C Ehresmann and B Ehresmann},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1280807},

isbn = {1280807},

year  = {1992},

date = {1992-01-01},

journal = {Nucleic Acids Res},

volume = {20},

number = {21},

pages = {5633-5640},

abstract = {We previously showed that: (i) E.coli threonyl-tRNA synthetase (ThrRS) binds to the leader of its mRNA and represses translation by preventing ribosome binding to its loading site; (ii) the translational operator shares sequence and structure similarities with tRNA(Thr); (iii) it is possible to switch the specificity of the translational control from ThrRS to methionyl-tRNA synthetase (MetRS) by changing the CGU anticodon-like sequence to CAU, the tRNA(Met) anticodon. Here, we show that the wild type (CGU) and the mutated (CAU) operators act as competitive inhibitors of tRNA(Thr) and tRNA(fMet) for aminoacylation catalyzed by E.coli ThrRS and MetRS, respectively. The apparent Kd of the MetRS/CAU operator complex is one order magnitude higher than that of the ThrRS/CGU operator complex. Although ThrRS and MetRS shield the anticodon- and acceptor-like domains of their respective operators, the relative contribution of these two domains differs significantly. As in the threonine system, the interaction of MetRS with the CAU operator occludes ribosome binding to its loading site. The present data demonstrate that the anticodon-like sequence is one major determinant for the identity of the operator and the regulation specificity. It further shows that the tRNA-like operator obeys to tRNA identity rules.},

note = {0305-1048 

Journal Article},

keywords = {Acylation  Anticodon  Base Sequence  Binding, Bacterial  Methionine-tRNA Ligase/metabolism  Molecular Sequence Data  Mutation  Nucleic Acid Conformation  *Operator Regions (Genetics)  RNA, Bacterial/metabolism  RNA, Competitive  Escherichia coli/enzymology/*genetics  *Gene Expression Regulation, Genetic, Met/metabolism  RNA, Non-U.S. Gov't  Threonine-tRNA Ligase/antagonists & inhibitors/*genetics/metabolism  Translation, ROMBY, Thr/metabolism  Repressor Proteins/*metabolism  Ribosomes/metabolism  Support, Transfer, Transfer/*metabolism  RNA, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Rippe K, Fritsch V, Westhof E, Jovin T M

Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex Article de journal

Dans: EMBO J, vol. 11, no. 10, p. 3777-3786, 1992, ISBN: 1396571, (0261-4189 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence Circular Dichroism DNA/*chemistry Hydrogen Bonding Hydrogen-Ion Concentration Indicators and Reagents Magnesium Chloride Models, Fluorescence Spectrophotometry, MARQUET, Molecular Molecular Sequence Data *Nucleic Acid Conformation Oligodeoxyribonucleotides/*chemistry Spectrometry, PAILLART, Ultraviolet Structure-Activity Relationship Thermodynamics, Unité ARN, WESTHOF

@article{,

title = {Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex},

author = {K Rippe and V Fritsch and E Westhof and T M Jovin},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1396571},

isbn = {1396571},

year  = {1992},

date = {1992-01-01},

journal = {EMBO J},

volume = {11},

number = {10},

pages = {3777-3786},

abstract = {The oligonucleotides d[(G-A)7G] and d[(G-A)12G] self-associate under physiological conditions (10 mM MgCl2, neutral pH) into a stable double-helical structure (psRR-DNA) in which the two polypurine strands are in a parallel orientation in contrast to the antiparallel disposition of conventional B-DNA. We have characterized psRR-DNA by gel electrophoresis, UV absorption, vacuum UV circular dichroism, monomer-excimer fluorescence of oligonucleotides end-labelled with pyrene, and chemical probing with diethyl pyrocarbonate and dimethyl sulfate. The duplex is stable at pH 4-9, suggesting that the structure is compatible with, but does not require, protonation of the A residues. The data support a model derived from force-field analysis in which the parallel-stranded d(G-A)n helix is right-handed and constituted of alternating, symmetrical Gsyn.Gsyn and Aanti.Aanti base pairs with N1H.O6 and N6H.N7 hydrogen bonds, respectively. This dinucleotide structure may be the source of a negative peak observed at 190 nm in the vacuum UV CD spectrum, a feature previously reported only for left-handed Z-DNA. The related sequence d[(GAAGGA)4G] also forms a parallel-stranded duplex but one that is less stable and probably involves a slightly different secondary structure. We discuss the potential intervention of psRR-DNA in recombination, gene expression and the stabilization of genomic structure.},

note = {0261-4189 

Journal Article},

keywords = {Base Sequence  Circular Dichroism  DNA/*chemistry  Hydrogen Bonding  Hydrogen-Ion Concentration  Indicators and Reagents  Magnesium Chloride  Models, Fluorescence  Spectrophotometry, MARQUET, Molecular  Molecular Sequence Data  *Nucleic Acid Conformation  Oligodeoxyribonucleotides/*chemistry  Spectrometry, PAILLART, Ultraviolet  Structure-Activity Relationship  Thermodynamics, Unité ARN, WESTHOF},

pubstate = {published},

tppubtype = {article}

}

Fermer

Przykorska A, el Adlouni C, Keith G, Szarkowski J W, Dirheimer G

Structural specificity of Rn nuclease I as probed on yeast tRNA(Phe) and tRNA(Asp) Article de journal

Dans: Nucleic Acids Res, vol. 20, no. 4, p. 659-663, 1992, ISBN: 1542562, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/*metabolism RNA, Base Composition Base Sequence Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Yeasts/genetics, Pancreatic/*metabolism Secale cereale Substrate Specificity Support, Phe/chemistry/genetics/*metabolism Ribonuclease, Transfer, Unité ARN

Perret V, Florentz C, Puglisi J D, Giege R

Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities Article de journal

Dans: J Mol Biol, vol. 226, no. 2, p. 323-333, 1992, ISBN: 1640453, (0022-2836 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Amino Acid Activation Aspartate-tRNA Ligase/*metabolism Base Sequence Molecular Sequence Data Nucleic Acid Conformation Phenylalanine-tRNA Ligase/*metabolism RNA, Asp/metabolism/*ultrastructure RNA, FLORENTZ, Fungal/metabolism/ultrastructure RNA, Non-U.S. Gov't, Phe/metabolism/*ultrastructure Saccharomyces cerevisiae Structure-Activity Relationship Substrate Specificity Support, Transfer, Unité ARN

@article{,

title = {Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities},

author = {V Perret and C Florentz and J D Puglisi and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1640453},

isbn = {1640453},

year  = {1992},

date = {1992-01-01},

journal = {J Mol Biol},

volume = {226},

number = {2},

pages = {323-333},

abstract = {The structure and function of in vitro transcribed tRNA(Asp) variants with inserted conformational features characteristic of yeast tRNA(Phe), such as the length of the variable region or the arrangement of the conserved residues in the D-loop, have been investigated. Although they exhibit significant conformational alterations as revealed by Pb2+ treatment, these variants are still efficiently aspartylated by yeast aspartyl-tRNA synthetase. Thus, this synthetase can accommodate a variety of tRNA conformers. In a second series of variants, the identity determinants of yeast tRNA(Phe) were transplanted into the previous structural variants of tRNA(Asp). The phenylalanine acceptance of these variants improves with increasing the number of structural characteristics of tRNA(Phe), suggesting that phenylalanyl-tRNA synthetase is sensitive to the conformational frame embedding the cognate identity nucleotides. These results contrast with the efficient transplantation of tRNA(Asp) identity elements into yeast tRNA(Phe). This indicates that synthetases respond differently to the detailed conformation of their tRNA substrates. Efficient aminoacylation is not only dependent on the presence of the set of identity nucleotides, but also on a precise conformation of the tRNA.},

note = {0022-2836 

Journal Article},

keywords = {Amino Acid Activation  Aspartate-tRNA Ligase/*metabolism  Base Sequence  Molecular Sequence Data  Nucleic Acid Conformation  Phenylalanine-tRNA Ligase/*metabolism  RNA, Asp/metabolism/*ultrastructure  RNA, FLORENTZ, Fungal/metabolism/ultrastructure  RNA, Non-U.S. Gov't, Phe/metabolism/*ultrastructure  Saccharomyces cerevisiae  Structure-Activity Relationship  Substrate Specificity  Support, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Pauly M, Treger M, Westhof E, Chambon P

The initiation accuracy of the SV40 early transcription is determined by the functional domains of two TATA elements Article de journal

Dans: Nucleic Acids Res, vol. 20, no. 5, p. 975-982, 1992, ISBN: 1312710, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA Mutational Analysis DNA, Genetic/*genetics, Non-U.S. Gov't TATA Box/*genetics Transcription, Unité ARN, Viral/*genetics Hela Cells Human Molecular Sequence Data Nucleic Acid Conformation Simian virus 40/*genetics Support, Viral/chemistry/genetics Electrophoresis Genes, WESTHOF

Nothwang H G, Coux O, Keith G, Silva-Pereira I, Scherrer K

The major RNA in prosomes of HeLa cells and duck erythroblasts is tRNA(Lys,3) Article de journal

Dans: Nucleic Acids Res, vol. 20, no. 8, p. 1959-1965, 1992, ISBN: 1579498, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Blotting, Gel, Lys/*analysis/metabolism Ribonucleoproteins/*chemistry/drug effects Support, Non-U.S. Gov't Zinc/pharmacology, Northern Ducks Electrophoresis, Transfer, Two-Dimensional Erythroblasts Hela Cells Human Molecular Sequence Data RNA Nucleotidyltransferases/metabolism RNA, Unité ARN

Myslinski E, Krol A, Carbon P

Optimal tRNA((Ser)Sec) gene activity requires an upstream SPH motif Article de journal

Dans: Nucleic Acids Res, vol. 20, no. 2, p. 203-209, 1992, ISBN: 1311068, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*genetics Recombinant Fusion Proteins/genetics/metabolism Simian virus 40/*genetics Support, Animals Base Sequence DNA Mutational Analysis DNA-Binding Proteins/genetics Enhancer Elements (Genetics)/*genetics/physiology Gene Expression Regulation/*genetics Molecular Sequence Data Promoter Regions (Genetics)/genetics RNA, Non-U.S. Gov't TATA Box/genetics Xenopus laevis/*genetics, Small Nuclear/genetics RNA, Transfer, Unité ARN

@article{,

title = {Optimal tRNA((Ser)Sec) gene activity requires an upstream SPH motif},

author = {E Myslinski and A Krol and P Carbon},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1311068},

isbn = {1311068},

year  = {1992},

date = {1992-01-01},

journal = {Nucleic Acids Res},

volume = {20},

number = {2},

pages = {203-209},

abstract = {The X. laevis tRNA((Ser)Sec) gene is different from the other tRNA genes in that its promoter contains two external elements, a PSE and a TATA box functionally equivalent to those of the U6 snRNA gene. Of the two internal promoters governing classical tRNA gene transcription, only subsists the internal B box. In this report, we show that the tRNA((Ser)Sec) contains in addition an activator element (AE) which we have mapped by extensive mutagenesis. Activation is only dependent on a 15 bp fragment residing between -209 and -195 and containing an SPH motif. In vitro, this element forms a complex with a nuclear protein which is different from the TEF-1 transcriptional activator that binds the SV40 Sph motifs. This AE is versatile since it shows capacity of activating a variety of genes in vivo, including U1 and U6 snRNAs and HSV thymidine kinase. Unexpectedly for an snRNA-related gene, the tRNA((Ser)Sec) is deprived of octamer or octamer-like motifs. The X.laevis tRNA((Ser)Sec) gene represents the first example of a Pol III snRNA-type gene whose activation of transcription is completely octamer-independent.},

note = {0305-1048 

Journal Article},

keywords = {Amino Acid-Specific/*genetics  Recombinant Fusion Proteins/genetics/metabolism  Simian virus 40/*genetics  Support, Animals  Base Sequence  DNA Mutational Analysis  DNA-Binding Proteins/genetics  Enhancer Elements (Genetics)/*genetics/physiology  Gene Expression Regulation/*genetics  Molecular Sequence Data  Promoter Regions (Genetics)/genetics  RNA, Non-U.S. Gov't  TATA Box/genetics  Xenopus laevis/*genetics, Small Nuclear/genetics  RNA, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Murgo S, Krol A, Carbon P

The differential transcriptional activity of two amphibian U1 small-nuclear RNA genes correlates with structural differences in the proximal sequence element Article de journal

Dans: Eur J Biochem, vol. 203, no. 3, p. 443-447, 1992, ISBN: 1735429, (0014-2956 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Ambystoma Animals Base Sequence Microinjections Molecular Sequence Data Mutagenesis, Genetic Xenopus laevis, Non-U.S. Gov't *Transcription, Nucleic Acid Sequence Homology, Nucleic Acid Support, Site-Directed Phylogeny RNA, Small Nuclear/*genetics *Regulatory Sequences, Unité ARN

@article{,

title = {The differential transcriptional activity of two amphibian U1 small-nuclear RNA genes correlates with structural differences in the proximal sequence element},

author = {S Murgo and A Krol and P Carbon},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1735429},

isbn = {1735429},

year  = {1992},

date = {1992-01-01},

journal = {Eur J Biochem},

volume = {203},

number = {3},

pages = {443-447},

abstract = {We previously analyzed the transcription of an axolotl U1 small-nuclear RNA (snRNA) gene (AmU1) by microinjection into Xenopus laevis oocytes. In such an assay, AmU1 showed a low template activity compared to that of an X. laevis U1 snRNA gene (XlU1B2). Swapping the proximal sequence element (PSE) with that of XlU1B2 was required for AmU1 to acquire a transcription level equal to that of XlU1B2. In the present work, we examine the functional importance of the nucleotides that are common or different in both PSEs with the aim of identifying which nucleotides within the Xenopus U1 PSE are critical for this enhancement of Ambystoma mexicanum U1 snRNA transcription. The PSE mutation analysis showed that the central, phylogenetically conserved C-58/C-57 doublet is absolutely required for U1 promoter activity. In the 3' portion of this element, a CGC to ATG change (positions -54/-52) which partially restores the XlU1B2 PSE sequence, enables the AmU1 gene to gain the same transcriptional activity as XlU1B2. Remarkably, in this clustered point mutation, the sole C-54 to A-54 change is sufficient to obtain this increased level. Therefore, the activity of the AmU1 gene in injected Xenopus oocytes is strongly affected by a single sequence difference between AmU1 and XlU1B2 PSEs. This finding underscores the crucial importance of the nucleotide identity at position -54 to the function of the Xenopus U1 PSE.},

note = {0014-2956 

Journal Article},

keywords = {Ambystoma  Animals  Base Sequence  Microinjections  Molecular Sequence Data  Mutagenesis, Genetic  Xenopus laevis, Non-U.S. Gov't  *Transcription, Nucleic Acid  Sequence Homology, Nucleic Acid  Support, Site-Directed  Phylogeny  RNA, Small Nuclear/*genetics  *Regulatory Sequences, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Michel F, Jaeger L, Westhof E, Kuras R, Tihy F, Xu M Q, Shub D A

Activation of the catalytic core of a group I intron by a remote 3' splice junction Article de journal

Dans: Genes Dev, vol. 6, no. 8, p. 1373-1385, 1992, ISBN: 1644285, (0890-9369 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA Mutational Analysis Escherichia coli/genetics Genes, Catalytic/genetics/*metabolism RNA, Messenger/genetics/*metabolism Support, P.H.S. T-Phages/genetics, U.S. Gov't, Unité ARN, Viral/*genetics Introns/genetics/*physiology Magnesium/metabolism Molecular Sequence Data Mutation/genetics Nucleic Acid Conformation Plasmids/genetics RNA Splicing/*genetics RNA

Meng Q C, King S J, Branham K E, DeLucas L J, Lorber B, Oparil S

Preparative isolation of angiotensin-converting enzyme from human lung. Article de journal

Dans: J Chromatogr, vol. 579, no. 1, p. 63-71, 1992.

Résumé | Liens | BibTeX | Étiquettes: Unité ARN

Lorber B, Giege R

Preparation and handling of biological macromolecules for crystallization. Chapitre d'ouvrage

Dans: Ducruix, A; Giegé, R (Ed.): Crystallization of Nucleic Acids and Proteins: A Practical Approach, p. 19-45, Oxford University Press, USA, 1992.

Liens | BibTeX | Étiquettes: Unité ARN

Lorber B, Giege R

A versatile reactor for temperature controlled crystallization of biological macromolecules. Article de journal

Dans: J Crystal Growth, vol. 122, no. 1-4, p. 168-175, 1992, ISBN: 10.1016/0022-0248(92)90240-J.

Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Unité ARN

Lescure A, Tebb G, Mattaj I W, Krol A, Carbon P

A factor with Sp1 DNA-binding specificity stimulates Xenopus U6 snRNA in vivo transcription by RNA polymerase III Article de journal

Dans: J Mol Biol, vol. 228, no. 2, p. 387-394, 1992, ISBN: 1453450, (0022-2836 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Binding Sites Dna Molecular Sequence Data RNA Polymerase III/*metabolism RNA, Genetic Xenopus, LESCURE, Non-U.S. Gov't Transcription Factor, Nucleic Acid Support, Small Nuclear/*genetics *Regulatory Sequences, Sp1/metabolism *Transcription, Unité ARN

Lescure A, Murgo S, Carbon P, Krol A

The proximal promoter and the start site cooperate to specify correct U1 snRNA transcription initiation by RNA polymerase II Article de journal

Dans: Nucleic Acids Res, vol. 20, no. 7, p. 1573-1578, 1992, ISBN: 1579449, (0305-1048 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence DNA/metabolism DNA Mutational Analysis Molecular Sequence Data Promoter Regions (Genetics)/*genetics RNA Polymerase II/*metabolism RNA, Genetic/*genetics Xenopus laevis/genetics, KROL, LESCURE, Non-U.S. Gov't Transcription, Small Nuclear/*genetics Support, Unité ARN

Lavignon M, Tounekti N, Rayner B, Imbach J L, Keith G, Paoletti J, Malvy C

Inhibition of murine leukemia viruses by nuclease-resistant alpha-oligonucleotides Article de journal

Dans: Antisense Res Dev, vol. 2, no. 4, p. 315-324, 1992, ISBN: 1292779, (1050-5261 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: 3T3 Cells Animals Base Sequence Binding Sites Culture Media Friend murine leukemia virus/*drug effects/genetics/physiology Mice Molecular Sequence Data Moloney murine leukemia virus/*drug effects/genetics/physiology Oligonucleotides, Antisense/metabolism/*pharmacology RNA, Genetic/drug effects, Genetic/drug effects Translation, Messenger/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Transcription, Unité ARN, Viral/chemistry/genetics/metabolism Support

Heitzler J, Marechal-Drouard L, Dirheimer G, Keith G

Use of a dot blot hybridization method for identification of pure tRNA species on different membranes Article de journal

Dans: Biochim Biophys Acta-Gene Regul Mech, vol. 1129, no. 3, p. 273-277, 1992, ISBN: 1536878, (0006-3002 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Artificial Nucleic Acid Hybridization RNA, Autoradiography *Membranes, Fungal/genetics RNA, Met/genetics Saccharomyces cerevisiae/genetics Support, Non-U.S. Gov't, Transfer, Transfer/*genetics RNA, Unité ARN

Graffe M, Dondon J, Caillet J, Romby P, Ehresmann C, Ehresmann B, Springer M

The specificity of translational control switched with transfer RNA identity rules Article de journal

Dans: Science, vol. 255, no. 5047, p. 994-996, 1992, ISBN: 1372129, (0036-8075 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Bacterial Genes, Bacterial Molecular Sequence Data Nucleic Acid Conformation RNA, Bacterial Proteins/metabolism Base Sequence DNA Mutational Analysis *Gene Expression Regulation, Bacterial/metabolism RNA, Genetic, Messenger/*metabolism/ultrastructure RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics/metabolism *Translation, ROMBY, Structural, Thr/*metabolism Support, Transfer, Unité ARN

Glasser A L, el Adlouni C, Keith G, Sochacka E, Malkiewicz A, Santos M, Tuite M F, Desgres J

Presence and coding properties of 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um) in the wobble position of the anticodon of tRNA(Leu) (U*AA) from brewer's yeast Article de journal

Dans: FEBS Lett, vol. 314, no. 3, p. 381-385, 1992, ISBN: 1468572, (0014-5793 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: *Anticodon Chromatography, Fungal/genetics RNA, High Pressure Liquid Fungal Proteins/biosynthesis Molecular Structure RNA, Leu/*genetics Saccharomyces cerevisiae/*genetics Spectrophotometry, Mass Support, Non-U.S. Gov't Uridine/*analogs & derivatives/analysis/chemistry/genetics, Transfer, Ultraviolet Spectrum Analysis, Unité ARN

Garcia A, Giege R

Footprinting evidence for close contacts of the yeast tRNA(Asp) anticodon region with aspartyl-tRNA synthetase Article de journal

Dans: Biochem Biophys Res Commun, vol. 186, no. 2, p. 956-962, 1992, ISBN: 1497679, (0006-291x Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Alkylation Anticodon/*metabolism Aspartate-tRNA Ligase/*metabolism Base Sequence Molecular Sequence Data Nucleic Acid Conformation Protein Binding RNA, Asp/genetics/isolation & purification/*metabolism Saccharomyces cerevisiae/enzymology/*genetics Sulfuric Acid Esters/metabolism/pharmacology Support, Non-U.S. Gov't, Transfer, Unité ARN

Frugier M, Florentz C, Giege R

Anticodon-independent aminoacylation of an RNA minihelix with valine Article de journal

Dans: Proc Natl Acad Sci U S A, vol. 89, no. 9, p. 3990-3994, 1992, ISBN: 1570324, (0027-8424 Journal Article).

Résumé | Liens | BibTeX | Étiquettes: *Amino Acid Activation Anticodon Base Sequence Hydrogen Bonding In Vitro Molecular Sequence Data RNA, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Valine-tRNA Ligase/*metabolism, Transfer, Unité ARN, Val/chemistry/*metabolism Saccharomyces cerevisiae Structure-Activity Relationship Support

Eiler S, Boeglin M, Martin F, Eriani G, Gangloff J, Thierry J C, Moras D

Crystallization of aspartyl-tRNA synthetase-tRNA(Asp) complex from Escherichia coli and first crystallographic results Article de journal

Dans: J Mol Biol, vol. 224, no. 4, p. 1171-1173,

Modèles Insectes d’Immunité Innée

Publications

1993

1992