Publications
2000
Benito Y, Kolb F A, Romby P, Lina G, Etienne J, Vandenesch F
In: RNA, vol. 6, no. 5, pp. 668-679, 2000, ISBN: 10836788, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Antisense/*chemistry/genetics/metabolism RNA, Bacterial Models, Bacterial/*chemistry/genetics/metabolism Ribosomes/metabolism Staphylococcal Protein A/*genetics Staphylococcus aureus/*chemistry/*genetics/metabolism Support, Base Sequence Binding Sites/genetics DNA Primers/genetics Escherichia coli/metabolism Gene Expression Genes, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, ROMBY, Unité ARN
@article{,
title = {Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression},
author = {Y Benito and F A Kolb and P Romby and G Lina and J Etienne and F Vandenesch},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10836788},
isbn = {10836788},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {5},
pages = {668-679},
abstract = {RNAIII, a 514-nt RNA molecule, regulates the expression of many Staphylococcus aureus genes encoding exoproteins and cell-wall-associated proteins. We have studied the structure of RNAIII in solution, using a combination of chemical and enzymatic probes. A model of the secondary structure was derived from experimental data with the help of computer simulation of RNA folding. The model contains 14 hairpin structures connected by unpaired nucleotides. The data also point to three helices formed by distant nucleotides that close off structural domains. This model was generally compatible with the results of in vivo probing experiments with dimethylsulfate in late exponential-phase cultures. Toe-printing experiments revealed that the ribosome binding site of hld, which is encoded by RNAIII, was accessible to the Escherichia coli 30S ribosomal subunit, suggesting that the in vitro structure represented a translatable form of RNAIII. We also found that, within the 3' end of RNAIII, the conserved hairpin 13 and the terminator form an intrinsic structural domain that exerts specific regulatory activity on protein A gene expression.},
note = {1355-8382
Journal Article},
keywords = {Antisense/*chemistry/genetics/metabolism RNA, Bacterial Models, Bacterial/*chemistry/genetics/metabolism Ribosomes/metabolism Staphylococcal Protein A/*genetics Staphylococcus aureus/*chemistry/*genetics/metabolism Support, Base Sequence Binding Sites/genetics DNA Primers/genetics Escherichia coli/metabolism Gene Expression Genes, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1996
Giege R, Florentz C, Kern D, Gangloff J, Eriani G, Moras D
Aspartate identity of transfer RNAs Journal Article
In: Biochimie, vol. 78, no. 7, pp. 605-623, 1996, ISBN: 8955904, (0300-9084 Journal Article Review Review, Tutorial).
Abstract | Links | BibTeX | Tags: Asp/*chemistry Saccharomyces cerevisiae Structure-Activity Relationship Support, Aspartate-tRNA Ligase/chemistry/metabolism Aspartic Acid/analysis Base Sequence Escherichia coli Models, ERIANI, FLORENTZ, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermus thermophilus, Transfer, Unité ARN
@article{,
title = {Aspartate identity of transfer RNAs},
author = {R Giege and C Florentz and D Kern and J Gangloff and G Eriani and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955904},
isbn = {8955904},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {605-623},
abstract = {Structure/function relationships accounting for specific tRNA charging by class II aspartyl-tRNA synthetases from Saccharomyces cerevisiae, Escherichia coli and Thermus thermophilus are reviewed. Effects directly linked to tRNA features are emphasized and aspects about synthetase contribution in expression of tRNA(Asp) identity are also covered. Major identity nucleotides conferring aspartate specificity to yeast, E coli and T thermophilus tRNAs comprise G34, U35, C36, C38 and G73, a set of nucleotides conserved in tRNA(Asp) molecules of other biological origin. Aspartate specificity can be enhanced by negative discrimination preventing, eg mischarging of native yeast tRNA(Asp by yeast arginyl-tRNA synthetase. In the yeast system crystallography shows that identity nucleotides are in contact with identity amino acids located in the catalytic and anticodon binding domains of the synthetase. Specificity of RNA/protein interaction involves a conformational change of the tRNA that optimizes the H-bonding potential of the identity signals on both partners of the complex. Mutation of identity nucleotides leads to decreased aspartylation efficiencies accompanied by a loss of specific H-bonds and an altered adaptation of tRNA on the synthetase. Species-specific characteristics of aspartate systems are the number, location and nature of minor identity signals. These features and the structural variations in aspartate tRNAs and synthetases are correlated with mechanistic differences in the aminoacylation reactions catalyzed by the various aspartyl-tRNA synthetases. The reality of the aspartate identity set is verified by its functional expression in a variety of RNA frameworks. Inversely a number of identities can be expressed within a tRNA(Asp) framework. From this emerged the concept of the RNA structural frameworks underlying expression of identities which is illustrated with data obtained with engineered tRNAs. Efficient aspartylation of minihelices is explained by the primordial role of G73. From this and other considerations it is suggested that aspartate identity appeared early in the history of tRNA aminoacylation systems.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Asp/*chemistry Saccharomyces cerevisiae Structure-Activity Relationship Support, Aspartate-tRNA Ligase/chemistry/metabolism Aspartic Acid/analysis Base Sequence Escherichia coli Models, ERIANI, FLORENTZ, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermus thermophilus, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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 Journal Article
In: J Mol Biol, vol. 235, no. 2, pp. 508-531, 1994, ISBN: 8289279, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
1993
Baron C, Westhof E, Bock A, Giege R
Solution structure of selenocysteine-inserting tRNA(Sec) from Escherichia coli. Comparison with canonical tRNA(Ser) Journal Article
In: J Mol Biol, vol. 231, no. 2, pp. 274-292, 1993, ISBN: 8510147, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}