Publications
2000
Kolb F A, Engdahl H M, Slagter-Jager J G, Ehresmann B, Ehresmann C, Westhof E, Wagner E G, Romby P
Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA Article de journal
Dans: EMBO J, vol. 19, no. 21, p. 5905-5915, 2000, ISBN: 11060041, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antisense/*chemistry/*genetics/metabolism RNA, Bacterial Models, Bacterial Proteins/genetics Base Sequence Binding, Bacterial/chemistry/genetics/metabolism Support, Competitive DNA Primers/genetics Escherichia coli/chemistry/genetics/metabolism Genes, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't, ROMBY, Unité ARN
@article{,
title = {Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA},
author = {F A Kolb and H M Engdahl and J G Slagter-Jager and B Ehresmann and C Ehresmann and E Westhof and E G Wagner and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11060041},
isbn = {11060041},
year = {2000},
date = {2000-01-01},
journal = {EMBO J},
volume = {19},
number = {21},
pages = {5905-5915},
abstract = {The antisense RNA, CopA, regulates the replication frequency of plasmid R1 through inhibition of RepA translation by rapid and specific binding to its target RNA (CopT). The stable CopA-CopT complex is characterized by a four-way junction structure and a side-by-side alignment of two long intramolecular helices. The significance of this structure for binding in vitro and control in vivo was tested by mutations in both CopA and CopT. High rates of stable complex formation in vitro and efficient inhibition in vivo required initial loop-loop complexes to be rapidly converted to extended interactions. These interactions involve asymmetric helix progression and melting of the upper stems of both RNAs to promote the formation of two intermolecular helices. Data presented here delineate the boundaries of these helices and emphasize the need for unimpeded helix propagation. This process is directional, i.e. one of the two intermolecular helices (B) must form first to allow formation of the other (B'). A binding pathway, characterized by a hierarchy of intermediates leading to an irreversible and inhibitory RNA-RNA complex, is proposed.},
note = {0261-4189
Journal Article},
keywords = {Antisense/*chemistry/*genetics/metabolism RNA, Bacterial Models, Bacterial Proteins/genetics Base Sequence Binding, Bacterial/chemistry/genetics/metabolism Support, Competitive DNA Primers/genetics Escherichia coli/chemistry/genetics/metabolism Genes, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1997
Aphasizhev R, Théobald-Dietrich A, Kostyuk D, Kochetkov S N, Kisselev L, Giege R, Fasiolo F
Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides Article de journal
Dans: RNA, vol. 3, no. 8, p. 893-904, 1997, ISBN: 9257648, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/metabolism RNA, Base Sequence DNA-Directed RNA Polymerases/genetics/metabolism Deoxyribonucleotides/chemistry/*metabolism Models, Genetic, Met/chemistry/genetics/metabolism Structure-Activity Relationship Support, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Transfer/*chemistry/genetics/*metabolism RNA, Unité ARN
@article{,
title = {Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides},
author = {R Aphasizhev and A Théobald-Dietrich and D Kostyuk and S N Kochetkov and L Kisselev and R Giege and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9257648},
isbn = {9257648},
year = {1997},
date = {1997-01-01},
journal = {RNA},
volume = {3},
number = {8},
pages = {893-904},
abstract = {The contribution of the ribose 2'-hydroxyls to RNA structure and function has been analyzed, but still remains controversial. In this work, we report the use of a mutant T7 RNA polymerase as a tool in RNA studies, applied to the aspartate and methionine tRNA aminoacylation systems from yeast. Our approach consists of determining the effect of substituting natural ribonucleotides by deoxyribonucleotides in RNA and, thereby, defining the subset of important 2'-hydroxyl groups. We show that deoxyribose-containing RNA can be folded in a global conformation similar to that of natural RNA. Melting curves of tRNAs, obtained by temperature-gradient gel electrophoresis, indicate that in deoxyribo-containing molecules, the thermal stability of the tertiary network drops down, whereas the stability of the secondary structure remains unaltered. Nuclease footprinting reveals a significant increase in the accessibility of both single- and double-stranded regions. As to the functionality of the deoxyribose-containing tRNAs, their in vitro aminoacylation efficiency indicates striking differential effects depending upon the nature of the substituted ribonucleotides. Strongest decrease in charging occurs for yeast initiator tRNA(Met) transcripts containing dG or dC residues and for yeast tRNA(Asp) transcripts with dU or dG. In the aspartate system, the decreased aminoacylation capacities can be correlated with the substitution of the ribose moieties of U11 and G27, disrupting two hydrogen bond contacts with the synthetase. Altogether, this suggests that specific 2'-hydroxyl groups in tRNAs can act as determinants specifying aminoacylation identity.},
note = {1355-8382
Journal Article},
keywords = {Asp/chemistry/genetics/metabolism RNA, Base Sequence DNA-Directed RNA Polymerases/genetics/metabolism Deoxyribonucleotides/chemistry/*metabolism Models, Genetic, Met/chemistry/genetics/metabolism Structure-Activity Relationship Support, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Transfer/*chemistry/genetics/*metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1996
Serganov A A, Masquida B, Westhof E, Cachia C, Portier C, Garber M, Ehresmann B, Ehresmann C
The 16S rRNA binding site of Thermus thermophilus ribosomal protein S15: comparison with Escherichia coli S15, minimum site and structure Article de journal
Dans: RNA, vol. 2, no. 11, p. 1124-1138, 1996, ISBN: 8903343, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/genetics/*metabolism Ribosomal Proteins/*metabolism Species Specificity Support, Bacterial/chemistry/genetics/*metabolism RNA, Base Sequence Binding Sites/genetics Comparative Study Computer Simulation Conserved Sequence Escherichia coli/genetics/*metabolism Magnesium/metabolism Models, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermodynamics Thermus thermophilus/genetics/*metabolism, Ribosomal, Unité ARN
@article{,
title = {The 16S rRNA binding site of Thermus thermophilus ribosomal protein S15: comparison with Escherichia coli S15, minimum site and structure},
author = {A A Serganov and B Masquida and E Westhof and C Cachia and C Portier and M Garber and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8903343},
isbn = {8903343},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {11},
pages = {1124-1138},
abstract = {Binding of Escherichia coli and Thermus thermophilus ribosomal proteins S15 to a 16S ribosomal RNA fragment from T. thermophilus (nt 559-753) has been investigated in detail by extensive deletion analysis, filter-binding assays, gel mobility shift, structure probing, footprinting with chemical, enzymatic, and hydroxyl radical probes. Both S15 proteins recognize two distinct sites. The first one maps in the bottom of helix 638-655/717-734 (H22) and in the three-way junction between helix 560-570/737-747 (H20), helix 571-600/606-634 (H21), and H22. The second is located in a conserved purine-rich region in the center of H22. The first site provides a higher contribution to the free energy of binding than the second one, and both are required for efficient binding. A short RNA fragment of 56 nt containing these elements binds S15 with high affinity. The structure of the rRNA is constrained by the three-way junction and requires both magnesium and S15 to be stabilized. A 3D model, derived by computer modeling with the use of experimental data, suggests that the bound form adopts a Y-shaped conformation, with a quasi-coaxial stacking of H22 on H20, and H21 forming an acute angle with H22. In this model, S15 binds to the shallow groove of the RNA on the exterior side of the Y-shaped structure, making contact with the two sites, which are separated by one helix turn.},
note = {1355-8382
Journal Article},
keywords = {16S/chemistry/genetics/*metabolism Ribosomal Proteins/*metabolism Species Specificity Support, Bacterial/chemistry/genetics/*metabolism RNA, Base Sequence Binding Sites/genetics Comparative Study Computer Simulation Conserved Sequence Escherichia coli/genetics/*metabolism Magnesium/metabolism Models, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't Thermodynamics Thermus thermophilus/genetics/*metabolism, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}