Méteignier Louis-Valentin, Ghandour Rabea, Zimmerman Aude, Kuhn Lauriane, Meurer Jörg, Zoschke Reimo, Hammani Kamel
Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo Article de journal
Dans: Nucleic Acids Research, vol. 49, no. 2, p. 1114–1132, 2021, ISSN: 1362-4962.
Résumé | Liens | BibTeX | Étiquettes: 16S, 23S, Arabidopsis, Arabidopsis Proteins, Chloroplast Proteins, Chloroplasts, Gene Expression Regulation, Organelle Biogenesis, Peptide Termination Factors, Plant, Polyribosomes, PPSE, Protein Biosynthesis, Recombinant Proteins, Ribonucleoproteins, Ribosomal, ribosomes, RNA, Substrate Specificity
@article{meteignier_arabidopsis_2021,
title = {Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo},
author = {Louis-Valentin Méteignier and Rabea Ghandour and Aude Zimmerman and Lauriane Kuhn and Jörg Meurer and Reimo Zoschke and Kamel Hammani},
doi = {10.1093/nar/gkaa1244},
issn = {1362-4962},
year = {2021},
date = {2021-01-01},
journal = {Nucleic Acids Research},
volume = {49},
number = {2},
pages = {1114--1132},
abstract = {The mitochondrial transcription termination factor proteins are nuclear-encoded nucleic acid binders defined by degenerate tandem helical-repeats of ∼30 amino acids. They are found in metazoans and plants where they localize in organelles. In higher plants, the mTERF family comprises ∼30 members and several of these have been linked to plant development and response to abiotic stress. However, knowledge of the molecular basis underlying these physiological effects is scarce. We show that the Arabidopsis mTERF9 protein promotes the accumulation of the 16S and 23S rRNAs in chloroplasts, and interacts predominantly with the 16S rRNA in vivo and in vitro. Furthermore, mTERF9 is found in large complexes containing ribosomes and polysomes in chloroplasts. The comprehensive analysis of mTERF9 in vivo protein interactome identified many subunits of the 70S ribosome whose assembly is compromised in the null mterf9 mutant, putative ribosome biogenesis factors and CPN60 chaperonins. Protein interaction assays in yeast revealed that mTERF9 directly interact with these proteins. Our data demonstrate that mTERF9 integrates protein-protein and protein-RNA interactions to promote chloroplast ribosomal assembly and translation. Besides extending our knowledge of mTERF functional repertoire in plants, these findings provide an important insight into the chloroplast ribosome biogenesis.},
keywords = {16S, 23S, Arabidopsis, Arabidopsis Proteins, Chloroplast Proteins, Chloroplasts, Gene Expression Regulation, Organelle Biogenesis, Peptide Termination Factors, Plant, Polyribosomes, PPSE, Protein Biosynthesis, Recombinant Proteins, Ribonucleoproteins, Ribosomal, ribosomes, RNA, Substrate Specificity},
pubstate = {published},
tppubtype = {article}
}
Niehus Sebastian, Giammarinaro Philippe, Liégeois Samuel, Quintin Jessica, Ferrandon Dominique
Fly culture collapse disorder: detection, prophylaxis and eradication of the microsporidian parasite Tubulinosema ratisbonensis infecting Drosophila melanogaster Article de journal
Dans: Fly (Austin), vol. 6, no. 3, p. 193–204, 2012, ISSN: 1933-6942.
Résumé | Liens | BibTeX | Étiquettes: Animals, Apansporoblastina, Apansporoblastina/*genetics/physiology, Base Sequence, cure, Disinfection, Disinfection/methods, DNA, DNA Primers, Drosophila melanogaster/*microbiology, ferrandon, fumagillin, Fungal, Fungal/chemistry, M3i, microsporidia, obligate intracellular parasitism, PCR detection, Phylogeny, Polymerase Chain Reaction, Polymerase Chain Reaction/methods, prophylaxis, Ribosomal, Ribosomal/chemistry, Sequence Alignment, Tubulinosema ratisbonensis
@article{niehus_fly_2012b,
title = {Fly culture collapse disorder: detection, prophylaxis and eradication of the microsporidian parasite Tubulinosema ratisbonensis infecting Drosophila melanogaster},
author = {Sebastian Niehus and Philippe Giammarinaro and Samuel Liégeois and Jessica Quintin and Dominique Ferrandon},
doi = {10.4161/fly.20896},
issn = {1933-6942},
year = {2012},
date = {2012-01-01},
journal = {Fly (Austin)},
volume = {6},
number = {3},
pages = {193--204},
abstract = {Drosophila melanogaster is a robust model to investigate many biological problems. It is however prone to some infections, which may endanger fly stocks if left unchecked for. One such infection is caused by an obligate fungal intracellular parasite, Tubulinosema ratisbonensis, which can be found in laboratory stocks. Here, we identify and briefly characterize a T. ratisbonensis strain that was infesting our Drosophila cultures and that required intensive measures to contain and eradicate the infection. We describe the phenotypes of infested stocks. We also report PCR-based techniques that allow the detection of infested stocks with a high sensitivity. We have developed a high-throughput qPCR assay that allows the efficient parallel screening of a large number of potentially-infested stocks. We also have investigated several prophylactic measures to prevent the further contamination of stocks, namely UV-exposure, ethanol treatment, bleaching, and desiccation. Bleaching was found to kill all spores. Other treatments were less effective but were found to be sufficient to prevent further contamination of noninfested stocks. Two treatments were efficacious in curing infested stocks (1) bleaching of eggs and subsequent raising of the larvae in clean vials; (2) fumagillin treatment. These cures only work on stocks that have not become too weak to withstand the procedures.},
keywords = {Animals, Apansporoblastina, Apansporoblastina/*genetics/physiology, Base Sequence, cure, Disinfection, Disinfection/methods, DNA, DNA Primers, Drosophila melanogaster/*microbiology, ferrandon, fumagillin, Fungal, Fungal/chemistry, M3i, microsporidia, obligate intracellular parasitism, PCR detection, Phylogeny, Polymerase Chain Reaction, Polymerase Chain Reaction/methods, prophylaxis, Ribosomal, Ribosomal/chemistry, Sequence Alignment, Tubulinosema ratisbonensis},
pubstate = {published},
tppubtype = {article}
}
Parisien M, Cruz J A, Westhof E, Major F
New metrics for comparing and assessing discrepancies between RNA 3D structures and models Article de journal
Dans: RNA, vol. 15, no. 10, p. 1875-1885, 2009, ISBN: 19710185, (1469-9001 (Electronic) 1355-8382 (Linking) Comparative Study Journal Article Research Support, Non-U.S. Gov't).
Résumé | Liens | BibTeX | Étiquettes: 28S/*chemistry Rats, Animals Base Pairing Calibration *Models, Molecular *Nucleic Acid Conformation RNA, Ribosomal, Unité ARN, WESTHOF
@article{,
title = {New metrics for comparing and assessing discrepancies between RNA 3D structures and models},
author = {M Parisien and J A Cruz and E Westhof and F Major},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19710185},
isbn = {19710185},
year = {2009},
date = {2009-01-01},
journal = {RNA},
volume = {15},
number = {10},
pages = {1875-1885},
abstract = {To benchmark progress made in RNA three-dimensional modeling and assess newly developed techniques, reliable and meaningful comparison metrics and associated tools are necessary. Generally, the average root-mean-square deviations (RMSDs) are quoted. However, RMSD can be misleading since errors are spread over the whole molecule and do not account for the specificity of RNA base interactions. Here, we introduce two new metrics that are particularly suitable to RNAs: the deformation index and deformation profile. The deformation index is calibrated by the interaction network fidelity, which considers base-base-stacking and base-base-pairing interactions within the target structure. The deformation profile highlights dissimilarities between structures at the nucleotide scale for both intradomain and interdomain interactions. Our results show that there is little correlation between RMSD and interaction network fidelity. The deformation profile is a tool that allows for rapid assessment of the origins of discrepancies.},
note = {1469-9001 (Electronic)
1355-8382 (Linking)
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {28S/*chemistry Rats, Animals Base Pairing Calibration *Models, Molecular *Nucleic Acid Conformation RNA, Ribosomal, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Benelli D, Marzi S, Mancone C, Alonzi T, la Teana A, Londei P
Function and ribosomal localization of aIF6, a translational regulator shared by archaea and eukarya Article de journal
Dans: Nucleic Acids Res, vol. 37, no. 1, p. 256-267, 2009, ISBN: 19036786, (1362-4962 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Résumé | Liens | BibTeX | Étiquettes: 23S/chemistry/metabolism Ribosomal Proteins/metabolism Ribosome Subunits, Archaeal Proteins/analysis/chemistry/*metabolism Base Sequence Binding Sites Cell Cycle Cloning, Archaeal/*metabolism Ribosomes/metabolism Sulfolobus solfataricus/*genetics/metabolism, Large, Molecular Eukaryotic Initiation Factors/chemistry Models, Molecular Molecular Sequence Data Prokaryotic Initiation Factors/analysis/chemistry/*metabolism *Protein Biosynthesis RNA, Ribosomal, ROMBY, Unité ARN
@article{,
title = {Function and ribosomal localization of aIF6, a translational regulator shared by archaea and eukarya},
author = {D Benelli and S Marzi and C Mancone and T Alonzi and A la Teana and P Londei},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19036786},
isbn = {19036786},
year = {2009},
date = {2009-01-01},
journal = {Nucleic Acids Res},
volume = {37},
number = {1},
pages = {256-267},
abstract = {The translation factor IF6 is shared by the Archaea and the Eukarya, but is not found in Bacteria. The properties of eukaryal IF6 (eIF6) have been extensively studied, but remain somewhat elusive. eIF6 behaves as a ribosome-anti-association factor and is involved in miRNA-mediated gene silencing; however, it also seems to participate in ribosome synthesis and export. Here we have determined the function and ribosomal localization of the archaeal (Sulfolobus solfataricus) IF6 homologue (aIF6). We find that aIF6 binds specifically to the 50S ribosomal subunits, hindering the formation of 70S ribosomes and strongly inhibiting translation. aIF6 is uniformly expressed along the cell cycle, but it is upregulated following both cold- and heat shock. The aIF6 ribosomal binding site lies in the middle of the 30-S interacting surface of the 50S subunit, including a number of critical RNA and protein determinants involved in subunit association. The data suggest that the IF6 protein evolved in the archaeal-eukaryal lineage to modulate translational efficiency under unfavourable environmental conditions, perhaps acquiring additional functions during eukaryotic evolution.},
note = {1362-4962 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {23S/chemistry/metabolism Ribosomal Proteins/metabolism Ribosome Subunits, Archaeal Proteins/analysis/chemistry/*metabolism Base Sequence Binding Sites Cell Cycle Cloning, Archaeal/*metabolism Ribosomes/metabolism Sulfolobus solfataricus/*genetics/metabolism, Large, Molecular Eukaryotic Initiation Factors/chemistry Models, Molecular Molecular Sequence Data Prokaryotic Initiation Factors/analysis/chemistry/*metabolism *Protein Biosynthesis RNA, Ribosomal, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lescoute A, Westhof E
The interaction networks of structured RNAs Article de journal
Dans: Nucleic Acids Res, vol. 34, no. 22, p. 6587-6604, 2006, ISBN: 17135184, (1362-4962 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry RNA, 23S/chemistry Ribonuclease P/chemistry, Base Pairing Base Sequence Introns *Models, Catalytic/chemistry RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA/*chemistry RNA, Ribosomal, Unité ARN, WESTHOF
@article{,
title = {The interaction networks of structured RNAs},
author = {A Lescoute and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17135184},
isbn = {17135184},
year = {2006},
date = {2006-01-01},
journal = {Nucleic Acids Res},
volume = {34},
number = {22},
pages = {6587-6604},
abstract = {All pairwise interactions occurring between bases which could be detected in three-dimensional structures of crystallized RNA molecules are annotated on new planar diagrams. The diagrams attempt to map the underlying complex networks of base-base interactions and, especially, they aim at conveying key relationships between helical domains: co-axial stacking, bending and all Watson-Crick as well as non-Watson-Crick base pairs. Although such wiring diagrams cannot replace full stereographic images for correct spatial understanding and representation, they reveal structural similarities as well as the conserved patterns and distances between motifs which are present within the interaction networks of folded RNAs of similar or unrelated functions. Finally, the diagrams could help devising methods for meaningfully transforming RNA structures into graphs amenable to network analysis.},
note = {1362-4962 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {16S/chemistry RNA, 23S/chemistry Ribonuclease P/chemistry, Base Pairing Base Sequence Introns *Models, Catalytic/chemistry RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA/*chemistry RNA, Ribosomal, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Kondo J, Urzhumtsev A, Westhof E
Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site Article de journal
Dans: Nucleic Acids Res, vol. 34, no. 2, p. 676-685, 2006, ISBN: 16452297, (1362-4962 (Electronic) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry RNA, 18S/*chemistry Research Support, Animals Comparative Study Crystallography, Bacterial/chemistry RNA, Molecular Nebramycin/analogs & derivatives/chemistry Nucleic Acid Conformation RNA, Non-U.S. Gov't Ribosomes/chemistry Tetrahymena thermophila/genetics, Protozoan/chemistry RNA, Ribosomal, Unité ARN, WESTHOF, X-Ray Genetic Code Humans *Models
@article{,
title = {Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site},
author = {J Kondo and A Urzhumtsev and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16452297},
isbn = {16452297},
year = {2006},
date = {2006-01-01},
journal = {Nucleic Acids Res},
volume = {34},
number = {2},
pages = {676-685},
abstract = {The decoding A site of the small ribosomal subunit is an RNA molecular switch, which monitors codon-anticodon interactions to guarantee translation fidelity. We have solved the crystal structure of an RNA fragment containing two Homo sapiens cytoplasmic A sites. Each of the two A sites presents a different conformational state. In one state, adenines A1492 and A1493 are fully bulged-out with C1409 forming a wobble-like pair to A1491. In the second state, adenines A1492 and A1493 form non-Watson-Crick pairs with C1409 and G1408, respectively while A1491 bulges out. The first state of the eukaryotic A site is, thus, basically the same as in the bacterial A site with bulging A1492 and A1493. It is the state used for recognition of the codon/anticodon complex. On the contrary, the second state of the H.sapiens cytoplasmic A site is drastically different from any of those observed for the bacterial A site without bulging A1492 and A1493.},
note = {1362-4962 (Electronic)
Journal Article},
keywords = {16S/chemistry RNA, 18S/*chemistry Research Support, Animals Comparative Study Crystallography, Bacterial/chemistry RNA, Molecular Nebramycin/analogs & derivatives/chemistry Nucleic Acid Conformation RNA, Non-U.S. Gov't Ribosomes/chemistry Tetrahymena thermophila/genetics, Protozoan/chemistry RNA, Ribosomal, Unité ARN, WESTHOF, X-Ray Genetic Code Humans *Models},
pubstate = {published},
tppubtype = {article}
}
Jenner L, Romby P, Rees B, Schulze-Briese C, Springer M, Ehresmann C, Ehresmann B, Moras D, Yusupova G, Yusupov M
Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding Article de journal
Dans: Science, vol. 308, no. 5718, p. 120-123, 2005, ISBN: 15802605, (1095-9203 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/metabolism RNA, Bacterial/*chemistry/metabolism RNA, Messenger/*chemistry/metabolism RNA, Met/chemistry/metabolism *Regulatory Sequences, Molecular Nucleic Acid Conformation *Protein Biosynthesis RNA, Non-U.S. Gov't Ribosomal Proteins/metabolism Ribosomes/*metabolism Thermus thermophilus/genetics/*metabolism Threonine-tRNA Ligase/genetics/metabolism, Ribonucleic Acid Repressor Proteins/*metabolism Research Support, Ribosomal, ROMBY, ROMBY Bacterial Proteins/metabolism Base Pairing Binding Sites Crystallization Crystallography, Transfer, Unité ARN, X-Ray Fourier Analysis Models
@article{,
title = {Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding},
author = {L Jenner and P Romby and B Rees and C Schulze-Briese and M Springer and C Ehresmann and B Ehresmann and D Moras and G Yusupova and M Yusupov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15802605},
isbn = {15802605},
year = {2005},
date = {2005-01-01},
journal = {Science},
volume = {308},
number = {5718},
pages = {120-123},
abstract = {The ribosome of Thermus thermophilus was cocrystallized with initiator transfer RNA (tRNA) and a structured messenger RNA (mRNA) carrying a translational operator. The path of the mRNA was defined at 5.5 angstroms resolution by comparing it with either the crystal structure of the same ribosomal complex lacking mRNA or with an unstructured mRNA. A precise ribosomal environment positions the operator stem-loop structure perpendicular to the surface of the ribosome on the platform of the 30S subunit. The binding of the operator and of the initiator tRNA occurs on the ribosome with an unoccupied tRNA exit site, which is expected for an initiation complex. The positioning of the regulatory domain of the operator relative to the ribosome elucidates the molecular mechanism by which the bound repressor switches off translation. Our data suggest a general way in which mRNA control elements must be placed on the ribosome to perform their regulatory task.},
note = {1095-9203
Journal Article},
keywords = {16S/chemistry/metabolism RNA, Bacterial/*chemistry/metabolism RNA, Messenger/*chemistry/metabolism RNA, Met/chemistry/metabolism *Regulatory Sequences, Molecular Nucleic Acid Conformation *Protein Biosynthesis RNA, Non-U.S. Gov't Ribosomal Proteins/metabolism Ribosomes/*metabolism Thermus thermophilus/genetics/*metabolism Threonine-tRNA Ligase/genetics/metabolism, Ribonucleic Acid Repressor Proteins/*metabolism Research Support, Ribosomal, ROMBY, ROMBY Bacterial Proteins/metabolism Base Pairing Binding Sites Crystallization Crystallography, Transfer, Unité ARN, X-Ray Fourier Analysis Models},
pubstate = {published},
tppubtype = {article}
}
Francois B, Russell R J, Murray J B, Aboul-ela F, Masquida B, Vicens Q, Westhof E
Dans: Nucleic Acids Res, vol. 33, no. 17, p. 5677-5690, 2005, ISBN: 16214802, (1362-4962 (Electronic) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry Research Support, Adenine/chemistry Aminoglycosides/*chemistry Anti-Bacterial Agents/*chemistry Anticodon/chemistry Base Sequence Binding Sites Codon/chemistry Crystallography, Molecular Oligoribonucleotides/*chemistry Paromomycin/analogs & derivatives/chemistry RNA, Non-U.S. Gov't Ribosomes/chemistry Ribostamycin/chemistry, Ribosomal, Unité ARN, WESTHOF, X-Ray Framycetin/chemistry Gentamicins/chemistry Kanamycin/chemistry *Models
@article{,
title = {Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding},
author = {B Francois and R J Russell and J B Murray and F Aboul-ela and B Masquida and Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16214802},
isbn = {16214802},
year = {2005},
date = {2005-01-01},
journal = {Nucleic Acids Res},
volume = {33},
number = {17},
pages = {5677-5690},
abstract = {The crystal structures of six complexes between aminoglycoside antibiotics (neamine, gentamicin C1A, kanamycin A, ribostamycin, lividomycin A and neomycin B) and oligonucleotides containing the decoding A site of bacterial ribosomes are reported at resolutions between 2.2 and 3.0 A. Although the number of contacts between the RNA and the aminoglycosides varies between 20 and 31, up to eight direct hydrogen bonds between rings I and II of the neamine moiety are conserved in the observed complexes. The puckered sugar ring I is inserted into the A site helix by stacking against G1491 and forms a pseudo base pair with two H-bonds to the Watson-Crick sites of the universally conserved A1408. This central interaction helps to maintain A1492 and A1493 in a bulged-out conformation. All these structures of the minimal A site RNA complexed to various aminoglycosides display crystal packings with intermolecular contacts between the bulging A1492 and A1493 and the shallow/minor groove of Watson-Crick pairs in a neighbouring helix. In one crystal, one empty A site is observed. In two crystals, two aminoglycosides are bound to the same A site with one bound specifically and the other bound in various ways in the deep/major groove at the edge of the A sites.},
note = {1362-4962 (Electronic)
Journal Article},
keywords = {16S/*chemistry Research Support, Adenine/chemistry Aminoglycosides/*chemistry Anti-Bacterial Agents/*chemistry Anticodon/chemistry Base Sequence Binding Sites Codon/chemistry Crystallography, Molecular Oligoribonucleotides/*chemistry Paromomycin/analogs & derivatives/chemistry RNA, Non-U.S. Gov't Ribosomes/chemistry Ribostamycin/chemistry, Ribosomal, Unité ARN, WESTHOF, X-Ray Framycetin/chemistry Gentamicins/chemistry Kanamycin/chemistry *Models},
pubstate = {published},
tppubtype = {article}
}
Mathy N, Pellegrini O, Serganov A, Patel D J, Ehresmann C, Portier C
Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation Article de journal
Dans: Mol Microbiol, vol. 52, no. 3, p. 661-675, 2004, ISBN: 15101974, (0950-382x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/genetics/*metabolism Recombinant Fusion Proteins/metabolism Ribosomal Proteins/chemistry/*genetics/*metabolism Sequence Alignment Support, Bacterial Models, EHRESMANN Amino Acid Sequence Base Sequence Escherichia coli Proteins/chemistry/genetics/*metabolism Gene Expression Regulation, Messenger/metabolism RNA, Molecular *Molecular Mimicry Molecular Sequence Data Mutagenesis, Non-U.S. Gov't Support, P.H.S., Ribosomal, Secondary RNA, Site-Directed Nucleic Acid Conformation Protein Structure, U.S. Gov't, Unité ARN
@article{,
title = {Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation},
author = {N Mathy and O Pellegrini and A Serganov and D J Patel and C Ehresmann and C Portier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15101974},
isbn = {15101974},
year = {2004},
date = {2004-01-01},
journal = {Mol Microbiol},
volume = {52},
number = {3},
pages = {661-675},
abstract = {The ribosomal protein S15 binds to 16S rRNA, during ribosome assembly, and to its own mRNA (rpsO mRNA), affecting autocontrol of its expression. In both cases, the RNA binding site is bipartite with a common subsite consisting of a G*U/G-C motif. The second subsite is located in a three-way junction in 16S rRNA and in the distal part of a stem forming a pseudoknot in Escherichia coli rpsO mRNA. To determine the extent of mimicry between these two RNA targets, we determined which amino acids interact with rpsO mRNA. A plasmid carrying rpsO (the S15 gene) was mutagenized and introduced into a strain lacking S15 and harbouring an rpsO-lacZ translational fusion. Analysis of deregulated mutants shows that each subsite of rpsO mRNA is recognized by a set of amino acids known to interact with 16S rRNA. In addition to the G*U/G-C motif, which is recognized by the same amino acids in both targets, the other subsite interacts with amino acids also involved in contacts with helix H22 of 16S rRNA, in the region adjacent to the three-way junction. However, specific S15-rpsO mRNA interactions can also be found, probably with A(-46) in loop L1 of the pseudoknot, demonstrating that mimicry between the two targets is limited.},
note = {0950-382x
Journal Article},
keywords = {16S/chemistry/genetics/*metabolism Recombinant Fusion Proteins/metabolism Ribosomal Proteins/chemistry/*genetics/*metabolism Sequence Alignment Support, Bacterial Models, EHRESMANN Amino Acid Sequence Base Sequence Escherichia coli Proteins/chemistry/genetics/*metabolism Gene Expression Regulation, Messenger/metabolism RNA, Molecular *Molecular Mimicry Molecular Sequence Data Mutagenesis, Non-U.S. Gov't Support, P.H.S., Ribosomal, Secondary RNA, Site-Directed Nucleic Acid Conformation Protein Structure, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Bielecki L, Westhof E
Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations Article de journal
Dans: J Mol Biol, vol. 335, no. 2, p. 555-571, 2004, ISBN: 14672663, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 5S/*chemistry/*metabolism Ribosomal Proteins/*chemistry/metabolism Support, Bacterial/chemistry RNA, Binding Sites Computer Simulation Guanine/chemistry/metabolism Hydrogen Bonding Magnesium/chemistry/*metabolism Models, Molecular Molecular Conformation Nucleic Acid Conformation Potassium/chemistry/*metabolism Protein Binding/genetics RNA, Non-U.S. Gov't Water/chemistry/metabolism, Ribosomal, Unité ARN, WESTHOF, WESTHOF Binding Sites Computer Simulation Guanine/chemistry/metabolism Hydrogen Bonding Magnesium/chemistry/*metabolism Models
@article{,
title = {Symmetric K+ and Mg2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations},
author = {P Auffinger and L Bielecki and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14672663},
isbn = {14672663},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {335},
number = {2},
pages = {555-571},
abstract = {Potassium binding to the 5S rRNA loop E motif has been studied by molecular dynamics at high (1.0 M) and low (0.2 M) concentration of added KCl in the presence and absence of Mg2+. A clear pattern of seven deep groove K+ binding sites or regions, in all cases connected with guanine N7/O6 atoms belonging to GpG, GpA, and GpU steps, was identified, indicating that the LE deep groove is significantly more ionophilic than the equivalent groove of regular RNA duplexes. Among all, two symmetry-related sites (with respect to the central G.A pair) were found to accommodate K+ ions with particularly long residence times. In a preceding molecular dynamics study by Auffinger et al. in the year 2003, these two sites were described as constituting important Mg2+ binding locations. Altogether, the data suggest that these symmetric sites correspond to the loop E main ion binding regions. Indeed, they are located in the deep groove of an important ribosomal protein binding motif associated with a fragile pattern of non-Watson-Crick pairs that has certainly to be stabilized by specific Mg2+ ions in order to be efficiently recognized by the protein. Besides, the other sites accommodate monovalent ions in a more diffuse way pointing out their lesser significance for the structure and function of this motif. Ion binding to the shallow groove and backbone atoms was generally found to be of minor importance since, at the low concentration, no well defined binding site could be characterized while high K+ concentration promoted mostly unspecific potassium binding to the RNA backbone. In addition, several K+ binding sites were located in positions equivalent to water molecules from the first hydration shell of divalent ions in simulations performed with magnesium, indicating that ion binding regions are able to accommodate both mono- and divalent ionic species. Overall, the simulations provide a more precise but, at the same time, a more intricate view of the relations of this motif with its ionic surrounding.},
note = {0022-2836
Journal Article},
keywords = {5S/*chemistry/*metabolism Ribosomal Proteins/*chemistry/metabolism Support, Bacterial/chemistry RNA, Binding Sites Computer Simulation Guanine/chemistry/metabolism Hydrogen Bonding Magnesium/chemistry/*metabolism Models, Molecular Molecular Conformation Nucleic Acid Conformation Potassium/chemistry/*metabolism Protein Binding/genetics RNA, Non-U.S. Gov't Water/chemistry/metabolism, Ribosomal, Unité ARN, WESTHOF, WESTHOF Binding Sites Computer Simulation Guanine/chemistry/metabolism Hydrogen Bonding Magnesium/chemistry/*metabolism Models},
pubstate = {published},
tppubtype = {article}
}
Vicens Q, Westhof E
Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide Article de journal
Dans: J Mol Biol, vol. 326, no. 4, p. 1175-1188, 2003, ISBN: 12589761, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/genetics/metabolism Support, Anti-Bacterial Agents/*chemistry/metabolism Binding Sites Crystallography, Bacterial Gentamicins/*chemistry/metabolism Human Models, Molecular Molecular Structure *Nucleic Acid Conformation Oligonucleotides/*chemistry/genetics/metabolism Protein Binding *Protein Conformation RNA, Non-U.S. Gov't, Ribosomal, Unité ARN, WESTHOF, X-Ray Drug Design Genes
@article{,
title = {Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide},
author = {Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12589761},
isbn = {12589761},
year = {2003},
date = {2003-01-01},
journal = {J Mol Biol},
volume = {326},
number = {4},
pages = {1175-1188},
abstract = {Aminoglycosides are antibacterial molecules that decrease translation accuracy by binding to the decoding aminoacyl-tRNA site (A site) on 16S ribosomal RNA. We have solved the crystal structure of an RNA fragment containing the A site bound to geneticin at 2.40A resolution. Geneticin, also known as G418, is a gentamicin-related aminoglycoside: it contains three rings that are functionalized by hydroxyl, ammonium and methyl groups. The detailed comparison of the distinctive behaviour of geneticin (binding to pro- and eukaryotic A sites) with the crystallographic, biochemical and microbiological results obtained so far for aminoglycoside-A site complexes offers new insights on the system. The two sugar rings constituting the neamine part common to most of the aminoglycosides bind to the A site, as already observed in the crystal structures solved previously with paromomycin and tobramycin. The essential hydrogen bonds involving ring I (to A1408) and ring II (to the phosphate oxygen atoms of the bulged adenine bases 1492 and 1493 and to G1494) are conserved and additional contacts are observed from ring III (to phosphate oxygen atoms of G1405 and U1406). The present work illustrates a molecular basis of the range in sensitiveness exhibited by geneticin towards common point A site mutations associated to resistance phenotypes. In addition, analysis and comparisons of the structures cast light on the role played by the conserved U1406.U1495 pair in the recognition of the A site by aminoglycosides.},
note = {0022-2836
Journal Article},
keywords = {16S/*chemistry/genetics/metabolism Support, Anti-Bacterial Agents/*chemistry/metabolism Binding Sites Crystallography, Bacterial Gentamicins/*chemistry/metabolism Human Models, Molecular Molecular Structure *Nucleic Acid Conformation Oligonucleotides/*chemistry/genetics/metabolism Protein Binding *Protein Conformation RNA, Non-U.S. Gov't, Ribosomal, Unité ARN, WESTHOF, X-Ray Drug Design Genes},
pubstate = {published},
tppubtype = {article}
}
Vicens Q, Westhof E
RNA as a drug target: the case of aminoglycosides Article de journal
Dans: Chembiochem, vol. 4, no. 10, p. 1018-1023, 2003, ISBN: 14523919, (1439-4227 Journal Article Review Review, Tutorial).
Liens | BibTeX | Étiquettes: 16S/*chemistry/drug effects/metabolism Substrate Specificity Technology, Aminoglycosides/*pharmacology Anti-Bacterial Agents/*pharmacology Binding Sites Drug Delivery Systems Models, Catalytic/chemistry/metabolism RNA, Molecular RNA/chemistry/metabolism RNA, Pharmaceutical Water/chemistry, Ribosomal, Unité ARN, WESTHOF
@article{,
title = {RNA as a drug target: the case of aminoglycosides},
author = {Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14523919},
isbn = {14523919},
year = {2003},
date = {2003-01-01},
journal = {Chembiochem},
volume = {4},
number = {10},
pages = {1018-1023},
note = {1439-4227
Journal Article
Review
Review, Tutorial},
keywords = {16S/*chemistry/drug effects/metabolism Substrate Specificity Technology, Aminoglycosides/*pharmacology Anti-Bacterial Agents/*pharmacology Binding Sites Drug Delivery Systems Models, Catalytic/chemistry/metabolism RNA, Molecular RNA/chemistry/metabolism RNA, Pharmaceutical Water/chemistry, Ribosomal, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Bielecki L, Westhof E
The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations Article de journal
Dans: Chem Biol, vol. 10, no. 6, p. 551-561, 2003, ISBN: 12837388, (1074-5521 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 5S/*chemistry/metabolism Support, Bacterial/*chemistry RNA, Binding Sites Cations, Divalent Computer Simulation Crystallization Electrostatics Hydrogen Bonding Magnesium/*chemistry/metabolism Models, Molecular Molecular Conformation Nucleic Acid Conformation RNA Stability RNA, Non-U.S. Gov't Thermodynamics Water/chemistry, Ribosomal, Unité ARN, WESTHOF
@article{,
title = {The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations},
author = {P Auffinger and L Bielecki and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12837388},
isbn = {12837388},
year = {2003},
date = {2003-01-01},
journal = {Chem Biol},
volume = {10},
number = {6},
pages = {551-561},
abstract = {Molecular dynamics simulations have been used to investigate the binding of Mg(2+) ions to the deep groove of the eubacterial 5S rRNA loop E. The simulations suggest that long-lived and specific water-mediated interactions established between the hydrated ions and the RNA atoms lining up the binding sites contribute to the stabilization of this motif. The Mg(2+) binding specificity is modulated by two factors: (i) a required electrostatic complementarity and (ii) a structural correspondence between the hydrated ion and its binding pocket that can be estimated by its degree of dehydration and the resulting number and lifetime of the intervening water-mediated contacts. Two distinct binding modes for pentahydrated Mg(2+) ions that result in a significant freezing of the tumbling motions of the ions are described, and mechanistic details related to the stabilization of nucleic acids by divalent ions are provided.},
note = {1074-5521
Journal Article},
keywords = {5S/*chemistry/metabolism Support, Bacterial/*chemistry RNA, Binding Sites Cations, Divalent Computer Simulation Crystallization Electrostatics Hydrogen Bonding Magnesium/*chemistry/metabolism Models, Molecular Molecular Conformation Nucleic Acid Conformation RNA Stability RNA, Non-U.S. Gov't Thermodynamics Water/chemistry, Ribosomal, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Perederina A., Nevskaya N., Nikonov O., Nikulin A., Dumas P., Yao M., Tanaka I., Garber M., Gongadze G., Nikonov S.
Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex Article de journal
Dans: RNA, vol. 8, no. 12, p. 1548-57, 2002, (1355-8382 Journal Article).
Résumé | BibTeX | Étiquettes: 5S/*chemistry/*metabolism, Acid, Amino, Bacterial, Base, Binding, Bonding, coli/genetics, Conformation, Data, Escherichia, Fragments/chemistry/metabolism, Gov't, Hydrogen, Models, Molecular, Non-U.S., Nucleic, Peptide, Protein, Proteins/*chemistry/*metabolism, Proteins/chemistry/metabolism, Ribosomal, RNA, Sequence, Sites, Support
@article{,
title = {Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex},
author = { A. Perederina and N. Nevskaya and O. Nikonov and A. Nikulin and P. Dumas and M. Yao and I. Tanaka and M. Garber and G. Gongadze and S. Nikonov},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {12},
pages = {1548-57},
abstract = {The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.},
note = {1355-8382
Journal Article},
keywords = {5S/*chemistry/*metabolism, Acid, Amino, Bacterial, Base, Binding, Bonding, coli/genetics, Conformation, Data, Escherichia, Fragments/chemistry/metabolism, Gov't, Hydrogen, Models, Molecular, Non-U.S., Nucleic, Peptide, Protein, Proteins/*chemistry/*metabolism, Proteins/chemistry/metabolism, Ribosomal, RNA, Sequence, Sites, Support},
pubstate = {published},
tppubtype = {article}
}
Vicens Q, Westhof E
Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site Article de journal
Dans: Chem Biol, vol. 9, no. 6, p. 747-755, 2002, ISBN: 12079787, (1074-5521 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry Support, Anti-Bacterial Agents/*chemistry Binding Sites Crystallography Escherichia coli/metabolism Models, Molecular Oligonucleotides/*chemistry Paromomycin/chemistry Protein Structure, Non-U.S. Gov't Tobramycin/*chemistry, Ribosomal, Secondary Protein Structure, Tertiary RNA, Unité ARN, WESTHOF
@article{,
title = {Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site},
author = {Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12079787},
isbn = {12079787},
year = {2002},
date = {2002-01-01},
journal = {Chem Biol},
volume = {9},
number = {6},
pages = {747-755},
abstract = {Aminoglycoside antibiotics target the decoding aminoacyl site (A site) on the 16S ribosomal RNA and induce miscoding during translation. Here, we present the crystal structure, at 2.54 A resolution, of an RNA oligonucleotide containing the A site sequence complexed to the 4,6-disubstituted 2-deoxystreptamine aminoglycoside tobramycin. The three aminosugar rings making up tobramycin interact with the deep-groove atoms directly or via water molecules and stabilize a fully bulged-out conformation of adenines A(1492) and A(1493). The comparison between this structure and the one previously solved in the presence of paromomycin confirms the importance of the functional groups on the common neamine part of these two antibiotics for binding to RNA. Furthermore, the analysis of the present structure provides a molecular explanation to some of the resistance mechanisms that have spread among bacteria and rendered aminoglycoside antibiotics inefficient.},
note = {1074-5521
Journal Article},
keywords = {16S/*chemistry Support, Anti-Bacterial Agents/*chemistry Binding Sites Crystallography Escherichia coli/metabolism Models, Molecular Oligonucleotides/*chemistry Paromomycin/chemistry Protein Structure, Non-U.S. Gov't Tobramycin/*chemistry, Ribosomal, Secondary Protein Structure, Tertiary RNA, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Perederina A, Nevskaya N, Nikonov O, Nikulin A, Dumas P, Yao M, Tanaka I, Garber M, Gongadze G, Nikonov S
Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex Article de journal
Dans: RNA, vol. 8, no. 12, p. 1548-1557, 2002, ISBN: 12515387, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 5S/*chemistry/*metabolism Ribosomal Proteins/*chemistry/*metabolism Support, Amino Acid Sequence Bacterial Proteins/chemistry/metabolism Base Sequence Binding Sites Escherichia coli/genetics Hydrogen Bonding Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Peptide Fragments/chemistry/metabolism Protein Conformation RNA, Non-U.S. Gov't, Ribosomal, Unité ARN
@article{,
title = {Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex},
author = {A Perederina and N Nevskaya and O Nikonov and A Nikulin and P Dumas and M Yao and I Tanaka and M Garber and G Gongadze and S Nikonov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12515387},
isbn = {12515387},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {12},
pages = {1548-1557},
abstract = {The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.},
note = {1355-8382
Journal Article},
keywords = {5S/*chemistry/*metabolism Ribosomal Proteins/*chemistry/*metabolism Support, Amino Acid Sequence Bacterial Proteins/chemistry/metabolism Base Sequence Binding Sites Escherichia coli/genetics Hydrogen Bonding Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Peptide Fragments/chemistry/metabolism Protein Conformation RNA, Non-U.S. Gov't, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Vicens Q, Westhof E
Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site Article de journal
Dans: Structure, vol. 9, no. 8, p. 647-658, 2001, ISBN: 11587639, (0969-2126 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry Ribosomes/*chemistry Spectrometry, Amino Acid Motifs Anti-Bacterial Agents/chemistry Base Sequence Binding Sites Crystallography, Mass, Matrix-Assisted Laser Desorption-Ionization Support, Molecular Molecular Sequence Data Mutation Paromomycin/*chemistry Protein Structure, Non-U.S. Gov't Tobramycin/chemistry Water/chemistry, Ribosomal, Secondary RNA, Unité ARN, X-Ray Escherichia coli/metabolism Magnetic Resonance Spectroscopy Models
@article{,
title = {Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site},
author = {Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11587639},
isbn = {11587639},
year = {2001},
date = {2001-01-01},
journal = {Structure},
volume = {9},
number = {8},
pages = {647-658},
abstract = {BACKGROUND: Aminoglycoside antibiotics interfere with translation in both gram-positive and gram-negative bacteria by binding to the tRNA decoding A site of the 16S ribosomal RNA. RESULTS: Crystals of complexes between oligoribonucleotides incorporating the sequence of the ribosomal A site of Escherichia coli and the aminoglycoside paromomycin have been solved at 2.5 A resolution. Each RNA fragment contains two A sites inserted between Watson-Crick pairs. The paromomycin molecules interact in an enlarged deep groove created by two bulging and one unpaired adenines. In both sites, hydroxyl and ammonium side chains of the antibiotic form 13 direct hydrogen bonds to bases and backbone atoms of the A site. In the best-defined site, 8 water molecules mediate 12 other hydrogen bonds between the RNA and the antibiotics. Ring I of paromomycin stacks over base G1491 and forms pseudo-Watson-Crick contacts with A1408. Both the hydroxyl group and one ammonium group of ring II form direct and water-mediated hydrogen bonds to the U1495oU1406 pair. The bulging conformation of the two adenines A1492 and A1493 is stabilized by hydrogen bonds between phosphate oxygens and atoms of rings I and II. The hydrophilic sites of the bulging A1492 and A1493 contact the shallow groove of G=C pairs in a symmetrical complex. CONCLUSIONS: Water molecules participate in the binding specificity by exploiting the antibiotic hydration shell and the typical RNA water hydration patterns. The observed contacts rationalize the protection, mutation, and resistance data. The crystal packing mimics the intermolecular contacts induced by aminoglycoside binding in the ribosome.},
note = {0969-2126
Journal Article},
keywords = {16S/*chemistry Ribosomes/*chemistry Spectrometry, Amino Acid Motifs Anti-Bacterial Agents/chemistry Base Sequence Binding Sites Crystallography, Mass, Matrix-Assisted Laser Desorption-Ionization Support, Molecular Molecular Sequence Data Mutation Paromomycin/*chemistry Protein Structure, Non-U.S. Gov't Tobramycin/chemistry Water/chemistry, Ribosomal, Secondary RNA, Unité ARN, X-Ray Escherichia coli/metabolism Magnetic Resonance Spectroscopy Models},
pubstate = {published},
tppubtype = {article}
}
Tishchenko S, Nikulin A, Fomenkova N, Nevskaya N, Nikonov O, Dumas P, Moine H, Ehresmann B, Ehresmann C, Piendl W, Lamzin V, Garber M, Nikonov S
Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii Article de journal
Dans: J Mol Biol, vol. 311, no. 2, p. 311-324, 2001, ISBN: 11478863, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/genetics/*metabolism RNA-Binding Proteins/chemistry/metabolism Ribosomal Proteins/*chemistry/*metabolism Ribosomes/chemistry/genetics/metabolism Sequence Alignment Substrate Specificity Support, Amino Acid Sequence Archaeal Proteins/chemistry/metabolism Bacteria/chemistry/genetics Base Sequence Binding Sites Conserved Sequence/genetics Crystallography, Archaeal/chemistry/genetics/metabolism RNA, Molecular Human Hydrogen Bonding Methanococcus/*chemistry/*genetics Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Protein Binding Protein Structure, Non-U.S. Gov't, Ribosomal, Secondary RNA, Unité ARN, X-Ray Evolution
@article{,
title = {Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii},
author = {S Tishchenko and A Nikulin and N Fomenkova and N Nevskaya and O Nikonov and P Dumas and H Moine and B Ehresmann and C Ehresmann and W Piendl and V Lamzin and M Garber and S Nikonov},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11478863},
isbn = {11478863},
year = {2001},
date = {2001-01-01},
journal = {J Mol Biol},
volume = {311},
number = {2},
pages = {311-324},
abstract = {The crystal structure of ribosomal protein S8 bound to its target 16 S rRNA from a hyperthermophilic archaeon Methanococcus jannaschii has been determined at 2.6 A resolution. The protein interacts with the minor groove of helix H21 at two sites located one helical turn apart, with S8 forming a bridge over the RNA major groove. The specificity of binding is essentially provided by the C-terminal domain of S8 and the highly conserved nucleotide core, characterized by two dinucleotide platforms, facing each other. The first platform (A595-A596), which is the less phylogenetically and structurally constrained, does not directly contact the protein but has an important shaping role in inducing cross-strand stacking interactions. The second platform (U641-A642) is specifically recognized by the protein. The universally conserved A642 plays a pivotal role by ensuring the cohesion of the complex organization of the core through an array of hydrogen bonds, including the G597-C643-U641 base triple. In addition, A642 provides the unique base-specific interaction with the conserved Ser105, while the Thr106 - Thr107 peptide link is stacked on its purine ring. Noteworthy, the specific recognition of this tripeptide (Thr-Ser-Thr/Ser) is parallel to the recognition of an RNA tetraloop by a dinucleotide platform in the P4-P6 ribozyme domain of group I intron. This suggests a general dual role of dinucleotide platforms in recognition of RNA or peptide motifs. One prominent feature is that conserved side-chain amino acids, as well as conserved bases, are essentially involved in maintaining tertiary folds. The specificity of binding is mainly driven by shape complementarity, which is increased by the hydrophobic part of side-chains. The remarkable similarity of this complex with its homologue in the T. thermophilus 30 S subunit indicates a conserved interaction mode between Archaea and Bacteria.},
note = {0022-2836
Journal Article},
keywords = {16S/*chemistry/genetics/*metabolism RNA-Binding Proteins/chemistry/metabolism Ribosomal Proteins/*chemistry/*metabolism Ribosomes/chemistry/genetics/metabolism Sequence Alignment Substrate Specificity Support, Amino Acid Sequence Archaeal Proteins/chemistry/metabolism Bacteria/chemistry/genetics Base Sequence Binding Sites Conserved Sequence/genetics Crystallography, Archaeal/chemistry/genetics/metabolism RNA, Molecular Human Hydrogen Bonding Methanococcus/*chemistry/*genetics Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Protein Binding Protein Structure, Non-U.S. Gov't, Ribosomal, Secondary RNA, Unité ARN, X-Ray Evolution},
pubstate = {published},
tppubtype = {article}
}
Serganov A, Benard L, Portier C, Ennifar E, Garber M, Ehresmann B, Ehresmann C
Role of conserved nucleotides in building the 16 S rRNA binding site for ribosomal protein S15 Article de journal
Dans: J Mol Biol, vol. 305, no. 4, p. 785-803, 2001, ISBN: 11162092, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/*genetics/*metabolism RNA-Binding Proteins/chemistry/metabolism Ribosomal Proteins/chemistry/*metabolism Sequence Alignment Support, Amino Acid Sequence Base Pairing Base Sequence Binding Sites Conserved Sequence/*genetics *Escherichia coli/chemistry/genetics/metabolism Models, ENNIFAR, Molecular Molecular Sequence Data Mutation/genetics Nuclease Protection Assays Phylogeny Protein Binding Protein Conformation Purines/metabolism RNA, Non-U.S. Gov't Thermodynamics Thermus thermophilus/chemistry, Ribosomal, Unité ARN
@article{,
title = {Role of conserved nucleotides in building the 16 S rRNA binding site for ribosomal protein S15},
author = {A Serganov and L Benard and C Portier and E Ennifar 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=11162092},
isbn = {11162092},
year = {2001},
date = {2001-01-01},
journal = {J Mol Biol},
volume = {305},
number = {4},
pages = {785-803},
abstract = {Ribosomal protein S15 recognizes a highly conserved target on 16 S rRNA, which consists of two distinct binding regions. Here, we used extensive site-directed mutagenesis on a Escherichia coli 16 S rRNA fragment containing the S15 binding site, to investigate the role of conserved nucleotides in protein recognition and to evaluate the relative contribution of the two sites. The effect of mutations on S15 recognition was studied by measuring the relative binding affinity, RNA probing and footprinting. The crystallographic structure of the Thermus thermophilus complex allowed molecular modelling of the E. coli complex and facilitated interpretation of biochemical data. Binding is essentially driven by site 1, which includes a three-way junction constrained by a conserved base triple and cross-strand stacking. Recognition is based mainly on shape complementarity, and the role of conserved nucleotides is to maintain a unique backbone geometry. The wild-type base triple is absolutely required for protein interaction, while changes in the conserved surrounding nucleotides are partially tolerated. Site 2, which provides functional groups in a conserved G-U/G-C motif, contributes only modestly to the stability of the interaction. Binding to this motif is dependent on binding at site 1 and is allowed only if the two sites are in the correct relative orientation. Non-conserved bulged nucleotides as well as a conserved purine interior loop, although not directly involved in recognition, are used to provide an appropriate flexibility between the two sites. In addition, correct binding at the two sites triggers conformational adjustments in the purine interior loop and in a distal region, which are known to be involved for subsequent binding of proteins S6 and S18. Thus, the role of site 1 is to anchor S15 to the rRNA, while binding at site 2 is aimed to induce a cascade of events required for subunit assembly.},
note = {0022-2836
Journal Article},
keywords = {16S/chemistry/*genetics/*metabolism RNA-Binding Proteins/chemistry/metabolism Ribosomal Proteins/chemistry/*metabolism Sequence Alignment Support, Amino Acid Sequence Base Pairing Base Sequence Binding Sites Conserved Sequence/*genetics *Escherichia coli/chemistry/genetics/metabolism Models, ENNIFAR, Molecular Molecular Sequence Data Mutation/genetics Nuclease Protection Assays Phylogeny Protein Binding Protein Conformation Purines/metabolism RNA, Non-U.S. Gov't Thermodynamics Thermus thermophilus/chemistry, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Nikulin A, Serganov A, Ennifar E, Tishchenko S, Nevskaya N, Shepard W, Portier C, Garber M, Ehresmann B, Ehresmann C, Nikonov S, Dumas P
Crystal structure of the S15-rRNA complex Article de journal
Dans: Nat Struct Biol, vol. 7, no. 4, p. 273-277, 2000, ISBN: 10742169, (1072-8368 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/genetics/*metabolism Ribosomal Proteins/*chemistry/*metabolism Structure-Activity Relationship Support, Amino Acid Sequence Base Pairing/drug effects/genetics Base Sequence Binding Sites/drug effects Conserved Sequence/genetics Crystallography, Bacterial/chemistry/genetics/metabolism RNA, ENNIFAR, Molecular Molecular Sequence Data *Nucleic Acid Conformation/drug effects Protein Conformation RNA, Non-U.S. Gov't Thermus thermophilus/*chemistry/genetics, Ribosomal, Unité ARN, X-Ray Magnesium/pharmacology Models
@article{,
title = {Crystal structure of the S15-rRNA complex},
author = {A Nikulin and A Serganov and E Ennifar and S Tishchenko and N Nevskaya and W Shepard and C Portier and M Garber and B Ehresmann and C Ehresmann and S Nikonov and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10742169},
isbn = {10742169},
year = {2000},
date = {2000-01-01},
journal = {Nat Struct Biol},
volume = {7},
number = {4},
pages = {273-277},
abstract = {In bacterial ribosomes, the small (30S) ribosomal subunit is composed of 16S rRNA and 21 distinct proteins. Ribosomal protein S15 is of particular interest because it binds primarily to 16S rRNA and is required for assembly of the small subunit and for intersubunit association, thus representing a key element in the assembly of a whole ribosome. Here we report the 2.8 inverted question mark resolution crystal structure of the highly conserved S15-rRNA complex. Protein S15 interacts in the minor groove with a G-U/G-C motif and a three-way junction. The latter is constrained by a conserved base triple and stacking interactions, and locked into place by magnesium ions and protein side chains, mainly through interactions with the unique three-dimensional geometry of the backbone. The present structure gives insights into the dual role of S15 in ribosome assembly and translational regulation.},
note = {1072-8368
Journal Article},
keywords = {16S/*chemistry/genetics/*metabolism Ribosomal Proteins/*chemistry/*metabolism Structure-Activity Relationship Support, Amino Acid Sequence Base Pairing/drug effects/genetics Base Sequence Binding Sites/drug effects Conserved Sequence/genetics Crystallography, Bacterial/chemistry/genetics/metabolism RNA, ENNIFAR, Molecular Molecular Sequence Data *Nucleic Acid Conformation/drug effects Protein Conformation RNA, Non-U.S. Gov't Thermus thermophilus/*chemistry/genetics, Ribosomal, Unité ARN, X-Ray Magnesium/pharmacology Models},
pubstate = {published},
tppubtype = {article}
}
Moine H, Squires C L, Ehresmann B, Ehresmann C
In vivo selection of functional ribosomes with variations in the rRNA-binding site of Escherichia coli ribosomal protein S8: evolutionary implications Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 97, no. 2, p. 605-610, 2000, ISBN: 10639126, (0027-8424http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10639126 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/genetics/metabolism Recombinant Fusion Proteins/genetics/metabolism Ribosomal Proteins/genetics/*metabolism Ribosomes/genetics/*metabolism Spectinomycin/pharmacology Support, Base Sequence Binding Sites/genetics Binding, Competitive Cell Division/genetics Cloning, Microbial Escherichia coli/drug effects/*genetics/metabolism Evolution, Molecular Drug Resistance, Molecular Protein Binding RNA, P.H.S. Variation (Genetics), Ribosomal, Ribosomal/genetics/*metabolism RNA, U.S. Gov't, Unité ARN
@article{,
title = {In vivo selection of functional ribosomes with variations in the rRNA-binding site of Escherichia coli ribosomal protein S8: evolutionary implications},
author = {H Moine and C L Squires and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10639126},
isbn = {10639126},
year = {2000},
date = {2000-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {97},
number = {2},
pages = {605-610},
abstract = {The highly conserved nature of rRNA sequences throughout evolution allows these molecules to be used to build philogenic trees of different species. It is unknown whether the stability of specific interactions and structural features of rRNA reflects an optimal adaptation to a functional task or an evolutionary trap. In the work reported here, we have applied an in vivo selection strategy to demonstrate that unnatural sequences do work as a functional replacement of the highly conserved binding site of ribosomal protein S8. However, growth competition experiments performed between Escherichia coli isolates containing natural and unnatural S8-binding sites showed that the fate of each isolate depended on the growth condition. In exponentially growing cells, one unnatural variant was found to be equivalent to wild type in competition experiments performed in rich media. In culture conditions leading to slow growth, however, cells containing the wild-type sequence were the ultimate winner of the competition, emphasizing that the wild-type sequence is, in fact, the most fit solution for the S8-binding site.},
note = {0027-8424http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10639126
Journal Article},
keywords = {16S/genetics/metabolism Recombinant Fusion Proteins/genetics/metabolism Ribosomal Proteins/genetics/*metabolism Ribosomes/genetics/*metabolism Spectinomycin/pharmacology Support, Base Sequence Binding Sites/genetics Binding, Competitive Cell Division/genetics Cloning, Microbial Escherichia coli/drug effects/*genetics/metabolism Evolution, Molecular Drug Resistance, Molecular Protein Binding RNA, P.H.S. Variation (Genetics), Ribosomal, Ribosomal/genetics/*metabolism RNA, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ennifar E, Nikulin A, Tishchenko S, Serganov A, Nevskaya N, Garber M, Ehresmann B, Ehresmann C, Nikonov S, Dumas P
The crystal structure of UUCG tetraloop Article de journal
Dans: J Mol Biol, vol. 304, no. 1, p. 35-42, 2000, ISBN: 11071808, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/genetics/*metabolism Ribosomal Proteins/chemistry/*metabolism Solvents Support, Base Sequence Crystallography, Biomolecular *Nucleic Acid Conformation RNA Stability RNA, ENNIFAR, Molecular Molecular Sequence Data Motion Nuclear Magnetic Resonance, Non-U.S. Gov't Thermodynamics, Ribosomal, Unité ARN, X-Ray Hydrogen Bonding Models
@article{,
title = {The crystal structure of UUCG tetraloop},
author = {E Ennifar and A Nikulin and S Tishchenko and A Serganov and N Nevskaya and M Garber and B Ehresmann and C Ehresmann and S Nikonov and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11071808},
isbn = {11071808},
year = {2000},
date = {2000-01-01},
journal = {J Mol Biol},
volume = {304},
number = {1},
pages = {35-42},
abstract = {All large structured RNAs contain hairpin motifs made of a stem closed by several looped nucleotides. The most frequent loop motif is the UUCG one. This motif belongs to the tetraloop family and has the peculiarity of being highly thermodynamically stable. Here, we report the first crystal structure of two UUCG tetraloops embedded in a larger RNA-protein complex solved at 2.8 A resolution. The two loops present in the asymmetric unit are in a different crystal packing environment but, nevertheless, have an identical conformation. The observed structure is globally close to that obtained in solution by nuclear magnetic resonance. However, subtle differences point to a more detailed picture of the role played by 2'-hydroxyl groups in stabilising this tetraloop.},
note = {0022-2836
Journal Article},
keywords = {16S/*chemistry/genetics/*metabolism Ribosomal Proteins/chemistry/*metabolism Solvents Support, Base Sequence Crystallography, Biomolecular *Nucleic Acid Conformation RNA Stability RNA, ENNIFAR, Molecular Molecular Sequence Data Motion Nuclear Magnetic Resonance, Non-U.S. Gov't Thermodynamics, Ribosomal, Unité ARN, X-Ray Hydrogen Bonding Models},
pubstate = {published},
tppubtype = {article}
}
Serganov A, Rak A, Garber M, Reinbolt J, Ehresmann B, Ehresmann C, Grunberg-Manago M, Portier C
Ribosomal protein S15 from Thermus thermophilus--cloning, sequencing, overexpression of the gene and RNA-binding properties of the protein Article de journal
Dans: Eur J Biochem, vol. 246, no. 2, p. 291-300, 1997, ISBN: 9208917, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/metabolism RNA-Binding Proteins/*genetics/metabolism Ribosomal Proteins/*genetics/metabolism Sequence Homology, Amino Acid Support, Amino Acid Sequence Base Sequence Cloning, Bacterial Escherichia coli/genetics Molecular Sequence Data Plasmids RNA, Molecular DNA, Non-U.S. Gov't Thermus thermophilus/*genetics, Ribosomal, Unité ARN
@article{,
title = {Ribosomal protein S15 from Thermus thermophilus--cloning, sequencing, overexpression of the gene and RNA-binding properties of the protein},
author = {A Serganov and A Rak and M Garber and J Reinbolt and B Ehresmann and C Ehresmann and M Grunberg-Manago and C Portier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9208917},
isbn = {9208917},
year = {1997},
date = {1997-01-01},
journal = {Eur J Biochem},
volume = {246},
number = {2},
pages = {291-300},
abstract = {A 6-kb DNA fragment from an extreme thermophile, Thermus thermophilus, carrying the genes for cytochrome oxidase ba3 subunit I (cbaA) and the ribosomal protein S15 (rpsO) was cloned into Escherichia coli. The gene rpsO was sequenced. The deduced amino acid sequence exhibits 59% identity to the corresponding protein from E. coli. Expression of rpsO in E. coli requires the use of a fully repressed inducible promoter because S15 from T. thermophilus is toxic for E. coli cells. When purified without denaturation from either overproducing E. coli strain or from T. thermophilus ribosomes, the S15 protein is stable and binds a cloned T. thermophilus 16S rRNA fragment (nucleotides 559-753), with low identical dissociation constants (2.5 nM), thus demonstrating that the thermophilic protein folds correctly in a mesophilic bacterium. The rRNA fragment bound corresponds in position and structure to the 16S rRNA fragment of E. coli. A similar high affinity was also found for the binding of S15 from T. thermophilus or E. coli to the corresponding E. coli 16S rRNA fragment, whereas a slightly lower affinity was observed in binding experiments between E. coli S15 and T. thermophilus 16S rRNA fragment. These results suggest that S15 from T. thermophilus recognizes similar determinants in both rRNA fragments. Competition experiments support this conclusion.},
note = {0014-2956
Journal Article},
keywords = {16S/metabolism RNA-Binding Proteins/*genetics/metabolism Ribosomal Proteins/*genetics/metabolism Sequence Homology, Amino Acid Support, Amino Acid Sequence Base Sequence Cloning, Bacterial Escherichia coli/genetics Molecular Sequence Data Plasmids RNA, Molecular DNA, Non-U.S. Gov't Thermus thermophilus/*genetics, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Moine H, Nurse K, Ehresmann B, Ehresmann C, Ofengand J
Conformational analysis of Escherichia coli 30S ribosomes containing the single-base mutations G530U, U1498G, G1401C, and C1501G and the double-base mutation G1401C/C1501G Article de journal
Dans: Biochemistry, vol. 36, no. 44, p. 13700-13709, 1997, ISBN: 9354641, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemical synthesis/*chemistry/genetics Ribosomes/chemistry/genetics Structure-Activity Relationship Support, Bacterial/*chemistry/genetics RNA, Base Sequence Cytosine Nucleotides/genetics Deoxyuridine Escherichia coli/genetics Guanine Nucleotides/genetics Molecular Sequence Data *Mutagenesis, Non-U.S. Gov't, Ribosomal, Site-Directed *Nucleic Acid Conformation RNA, Unité ARN
@article{,
title = {Conformational analysis of Escherichia coli 30S ribosomes containing the single-base mutations G530U, U1498G, G1401C, and C1501G and the double-base mutation G1401C/C1501G},
author = {H Moine and K Nurse and B Ehresmann and C Ehresmann and J Ofengand},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9354641},
isbn = {9354641},
year = {1997},
date = {1997-01-01},
journal = {Biochemistry},
volume = {36},
number = {44},
pages = {13700-13709},
abstract = {Biochemical and genetic studies have pointed out the importance of several sites in 16S ribosomal RNA of Escherichia coli in the decoding process. These sites consist of the core of the decoding center (1400/1500 region) and two other segments (530 and 1050/1200 regions). To detect a possible structural link between these functionally related regions, we analyzed their sensitivity to conformational changes induced by mutations which are located in each of these regions and are known to affect the decoding process. The conformations of five segments of 16S rRNA (1-106, 406-569, 780-978, 997-1247, and 1334-1519) were analyzed by chemical probing of 30S ribosomes containing the following mutations: G530U, U1498G, G1401C, C1501G, and G1401C/C1501G. Ribosomes reconstituted with natural wild-type 16S RNA showed only minor conformational differences with respect to ribosomes isolated from cells. When 16S RNA made in vitro replaced natural 16S RNA, a slightly looser conformation of the central core region was found. Mutant ribosomes made by reconstitution with mutant 16S RNA made in vitro showed conformational effects which were in all cases localized to the region of secondary structure surrounding the site of mutation. Although the core of the decoding center (1400/1500 region) and the two other sites (530 and 1050/1200 regions) participating in the decoding function have been functionally linked, our data indicate that they are structurally independent. They also provide evidence for an unusual structure of the 1400/1500 decoding center, possibly involving noncanonical interactions. Furthermore, the absence of any conformational effect induced by the G530U mutation except at the site of mutation itself points to its direct, as opposed to indirect, involvement in the decoding function of the ribosome.},
note = {0006-2960
Journal Article},
keywords = {16S/chemical synthesis/*chemistry/genetics Ribosomes/chemistry/genetics Structure-Activity Relationship Support, Bacterial/*chemistry/genetics RNA, Base Sequence Cytosine Nucleotides/genetics Deoxyuridine Escherichia coli/genetics Guanine Nucleotides/genetics Molecular Sequence Data *Mutagenesis, Non-U.S. Gov't, Ribosomal, Site-Directed *Nucleic Acid Conformation RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Moine H, Cachia C, Westhof E, Ehresmann B, Ehresmann C
The RNA binding site of S8 ribosomal protein of Escherichia coli: Selex and hydroxyl radical probing studies Article de journal
Dans: RNA, vol. 3, no. 3, p. 255-268, 1997, ISBN: 9056763, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/metabolism Ribosomal Proteins/chemistry/*metabolism Support, Autoradiography Base Sequence Binding Sites Consensus Sequence Escherichia coli Genetic Techniques Hydroxyl Radical/chemistry Models, Bacterial/*metabolism RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation Phylogeny Polymerase Chain Reaction RNA, Non-U.S. Gov't, Ribosomal, Unité ARN
@article{,
title = {The RNA binding site of S8 ribosomal protein of Escherichia coli: Selex and hydroxyl radical probing studies},
author = {H Moine and C Cachia and E Westhof and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9056763},
isbn = {9056763},
year = {1997},
date = {1997-01-01},
journal = {RNA},
volume = {3},
number = {3},
pages = {255-268},
abstract = {The RNA binding site of ribosomal protein S8 of Escherichia coli is confined to a small region within the stem of a hairpin in 16S rRNA (nt 588-605/633-651), and thus represents a model system for understanding RNA/protein interaction rules. The S8 binding site on 16S rRNA was suspected to contain noncanonical features difficult to prove with classical genetical or biochemical means. We performed in vitro iterative selection of RNA aptamers that bind S8. For the different aptamers, the interactions with the protein were probed with hydroxyl radicals. Aptamers that were recognized according to the same structural rules as wild-type RNA, but with variations not found in nature, were identified. These aptamers revealed features in the S8 binding site that had been concealed during previous characterizations by the high base conservation throughout evolution. Our data demonstrate that the core structure of the S8 binding site is composed of three interdependent bases (nt 597/641/643), with an essential intervening adenine nucleotide (position 642). The other elements important for the binding site are a base pair (598/640) above the three interdependent bases and a bulged base at position 595, the identity of which is not important. Possible implications on the geometry of the S8 binding site are discussed with the help of a three-dimensional model.},
note = {1355-8382
Journal Article},
keywords = {16S/chemistry/metabolism Ribosomal Proteins/chemistry/*metabolism Support, Autoradiography Base Sequence Binding Sites Consensus Sequence Escherichia coli Genetic Techniques Hydroxyl Radical/chemistry Models, Bacterial/*metabolism RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation Phylogeny Polymerase Chain Reaction RNA, Non-U.S. Gov't, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Masquida B, Felden B, Westhof E
Context dependent RNA-RNA recognition in a three-dimensional model of the 16S rRNA core Article de journal
Dans: Bioorg Med Chem, vol. 5, no. 6, p. 1021-1035, 1997, ISBN: 9222495, (0968-0896 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/*metabolism Ribosomal Proteins/chemistry Substrate Specificity Support, Base Sequence Escherichia coli/metabolism *Models, Molecular Molecular Sequence Data *Nucleic Acid Conformation Peptide Mapping RNA/*chemistry/*metabolism RNA, Non-U.S. Gov't, Ribosomal, Unité ARN
@article{,
title = {Context dependent RNA-RNA recognition in a three-dimensional model of the 16S rRNA core},
author = {B Masquida and B Felden and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9222495},
isbn = {9222495},
year = {1997},
date = {1997-01-01},
journal = {Bioorg Med Chem},
volume = {5},
number = {6},
pages = {1021-1035},
abstract = {A 3-D model of the core of the 16S rRNA of Escherichia coli containing 328 residues has been built in the protein map derived from neutron scattering data with the help of all the available phylogenetic, biochemical, and cross-linking data. The three pseudoknots of the 16S-core cluster, through the arrangement of complex three-, four- and five-way junctions, around the neck and at the subunit interface. The roles in assembly, initiation or elongation of the three pseudoknots in ribosomal dynamics are emphasized. The 530-loop, localized on the periphery of the 30S particle, could be built with and without a pseudoknot independently of the state of the particle. The pseudoknot of the central domain controls the dynamics of an helix connected to the subunit interface which could trigger some mechanism during translation. The process of the model construction is compatible with a folding scenario in which the 5'-terminal pseudoknot controls the assembly of the central junction and the subsequent folding of the 3'-major domain. The modelling, together with the phylogenetic analysis and the experimental data, point to several potential RNA-RNA contacts which depend on the structural and sequence context in which they occur.},
note = {0968-0896
Journal Article},
keywords = {16S/*chemistry/*metabolism Ribosomal Proteins/chemistry Substrate Specificity Support, Base Sequence Escherichia coli/metabolism *Models, Molecular Molecular Sequence Data *Nucleic Acid Conformation Peptide Mapping RNA/*chemistry/*metabolism RNA, Non-U.S. Gov't, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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}
}
O'Connor M., Brunelli C. A., Firpo M. A., Gregory S. T., Lieberman K. R., Lodmell J. S., Moine H., Ryk D. I. Van, Dahlberg A. E.
Genetic probes of ribosomal RNA function Article de journal
Dans: Biochem Cell Biol, vol. 73, no. 11-12, p. 859-68, 1995, (0829-8211 Journal Article Review Review, Tutorial).
Résumé | BibTeX | Étiquettes: 16S/genetics, Acid, Base, Conformation, Data, Gov't, Messenger/genetics, Molecular, Mutation, Non-U.S., Nucleic, P.H.S., Probes, Ribosomal, Ribosomal/*genetics, RNA, Sequence, Support, Transfer/genetics, U.S.
@article{,
title = {Genetic probes of ribosomal RNA function},
author = { M. O'Connor and C. A. Brunelli and M. A. Firpo and S. T. Gregory and K. R. Lieberman and J. S. Lodmell and H. Moine and D. I. Van Ryk and A. E. Dahlberg},
year = {1995},
date = {1995-01-01},
journal = {Biochem Cell Biol},
volume = {73},
number = {11-12},
pages = {859-68},
abstract = {We have used a genetic approach to uncover the functional roles of rRNA in protein synthesis. Mutations were constructed in a cloned rrn operon by site-directed mutagenesis or isolated by genetic selections following random mutagenesis. We have identified mutations that affect each step in the process of translation. The data are consistent with the results of biochemical and phylogenetic analyses but, in addition, have provided novel information on regions of rRNA not previously investigated.},
note = {0829-8211
Journal Article
Review
Review, Tutorial},
keywords = {16S/genetics, Acid, Base, Conformation, Data, Gov't, Messenger/genetics, Molecular, Mutation, Non-U.S., Nucleic, P.H.S., Probes, Ribosomal, Ribosomal/*genetics, RNA, Sequence, Support, Transfer/genetics, U.S.},
pubstate = {published},
tppubtype = {article}
}
O'Connor M, Brunelli C A, Firpo M A, Gregory S T, Lieberman K R, Lodmell J S, Moine H, Ryk D I Van, Dahlberg A E
Genetic probes of ribosomal RNA function Article de journal
Dans: Biochem Cell Biol, vol. 73, no. 11-12, p. 859-868, 1995, ISBN: 8722001, (0829-8211 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: 16S/genetics RNA, Base Sequence Molecular Sequence Data Mutation Nucleic Acid Conformation RNA Probes RNA, Messenger/genetics RNA, Non-U.S. Gov't Support, P.H.S., Ribosomal, Ribosomal/*genetics RNA, Transfer/genetics Support, U.S. Gov't, Unité ARN
@article{,
title = {Genetic probes of ribosomal RNA function},
author = {M O'Connor and C A Brunelli and M A Firpo and S T Gregory and K R Lieberman and J S Lodmell and H Moine and D I Van Ryk and A E Dahlberg},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8722001},
isbn = {8722001},
year = {1995},
date = {1995-01-01},
journal = {Biochem Cell Biol},
volume = {73},
number = {11-12},
pages = {859-868},
abstract = {We have used a genetic approach to uncover the functional roles of rRNA in protein synthesis. Mutations were constructed in a cloned rrn operon by site-directed mutagenesis or isolated by genetic selections following random mutagenesis. We have identified mutations that affect each step in the process of translation. The data are consistent with the results of biochemical and phylogenetic analyses but, in addition, have provided novel information on regions of rRNA not previously investigated.},
note = {0829-8211
Journal Article
Review
Review, Tutorial},
keywords = {16S/genetics RNA, Base Sequence Molecular Sequence Data Mutation Nucleic Acid Conformation RNA Probes RNA, Messenger/genetics RNA, Non-U.S. Gov't Support, P.H.S., Ribosomal, Ribosomal/*genetics RNA, Transfer/genetics Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Moine H., Dahlberg A. E.
Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis Article de journal
Dans: J Mol Biol, vol. 243, no. 3, p. 402-12, 1994, (0022-2836 Journal Article).
Résumé | BibTeX | Étiquettes: *Mutation, *Nucleic, *Translation, &, 16S/*chemistry/genetics, Acid, Base, beta-Galactosidase/genetics, Codon, coli/*genetics/growth, Conformation, Data, development, Escherichia, Genetic, Gov't, Molecular, Non-U.S., P.H.S., Ribosomal, Ribosomes/*metabolism, RNA, Sequence, Support, Terminator, U.S.
@article{,
title = {Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis},
author = { H. Moine and A. E. Dahlberg},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {243},
number = {3},
pages = {402-12},
abstract = {Helix 34 of E. coli 16 S rRNA (1046 to 1067 and 1189 to 1211) has been proposed to participate directly in the termination of translation at UGA stop codons. We have constructed mutations in this helix in plasmid-encoded rDNA to explore the specific functional roles of the sequence UCAUCA (1199 to 1204) and a secondary structure also involving positions 1054 and 1057-1058. The rRNA mutations were analyzed for their effects on in vivo translational accuracy (stop codon readthrough and frameshifting) as well as growth rate, ribosome synthesis and incorporation into polysomes. Mutations at positions 1054, 1057, 1058, 1199 and 1200 had significant effects on translational accuracy, causing non-specific readthrough of all three stop codons as well as enhanced +1 and -1 frameshifting. Mutations at 1202 and 1203, however, had no effect. The incorporation of deleterious mutant subunits into 70 S ribosomes and polysomes was severely reduced and was associated with a slower growth rate and increased synthesis of host-encoded ribosomes. These data support the proposal that helix 34 is an essential component of the decoding center of the 30 S ribosomal subunit and is not restricted in function to UGA-codon specific termination.},
note = {0022-2836
Journal Article},
keywords = {*Mutation, *Nucleic, *Translation, &, 16S/*chemistry/genetics, Acid, Base, beta-Galactosidase/genetics, Codon, coli/*genetics/growth, Conformation, Data, development, Escherichia, Genetic, Gov't, Molecular, Non-U.S., P.H.S., Ribosomal, Ribosomes/*metabolism, RNA, Sequence, Support, Terminator, U.S.},
pubstate = {published},
tppubtype = {article}
}
Vysotskaya V, Tischenko S, Garber M, Kern D, Mougel M, Ehresmann C, Ehresmann B
The ribosomal protein S8 from Thermus thermophilus VK1. Sequencing of the gene, overexpression of the protein in Escherichia coli and interaction with rRNA Article de journal
Dans: Eur J Biochem, vol. 223, no. 2, p. 437-445, 1994, ISBN: 7519982, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*metabolism Recombinant Proteins/metabolism Ribosomal Proteins/chemistry/*genetics/isolation & purification/metabolism Sequence Alignment Support, Amino Acid Sequence Base Sequence Blotting, Bacterial Molecular Sequence Data Molecular Weight Nucleic Acid Hybridization Polymerase Chain Reaction Promoter Regions (Genetics) Protein Binding Protein Structure, Bacterial/chemistry/genetics/isolation & purification Escherichia coli/genetics/metabolism *Gene Expression *Genes, Bacterial/metabolism RNA, Genetic, Molecular DNA, Non-U.S. Gov't Thermus thermophilus/*genetics Transcription, Ribosomal, Secondary RNA, Southern Cloning, Unité ARN
@article{,
title = {The ribosomal protein S8 from Thermus thermophilus VK1. Sequencing of the gene, overexpression of the protein in Escherichia coli and interaction with rRNA},
author = {V Vysotskaya and S Tischenko and M Garber and D Kern and M Mougel and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7519982},
isbn = {7519982},
year = {1994},
date = {1994-01-01},
journal = {Eur J Biochem},
volume = {223},
number = {2},
pages = {437-445},
abstract = {The gene of the ribosomal protein S8 from Thermus thermophilus VK1 has been isolated from a genomic library by hybridization of an oligonucleotide coding for the N-terminal amino acid sequence of the protein, amplified by PCR and sequenced. Nucleotide sequence reveals an open reading frame coding for a protein of 138 amino acid residues (M(r) 15,839). The codon usage shows that 94% of the codons possess G or C in the third position, and agrees with the preferential usage of codons of high G+C content in the bacteria of the genus Thermus. The amino acid sequence of the protein shows 48% identity with the protein from Escherichia coli. Ribosomal protein S8 from T. thermophilus has been expressed in E. coli under the control of the T7 promoter and purified to homogeneity by heat treatment of the extract followed by cation-exchange chromatography. Conditions were defined in which T. thermophilus protein S8 binds specifically an homologous 16S rRNA fragment containing the putative S8 binding site with an apparent association constant of 5 x 10(7) M-1. The overexpressed protein binds the rRNA with the same affinity as that extracted from T. thermophilus, indicating that the thermophilic protein is correctly folded in E. coli. The specificity of this binding is dependent on the ionic strength. The protein S8 from T. thermophilus recognizes the E. coli rRNA binding sites as efficiently as the S8 protein from E. coli. This result agrees with sequence comparisons of the S8 binding site on the small subunit rRNA from E. coli and from T. thermophilus, showing strong similarities in the regions involved in the interaction. It suggests that the structural features responsible for the recognition are conserved in the mesophilic and thermophilic eubacteria, despite structural peculiarities in the thermophilic partners conferring thermostability.},
note = {0014-2956
Journal Article},
keywords = {16S/*metabolism Recombinant Proteins/metabolism Ribosomal Proteins/chemistry/*genetics/isolation & purification/metabolism Sequence Alignment Support, Amino Acid Sequence Base Sequence Blotting, Bacterial Molecular Sequence Data Molecular Weight Nucleic Acid Hybridization Polymerase Chain Reaction Promoter Regions (Genetics) Protein Binding Protein Structure, Bacterial/chemistry/genetics/isolation & purification Escherichia coli/genetics/metabolism *Gene Expression *Genes, Bacterial/metabolism RNA, Genetic, Molecular DNA, Non-U.S. Gov't Thermus thermophilus/*genetics Transcription, Ribosomal, Secondary RNA, Southern Cloning, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Moine H, Dahlberg A E
Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis Article de journal
Dans: J Mol Biol, vol. 243, no. 3, p. 402-412, 1994, ISBN: 7966269, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/genetics Ribosomes/*metabolism Support, Base Sequence Codon, Genetic beta-Galactosidase/genetics, Non-U.S. Gov't Support, P.H.S. *Translation, Ribosomal, Terminator Escherichia coli/*genetics/growth & development Molecular Sequence Data *Mutation *Nucleic Acid Conformation RNA, U.S. Gov't, Unité ARN
@article{,
title = {Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis},
author = {H Moine and A E Dahlberg},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7966269},
isbn = {7966269},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {243},
number = {3},
pages = {402-412},
abstract = {Helix 34 of E. coli 16 S rRNA (1046 to 1067 and 1189 to 1211) has been proposed to participate directly in the termination of translation at UGA stop codons. We have constructed mutations in this helix in plasmid-encoded rDNA to explore the specific functional roles of the sequence UCAUCA (1199 to 1204) and a secondary structure also involving positions 1054 and 1057-1058. The rRNA mutations were analyzed for their effects on in vivo translational accuracy (stop codon readthrough and frameshifting) as well as growth rate, ribosome synthesis and incorporation into polysomes. Mutations at positions 1054, 1057, 1058, 1199 and 1200 had significant effects on translational accuracy, causing non-specific readthrough of all three stop codons as well as enhanced +1 and -1 frameshifting. Mutations at 1202 and 1203, however, had no effect. The incorporation of deleterious mutant subunits into 70 S ribosomes and polysomes was severely reduced and was associated with a slower growth rate and increased synthesis of host-encoded ribosomes. These data support the proposal that helix 34 is an essential component of the decoding center of the 30 S ribosomal subunit and is not restricted in function to UGA-codon specific termination.},
note = {0022-2836
Journal Article},
keywords = {16S/*chemistry/genetics Ribosomes/*metabolism Support, Base Sequence Codon, Genetic beta-Galactosidase/genetics, Non-U.S. Gov't Support, P.H.S. *Translation, Ribosomal, Terminator Escherichia coli/*genetics/growth & development Molecular Sequence Data *Mutation *Nucleic Acid Conformation RNA, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Allmang C, Mougel M, Westhof E, Ehresmann B, Ehresmann C
Role of conserved nucleotides in building the 16S rRNA binding site of E. coli ribosomal protein S8 Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 18, p. 3708-3714, 1994, ISBN: 7937081, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/*metabolism Ribosomal Proteins/*metabolism, Base Sequence Binding Sites Computer Simulation *Conserved Sequence Escherichia coli/metabolism Models, Molecular Molecular Sequence Data *Nucleic Acid Conformation Point Mutation/physiology RNA, Ribosomal, Unité ARN
@article{,
title = {Role of conserved nucleotides in building the 16S rRNA binding site of E. coli ribosomal protein S8},
author = {C Allmang and M Mougel and E Westhof and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7937081},
isbn = {7937081},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {18},
pages = {3708-3714},
abstract = {Ribosomal protein S8 specifically recognizes a helical and irregular region of 16S rRNA that is highly evolutionary constrained. Despite its restricted size, the precise conformation of this region remains a question of debate. Here, we used chemical probing to analyze the structural consequences of mutations in this RNA region. These data, combined with computer modelling and previously published data on protein binding were used to investigate the conformation of the RNA binding site. The experimental data confirm the model in which adenines A595, A640 and A642 bulge out in the deep groove. In addition to the already proposed non canonical U598-U641 interaction, the structure is stabilized by stacking interactions (between A595 and A640) and an array of hydrogen bonds involving bases and the sugar phosphate backbone. Mutations that alter the ability to form these interdependent interactions result in a local destabilization or reorganization. The specificity of recognition by protein S8 is provided by the irregular and distorted backbone and the two bulged adenines 640 and 642 in the deep groove. The third adenine (A595) is not a direct recognition site but must adopt a bulged position. The U598-U641 pair should not be directly in contact with the protein.},
note = {0305-1048
Journal Article},
keywords = {16S/*chemistry/*metabolism Ribosomal Proteins/*metabolism, Base Sequence Binding Sites Computer Simulation *Conserved Sequence Escherichia coli/metabolism Models, Molecular Molecular Sequence Data *Nucleic Acid Conformation Point Mutation/physiology RNA, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Muller G, Gaspin C, Etienne A, Westhof E
Automatic display of RNA secondary structures Article de journal
Dans: Comput Appl Biosci, vol. 9, no. 5, p. 551-561, 1993, ISBN: 7507400, (0266-7061 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/genetics RNA, 5S/chemistry/genetics Ribonuclease P *Software, Algorithms Bacillus subtilis/chemistry/genetics Base Sequence *Computer Graphics Endoribonucleases/genetics Escherichia coli/chemistry/genetics Molecular Sequence Data Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Bacterial/genetics RNA, Catalytic/genetics RNA, Ribosomal, Unité ARN
@article{,
title = {Automatic display of RNA secondary structures},
author = {G Muller and C Gaspin and A Etienne and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7507400},
isbn = {7507400},
year = {1993},
date = {1993-01-01},
journal = {Comput Appl Biosci},
volume = {9},
number = {5},
pages = {551-561},
abstract = {A set of programs written in C language with the GL library and under UNIX has been developed for generating compact, pleasant and non-overlapping displays of secondary structures of ribonucleic acids. The first program, rnasearch, implements a new search procedure that dynamically rearranges overlapping portions of the two-dimensional drawing while preserving clear and readable displays of the two-dimensional structure. The algorithm is fast (the execution time for the command rnasearch is 38.6 s for the 16S rRNA of Escherichia coli with 1542 bases), accepts outputs from two-dimensional prediction programs and therefore allows for rapid comparison between the various two-dimensional folds generated. A second program, rnadisplay, allows the graphical display of the computed two-dimensional structures on a graphics workstation. Otherwise, it is possible to obtain a paper output of the two-dimensional structure by using the program print2D which builds a Postscript file. Moreover the two-dimensional drawing can be labelled for representing data coming from chemical modifications and/or enzymatic cleavages. Application to a few secondary structures such as RNaseP, 5S rRNA and 16S rRNA are given.},
note = {0266-7061
Journal Article},
keywords = {16S/chemistry/genetics RNA, 5S/chemistry/genetics Ribonuclease P *Software, Algorithms Bacillus subtilis/chemistry/genetics Base Sequence *Computer Graphics Endoribonucleases/genetics Escherichia coli/chemistry/genetics Molecular Sequence Data Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Bacterial/genetics RNA, Catalytic/genetics RNA, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mougel M, Allmang C, Eyermann F, Cachia C, Ehresmann B, Ehresmann C
Minimal 16S rRNA binding site and role of conserved nucleotides in Escherichia coli ribosomal protein S8 recognition Article de journal
Dans: Eur J Biochem, vol. 215, no. 3, p. 787-792, 1993, ISBN: 7689052, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*metabolism Ribosomal Proteins/genetics/*metabolism Support, Adenine/metabolism Bacterial Proteins/metabolism Base Composition Base Sequence Binding Sites Conserved Sequence Escherichia coli/*metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Bacterial/metabolism RNA, Non-U.S. Gov't, Ribosomal, ROMBY, Unité ARN
@article{,
title = {Minimal 16S rRNA binding site and role of conserved nucleotides in Escherichia coli ribosomal protein S8 recognition},
author = {M Mougel and C Allmang and F Eyermann and C Cachia and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7689052},
isbn = {7689052},
year = {1993},
date = {1993-01-01},
journal = {Eur J Biochem},
volume = {215},
number = {3},
pages = {787-792},
abstract = {Escherichia coli ribosomal protein S8 was previously shown to bind a 16S rRNA fragment (nucleotides 584-756) with the same affinity as the complete 16S rRNA, and to shield an irregular helical region (region C) [Mougel, M., Eyermann, F., Westhof, E., Romby, P., Expert-Bezancon, Ebel, J. P., Ehresmann, B. & Ehresmann, C. (1987). J. Mol. Biol. 198, 91-107]. Region C was postulated to display characteristic features: three bulged adenines (A595, A640 and A642), a non-canonical U598-U641 pair surrounded by two G.C pairs. In order to delineate the minimal RNA binding site, deletions were introduced by site-directed mutagenesis and short RNA fragments were synthesized. Their ability to bind S8 was assayed by filter binding. Our results show that the RNA binding site can be restricted to a short helical stem (588-605/633-651) containing region C. The second part of the work focused on region C and on the role of conserved nucleotides as potential determinants of S8 recognition. Single and double mutations were introduced by site-directed mutagenesis in fragment 584-756, and their effect on S8 binding was measured. It was found that the three bulged positions are essential and that adenines are required at positions 640 and 642. U598 is also crucial and the highly conserved G597.C643 pair cannot be inverted. These conserved nucleotides are either directly involved in the recognition process as direct contacts or required to maintain a specific conformation. The strong evolutionary pressure and the small number of positive mutants stress the high stringency of the recognition process.},
note = {0014-2956
Journal Article},
keywords = {16S/*metabolism Ribosomal Proteins/genetics/*metabolism Support, Adenine/metabolism Bacterial Proteins/metabolism Base Composition Base Sequence Binding Sites Conserved Sequence Escherichia coli/*metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Bacterial/metabolism RNA, Non-U.S. Gov't, Ribosomal, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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, (0305-1048 Journal Article).
BibTeX | Étiquettes: &, 5S/*isolation, Acrylic, Human, Nuclear/*isolation, Nylons, purification, Resins, Ribosomal, RNA, Small, Transfer/*isolation, Yeasts/genetics
@article{,
title = {Rapid transfer of small RNAs from a polyacrylamide gel onto a nylon membrane using a gel dryer},
author = { M. L. Wilhelm and W. Baranowski and G. Keith and F. X. Wilhelm},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {15},
pages = {4106},
note = {0305-1048
Journal Article},
keywords = {&, 5S/*isolation, Acrylic, Human, Nuclear/*isolation, Nylons, purification, Resins, Ribosomal, RNA, Small, Transfer/*isolation, Yeasts/genetics},
pubstate = {published},
tppubtype = {article}
}
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
@article{,
title = {Rapid transfer of small RNAs from a polyacrylamide gel onto a nylon membrane using a gel dryer},
author = {M L Wilhelm and W Baranowski and G Keith and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1508703},
isbn = {1508703},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {15},
pages = {4106},
note = {0305-1048
Journal Article},
keywords = {5S/*isolation & purification RNA, Acrylic Resins Human Nylons RNA, Ribosomal, Small Nuclear/*isolation & purification RNA, Transfer/*isolation & purification Yeasts/genetics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}