Huntzinger E, Winter F, Moine H, Ehresmann C, Romby P
Probing RNA structures with enzymes and chemicals in vitro and in vivo Book Chapter
In: Hartmann, R K; Bindereif, A; Schon, A; Westhof, E (Ed.): Handbook of RNA biochemistry, vol. 1, pp. 151-171, Wiley-Vch Verlag, 2005.
Links | BibTeX | Tags: ROMBY, ROMBY thiouridine 6-thioguanosine structures relationships variants, Unité ARN
@inbook{,
title = {Probing RNA structures with enzymes and chemicals in vitro and in vivo},
author = {E Huntzinger and F Winter and H Moine and C Ehresmann and P Romby},
editor = {R K Hartmann and A Bindereif and A Schon and E Westhof},
url = {http://onlinelibrary.wiley.com/doi/10.1002/9783527619504.ch10/summary},
year = {2005},
date = {2005-01-01},
booktitle = {Handbook of RNA biochemistry},
volume = {1},
pages = {151-171},
publisher = {Wiley-Vch Verlag},
keywords = {ROMBY, ROMBY thiouridine 6-thioguanosine structures relationships variants, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Huntzinger E, Boisset S, Saveanu C, Benito Y, Geissmann T, Namane A, Lina G, Etienne J, Ehresmann B, Ehresmann C, Jacquier A, Vandenesch F, Romby P
Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression Journal Article
In: EMBO J, vol. 24, no. 4, pp. 824-835, 2005, ISBN: 15678100, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{,
title = {Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression},
author = {E Huntzinger and S Boisset and C Saveanu and Y Benito and T Geissmann and A Namane and G Lina and J Etienne and B Ehresmann and C Ehresmann and A Jacquier and F Vandenesch and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15678100},
isbn = {15678100},
year = {2005},
date = {2005-01-01},
journal = {EMBO J},
volume = {24},
number = {4},
pages = {824-835},
abstract = {Staphylococcus aureus RNAIII is one of the largest regulatory RNAs, which controls several virulence genes encoding exoproteins and cell-wall-associated proteins. One of the RNAIII effects is the repression of spa gene (coding for the surface protein A) expression. Here, we show that spa repression occurs not only at the transcriptional level but also by RNAIII-mediated inhibition of translation and degradation of the stable spa mRNA by the double-strand-specific endoribonuclease III (RNase III). The 3' end domain of RNAIII, partially complementary to the 5' part of spa mRNA, efficiently anneals to spa mRNA through an initial loop-loop interaction. Although this annealing is sufficient to inhibit in vitro the formation of the translation initiation complex, the coordinated action of RNase III is essential in vivo to degrade the mRNA and irreversibly arrest translation. Our results further suggest that RNase III is recruited for targeting the paired RNAs. These findings add further complexity to the expression of the S. aureus virulon.},
note = {0261-4189
Journal Article},
keywords = {ROMBY, Unité ARN},
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 Journal Article
In: Science, vol. 308, no. 5718, pp. 120-123, 2005, ISBN: 15802605, (1095-9203 Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
Dock-Bregeon A C, Romby P, Springer M
Threonyl-tRNA synthetase: a multifunctional enzyme in E.coli. Book Chapter
In: Ibba, M; Francklyn, C; Cusack, S (Ed.): The aminoacyl-tRNA synthetases, pp. 163-176, Landes Bioscience, 2005.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@inbook{,
title = {Threonyl-tRNA synthetase: a multifunctional enzyme in E.coli.},
author = {A C Dock-Bregeon and P Romby and M Springer},
editor = {M Ibba and C Francklyn and S Cusack},
url = {http://www.landesbioscience.com/curie/chapter/1876},
year = {2005},
date = {2005-01-01},
booktitle = {The aminoacyl-tRNA synthetases},
pages = {163-176},
publisher = {Landes Bioscience},
abstract = {Aminoacyl-tRNA synthetases were discovered in the mid-nineteenfifties1 as モactivating enzymesヤ that yielded モ… an enzyme bound, carboxyl-activated, aminoacid- AMP compoundヤ. These activating enzymes were fractionated such that Hoagland was able to say モseparate enzymes are involved in the activation of several aminoacids.ヤ2 At about the same time, F. Crick proposed his adaptor hypothesis.3 This brilliant hypothesis was confirmed when Hoagland et al4 discovered that their モactivating enzymesヤ were able to attach an amino acid to a small RNA, transfer RNA, that had all the properties of Crickメs adaptor.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Romby P, Springer M
Bacterial translational control at atomic resolution Journal Article
In: Trends Genet, vol. 19, no. 3, pp. 155-161, 2003, ISBN: 12615010, (0168-9525 Journal Article Review Review, Tutorial).
Abstract | Links | BibTeX | Tags: Bacterial *Gene Expression Regulation, Bacterial Models, Base Sequence Conserved Sequence Escherichia coli/*enzymology/*genetics *Gene Expression Regulation, Biological Models, Enzymologic Genes, Genetic, Messenger/genetics/*metabolism RNA, Molecular Molecular Mimicry Nucleic Acid Conformation Operator Regions (Genetics) RNA, Non-U.S. Gov't Threonine-tRNA Ligase/chemistry/*genetics/metabolism *Translation, ROMBY, Thr/*metabolism RNA-Binding Proteins/metabolism Support, Transfer, Unité ARN
@article{,
title = {Bacterial translational control at atomic resolution},
author = {P Romby and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12615010},
isbn = {12615010},
year = {2003},
date = {2003-01-01},
journal = {Trends Genet},
volume = {19},
number = {3},
pages = {155-161},
abstract = {Translational regulation allows rapid adaptation of protein synthesis to environmental conditions. In prokaryotes, the synthesis of many RNA-binding proteins is regulated by a translational feedback mechanism involving a competition between their natural substrate and their binding site on mRNA, which are often thought to resemble each other. This article describes the case of threonyl-tRNA synthetase, which represses the translation of its own mRNA. Recent data provide the first opportunity to describe at the atomic level both the extent and the limit of mimicry between the way this enzyme recognizes tRNA(Thr) and its regulatory site in mRNA. The data also give some clues about how the binding of the synthetase to its mRNA inhibits translation.},
note = {0168-9525
Journal Article
Review
Review, Tutorial},
keywords = {Bacterial *Gene Expression Regulation, Bacterial Models, Base Sequence Conserved Sequence Escherichia coli/*enzymology/*genetics *Gene Expression Regulation, Biological Models, Enzymologic Genes, Genetic, Messenger/genetics/*metabolism RNA, Molecular Molecular Mimicry Nucleic Acid Conformation Operator Regions (Genetics) RNA, Non-U.S. Gov't Threonine-tRNA Ligase/chemistry/*genetics/metabolism *Translation, ROMBY, Thr/*metabolism RNA-Binding Proteins/metabolism Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Caillet J, Nogueira T, Masquida B, Winter F, Graffe M, Dock-Bregeon A C, Torres-Larios A, Sankaranarayanan R, Westhof E, Ehresmann B, Ehresmann C, Romby P, Springer M
The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression Journal Article
In: Mol Microbiol, vol. 47, no. 4, pp. 961-974, 2003, ISBN: 12581352, (0950-382x Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acyl/chemistry/metabolism Ribosomes/metabolism Support, Bacterial Genes, Bacterial Macromolecular Systems Models, Bacterial/chemistry/metabolism RNA, Binding Sites Binding, Competitive Escherichia coli/*enzymology/*genetics Evolution, Messenger/metabolism RNA, Molecular Gene Expression Regulation, Molecular Molecular Mimicry Molecular Structure Mutation Operator Regions (Genetics) Protein Structure, Non-U.S. Gov't Threonine-tRNA Ligase/*chemistry/genetics/*metabolism, ROMBY, Tertiary Protein Subunits RNA, Transfer, Unité ARN, WESTHOF
@article{,
title = {The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression},
author = {J Caillet and T Nogueira and B Masquida and F Winter and M Graffe and A C Dock-Bregeon and A Torres-Larios and R Sankaranarayanan and E Westhof and B Ehresmann and C Ehresmann and P Romby and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12581352},
isbn = {12581352},
year = {2003},
date = {2003-01-01},
journal = {Mol Microbiol},
volume = {47},
number = {4},
pages = {961-974},
abstract = {In addition to its role in tRNA aminoacylation, Escherichia coli threonyl-tRNA synthetase is a regulatory protein which binds a site, called the operator, located in the leader of its own mRNA and inhibits translational initiation by competing with ribosome binding. This work shows that the two essential steps of regulation, operator recognition and inhibition of ribosome binding, are performed by different domains of the protein. The catalytic and the C-terminal domain of the protein are involved in binding the two anticodon arm-like structures in the operator whereas the N-terminal domain of the enzyme is responsible for the competition with the ribosome. This is the first demonstration of a modular structure for a translational repressor and is reminiscent of that of transcriptional regulators. The mimicry between the operator and tRNA, suspected on the basis of previous experiments, is further supported by the fact that identical regions of the synthetase recognize both the operator and the tRNA anticodon arm. Based on these results, and recent structural data, we have constructed a computer-derived molecular model for the operator-threonyl-tRNA synthetase complex, which sheds light on several essential aspects of the regulatory mechanism.},
note = {0950-382x
Journal Article},
keywords = {Amino Acyl/chemistry/metabolism Ribosomes/metabolism Support, Bacterial Genes, Bacterial Macromolecular Systems Models, Bacterial/chemistry/metabolism RNA, Binding Sites Binding, Competitive Escherichia coli/*enzymology/*genetics Evolution, Messenger/metabolism RNA, Molecular Gene Expression Regulation, Molecular Molecular Mimicry Molecular Structure Mutation Operator Regions (Genetics) Protein Structure, Non-U.S. Gov't Threonine-tRNA Ligase/*chemistry/genetics/*metabolism, ROMBY, Tertiary Protein Subunits RNA, Transfer, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Lindell M, Romby P, Wagner E G
Lead(II) as a probe for investigating RNA structure in vivo Journal Article
In: RNA, vol. 8, no. 4, pp. 534-541, 2002, ISBN: 11991646, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence Biochemistry/*methods Comparative Study Lead/*chemistry/*metabolism Molecular Sequence Data Nucleic Acid Conformation Porins/genetics RNA/*chemistry/*metabolism RNA, Messenger/chemistry/metabolism Support, Non-U.S. Gov't, ROMBY, Unité ARN
@article{,
title = {Lead(II) as a probe for investigating RNA structure in vivo},
author = {M Lindell and P Romby and E G Wagner},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11991646},
isbn = {11991646},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {4},
pages = {534-541},
abstract = {In this communication, we describe a simple and reliable method for RNA structure determination in vivo, using the divalent ion, lead(II), as a structural probe. Lead(II) is known to cleave RNA within single-stranded regions, loops, and bulges, whereas cleavages in double-stranded regions are weaker or absent. Because the ion easily entered bacterial cells, Escherichia coli cultures were treated by addition of 50-100 mM lead(II) acetate for 3-7 min, resulting in partial cleavage of RNA in vivo. Cleavage positions were mapped by reverse transcription analysis of total extracted RNA. Three RNAs were analyzed: tmRNA, CopT (the target of the antisense RNA CopA), and the leader region of the ompF mRNA. All three RNAs had previously been analyzed in vitro, and secondary structure models were available. The results presented here show that lead(II) cleavages in vivo yield detailed structural information for these RNAs, which was in good agreement with the models proposed based on in vitro work. These data illustrate the potential of lead(II) as a sequence-independent RNA structure probe for use in living cells.},
note = {1355-8382
Journal Article},
keywords = {Base Sequence Biochemistry/*methods Comparative Study Lead/*chemistry/*metabolism Molecular Sequence Data Nucleic Acid Conformation Porins/genetics RNA/*chemistry/*metabolism RNA, Messenger/chemistry/metabolism Support, Non-U.S. Gov't, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Brunel C, Marquet R, Romby P, Ehresmann C
RNA loop-loop interactions as dynamic functional motifs Journal Article
In: Biochimie, vol. 84, no. 9, pp. 925-944, 2002, ISBN: 12458085, (0300-9084 Journal Article Review Review Literature).
Abstract | Links | BibTeX | Tags: Animals Base Pairing Base Sequence Dimerization HIV-1/genetics Human Kinetics Molecular Sequence Data *Nucleic Acid Conformation RNA/genetics/*metabolism Support, MARQUET, Non-U.S. Gov't Thermodynamics, ROMBY, Unité ARN
@article{,
title = {RNA loop-loop interactions as dynamic functional motifs},
author = {C Brunel and R Marquet and P Romby and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12458085},
isbn = {12458085},
year = {2002},
date = {2002-01-01},
journal = {Biochimie},
volume = {84},
number = {9},
pages = {925-944},
abstract = {RNA loop-loop interactions are frequently used to trigger initial recognition between two RNA molecules. In this review, we present selected well-documented cases that illustrate the diversity of biological processes using RNA loop-loop recognition properties. The first one is related to natural antisense RNAs that play a variety of regulatory functions in bacteria and their extra-chromosomal elements. The second one concerns the dimerization of HIV-1 genomic RNA, which is responsible for the encapsidation of a diploid RNA genome. The third one concerns RNA interactions involving double-loop interactions. These are used by the bicoid mRNA to form dimers, a property that appears to be important for mRNA localization in drosophila embryo, and by bacteriophage phi29 pRNA which forms hexamers that participate in the translocation of the DNA genome through the portal vertex of the capsid. Despite the high diversity of systems and mechanisms, some common features can be highlighted. (1) Efficient recognition requires rapid bi-molecular binding rates, regardless of the RNA pairing scheme. (2) The initial recognition is favored by particular conformations of the loops enabling a proper presentation of nucleotides (generally a restricted number) that initiate the recognition process. (3) The fate of the initial reversible loop-loop complex is dictated by both functional and structural constraints. RNA structures have evolved either to "freeze" the initial complex, or to convert it into a more stable one, which involves propagation of intermolecular interactions along topologically feasible pathways. Stabilization of the initial complex may also be assisted by proteins and/or formation of additional contacts.},
note = {0300-9084
Journal Article
Review
Review Literature},
keywords = {Animals Base Pairing Base Sequence Dimerization HIV-1/genetics Human Kinetics Molecular Sequence Data *Nucleic Acid Conformation RNA/genetics/*metabolism Support, MARQUET, Non-U.S. Gov't Thermodynamics, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wagner E G, Altuvia S, Romby P
Antisense RNAs in bacteria and their genetic elements. Book Chapter
In: Dunlap, J C; Wu, C. -ting (Ed.): Advances in Genetics: Homology Effects., vol. 46, pp. 361-398, Academic Press, 2002, ISBN: 11931231, (0065-2660 Review Review, Academic).
Abstract | Links | BibTeX | Tags: Antisense/*genetics/metabolism RNA, Bacteria/*genetics/metabolism Bacteriophages/genetics Chromosomes, Bacterial Models, Bacterial/*genetics/metabolism Support, Bacterial/genetics Conjugation, Genetic DNA Replication/genetics DNA Transposable Elements/genetics Gene Expression Regulation, Genetic Mutation Plasmids/genetics RNA, Non-U.S. Gov't, ROMBY, Unité ARN
@inbook{,
title = {Antisense RNAs in bacteria and their genetic elements.},
author = {E G Wagner and S Altuvia and P Romby},
editor = {J C Dunlap and C.-ting Wu},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11931231},
isbn = {11931231},
year = {2002},
date = {2002-01-01},
booktitle = {Advances in Genetics: Homology Effects.},
volume = {46},
pages = {361-398},
publisher = {Academic Press},
abstract = {Antisense RNA-mediated regulation is widespread in bacteria. Most antisense RNA control systems have been found in plasmids, phages, and transposons. Fewer examples were identified in bacterial chromosomes. This chapter summarizes our current knowledge about antisense RNAs with respect to their occurrence, their biological roles, and their diverse mechanisms of action. Examples of cis- or trans-encoded antisense RNAs are discussed, and their properties compared. Most antisense RNAs are posttranscriptionally acting inhibitors of target genes, but a few examples of activator antisense RNAs are known. The implications of RNA structure on topologically and kinetically favored binding pathways are addressed, and solutions that have evolved to permit productive interactions between intricately folded RNAs are discussed. Finally, we describe how particular properties of individual antisense/target RNA systems match their respective biological roles.},
note = {0065-2660
Review
Review, Academic},
keywords = {Antisense/*genetics/metabolism RNA, Bacteria/*genetics/metabolism Bacteriophages/genetics Chromosomes, Bacterial Models, Bacterial/*genetics/metabolism Support, Bacterial/genetics Conjugation, Genetic DNA Replication/genetics DNA Transposable Elements/genetics Gene Expression Regulation, Genetic Mutation Plasmids/genetics RNA, Non-U.S. Gov't, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Torres-Larios A, Dock-Bregeon A C, Romby P, Rees B, Sankaranarayanan R, Caillet J, Springer M, Ehresmann C, Ehresmann B, Moras D
Structural basis of translational control by Escherichia coli threonyl tRNA synthetase Journal Article
In: Nat Struct Biol, vol. 9, no. 5, pp. 343-347, 2002, ISBN: 11953757, (1072-8368 Journal Article).
Abstract | Links | BibTeX | Tags: Anticodon/genetics Base Sequence Crystallography, Bacterial/chemistry/genetics/metabolism RNA, Genetic, Messenger/chemistry/genetics/*metabolism RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation Protein Conformation RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*chemistry/*metabolism *Translation, ROMBY, Transfer/chemistry/genetics/metabolism Sequence Alignment Structure-Activity Relationship Support, Unité ARN, X-Ray Escherichia coli/*enzymology/genetics Models
@article{,
title = {Structural basis of translational control by Escherichia coli threonyl tRNA synthetase},
author = {A Torres-Larios and A C Dock-Bregeon and P Romby and B Rees and R Sankaranarayanan and J Caillet and M Springer and C Ehresmann and B Ehresmann and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11953757},
isbn = {11953757},
year = {2002},
date = {2002-01-01},
journal = {Nat Struct Biol},
volume = {9},
number = {5},
pages = {343-347},
abstract = {Escherichia coli threonyl-tRNA synthetase (ThrRS) represses the translation of its own messenger RNA by binding to an operator located upstream of the initiation codon. The crystal structure of the complex between the core of ThrRS and the essential domain of the operator shows that the mRNA uses the recognition mode of the tRNA anticodon loop to initiate binding. The final positioning of the operator, upon which the control mechanism is based, relies on a characteristic RNA motif adapted to the enzyme surface. The finding of other thrS operators that have this conserved motif leads to a generalization of this regulatory mechanism to a subset of Gram-negative bacteria.},
note = {1072-8368
Journal Article},
keywords = {Anticodon/genetics Base Sequence Crystallography, Bacterial/chemistry/genetics/metabolism RNA, Genetic, Messenger/chemistry/genetics/*metabolism RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation Protein Conformation RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*chemistry/*metabolism *Translation, ROMBY, Transfer/chemistry/genetics/metabolism Sequence Alignment Structure-Activity Relationship Support, Unité ARN, X-Ray Escherichia coli/*enzymology/genetics Models},
pubstate = {published},
tppubtype = {article}
}
Tahiri-Alaoui A, Frigotto L, Manville N, Ibrahim J, Romby P, James W
High affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands Journal Article
In: Nucleic Acids Res, vol. 30, no. 10, pp. e45, 2002, ISBN: 12000850, (1362-4962 Journal Article).
Abstract | Links | BibTeX | Tags: Affinity Labels/isolation & purification Base Sequence Binding Sites Binding, Competitive Electrophoretic Mobility Shift Assay Ligands Molecular Sequence Data Nucleic Acid Conformation Oligonucleotides/chemistry/genetics/metabolism RNA/chemistry/isolation & purification/*metabolism Streptavidin/chemistry/*metabolism, ROMBY, Unité ARN
@article{,
title = {High affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands},
author = {A Tahiri-Alaoui and L Frigotto and N Manville and J Ibrahim and P Romby and W James},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12000850},
isbn = {12000850},
year = {2002},
date = {2002-01-01},
journal = {Nucleic Acids Res},
volume = {30},
number = {10},
pages = {e45},
abstract = {We have isolated 2'-Fluoro-substituted RNA aptamers that bind to streptavidin (SA) with an affinity around 7 +/- 1.8 nM, comparable with that of recently described peptide aptamers. Binding to SA was not prevented by prior saturation with biotin, enabling nucleic acid aptamers to form useful ternary complexes. Mutagenesis, secondary structure analysis, ribonuclease footprinting and deletion analysis provided evidence for the essential structural features of SA-binding aptamers. In order to provide a general method for the exploitation of these aptamers, we produced derivatives in which they were fused to the naturally structured RNA elements, CopT or CopA. In parallel, we produced derivatives of CD4-binding aptamers fused to the complementary CopA or CopT elements. When mixed, these two chimeric aptamers rapidly hybridized, by virtue of CopA-CopT complementarity, to form stable, bi-functional aptamers that we called 'adaptamers'. We show that a CD4-SA-binding adaptamer can be used to capture CD4 onto a SA-derivatized surface, illustrating their general utility as indirect affinity ligands.},
note = {1362-4962
Journal Article},
keywords = {Affinity Labels/isolation & purification Base Sequence Binding Sites Binding, Competitive Electrophoretic Mobility Shift Assay Ligands Molecular Sequence Data Nucleic Acid Conformation Oligonucleotides/chemistry/genetics/metabolism RNA/chemistry/isolation & purification/*metabolism Streptavidin/chemistry/*metabolism, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Sankaranarayanan R, Dock-Bregeon A C, Rees B, Bovee M, Caillet J, Romby P, Francklyn C S, Moras D
Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase Journal Article
In: Nat Struct Biol, vol. 7, no. 6, pp. 461-465, 2000, ISBN: 10881191, (1072-8368 Journal Article).
Abstract | Links | BibTeX | Tags: Binding Sites Catalytic Domain Crystallography, Molecular Molecular Sequence Data Protein Binding Protein Conformation Sequence Deletion/genetics Serine-tRNA Ligase/chemistry/metabolism Structure-Activity Relationship Substrate Specificity Support, Non-U.S. Gov't Threonine/analogs & derivatives/chemistry/*metabolism Threonine-tRNA Ligase/*chemistry/genetics/*metabolism Valine-tRNA Ligase/chemistry/metabolism Zinc/*metabolism, ROMBY, Unité ARN, X-Ray Dimerization Escherichia coli/*enzymology Kinetics Models
@article{,
title = {Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase},
author = {R Sankaranarayanan and A C Dock-Bregeon and B Rees and M Bovee and J Caillet and P Romby and C S Francklyn and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10881191},
isbn = {10881191},
year = {2000},
date = {2000-01-01},
journal = {Nat Struct Biol},
volume = {7},
number = {6},
pages = {461-465},
abstract = {Accurate translation of the genetic code depends on the ability of aminoacyl-tRNA synthetases to distinguish between similar amino acids. In order to investigate the basis of amino acid recognition and to understand the role played by the zinc ion present in the active site of threonyl-tRNA synthetase, we have determined the crystal structures of complexes of an active truncated form of the enzyme with a threonyl adenylate analog or threonine. The zinc ion is directly involved in threonine recognition, forming a pentacoordinate intermediate with both the amino group and the side chain hydroxyl. Amino acid activation experiments reveal that the enzyme shows no activation of isosteric valine, and activates serine at a rate 1,000-fold less than that of cognate threonine. This study demonstrates that the zinc ion is neither strictly catalytic nor structural and suggests how the zinc ion ensures that only amino acids that possess a hydroxyl group attached to the beta-position are activated.},
note = {1072-8368
Journal Article},
keywords = {Binding Sites Catalytic Domain Crystallography, Molecular Molecular Sequence Data Protein Binding Protein Conformation Sequence Deletion/genetics Serine-tRNA Ligase/chemistry/metabolism Structure-Activity Relationship Substrate Specificity Support, Non-U.S. Gov't Threonine/analogs & derivatives/chemistry/*metabolism Threonine-tRNA Ligase/*chemistry/genetics/*metabolism Valine-tRNA Ligase/chemistry/metabolism Zinc/*metabolism, ROMBY, Unité ARN, X-Ray Dimerization Escherichia coli/*enzymology Kinetics Models},
pubstate = {published},
tppubtype = {article}
}
Kolb F A, Malmgren C, Westhof E, Ehresmann C, Ehresmann B, Wagner E G, Romby P
In: RNA, vol. 6, no. 3, pp. 311-324, 2000, ISBN: 10744017, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Antisense/*metabolism RNA, Bacterial Proteins/*metabolism Base Pairing Base Sequence Binding Sites Cations, Divalent Computer Simulation Metals, Double-Stranded/metabolism RNA, Heavy/metabolism Models, Messenger/metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA Stability RNA, Non-U.S. Gov't, ROMBY, Spliced Leader/metabolism Support, Unité ARN
@article{,
title = {An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment},
author = {F A Kolb and C Malmgren and E Westhof and C Ehresmann and B Ehresmann and E G Wagner and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10744017},
isbn = {10744017},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {3},
pages = {311-324},
abstract = {The antisense RNA CopA binds to the leader region of the repA mRNA (target: CopT). Previous studies on CopA-CopT pairing in vitro showed that the dominant product of antisense RNA-mRNA binding is not a full RNA duplex. We have studied here the structure of CopA-CopT complex, combining chemical and enzymatic probing and computer graphic modeling. CopI, a truncated derivative of CopA unable to bind CopT stably, was also analyzed. We show here that after initial loop-loop interaction (kissing), helix propagation resulted in an extended kissing complex that involves the formation of two intermolecular helices. By introducing mutations (base-pair inversions) into the upper stem regions of CopA and CopT, the boundaries of the two newly formed intermolecular helices were delimited. The resulting extended kissing complex represents a new type of four-way junction structure that adopts an asymmetrical X-shaped conformation formed by two helical domains, each one generated by coaxial stacking of two helices. This structure motif induces a side-by-side alignment of two long intramolecular helices that, in turn, facilitates the formation of an additional intermolecular helix that greatly stabilizes the inhibitory CopA-CopT RNA complex. This stabilizer helix cannot form in CopI-CopT complexes due to absence of the sequences involved. The functional significance of the three-dimensional models of the extended kissing complex (CopI-CopT) and the stable complex (CopA-CopT) are discussed.},
note = {1355-8382
Journal Article},
keywords = {Antisense/*metabolism RNA, Bacterial Proteins/*metabolism Base Pairing Base Sequence Binding Sites Cations, Divalent Computer Simulation Metals, Double-Stranded/metabolism RNA, Heavy/metabolism Models, Messenger/metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA Stability RNA, Non-U.S. Gov't, ROMBY, Spliced Leader/metabolism Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Kolb F A, Engdahl H M, Slagter-Jager J G, Ehresmann B, Ehresmann C, Westhof E, Wagner E G, Romby P
Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA Journal Article
In: EMBO J, vol. 19, no. 21, pp. 5905-5915, 2000, ISBN: 11060041, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Antisense/*chemistry/*genetics/metabolism RNA, Bacterial Models, Bacterial Proteins/genetics Base Sequence Binding, Bacterial/chemistry/genetics/metabolism Support, Competitive DNA Primers/genetics Escherichia coli/chemistry/genetics/metabolism Genes, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't, ROMBY, Unité ARN
@article{,
title = {Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA},
author = {F A Kolb and H M Engdahl and J G Slagter-Jager and B Ehresmann and C Ehresmann and E Westhof and E G Wagner and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11060041},
isbn = {11060041},
year = {2000},
date = {2000-01-01},
journal = {EMBO J},
volume = {19},
number = {21},
pages = {5905-5915},
abstract = {The antisense RNA, CopA, regulates the replication frequency of plasmid R1 through inhibition of RepA translation by rapid and specific binding to its target RNA (CopT). The stable CopA-CopT complex is characterized by a four-way junction structure and a side-by-side alignment of two long intramolecular helices. The significance of this structure for binding in vitro and control in vivo was tested by mutations in both CopA and CopT. High rates of stable complex formation in vitro and efficient inhibition in vivo required initial loop-loop complexes to be rapidly converted to extended interactions. These interactions involve asymmetric helix progression and melting of the upper stems of both RNAs to promote the formation of two intermolecular helices. Data presented here delineate the boundaries of these helices and emphasize the need for unimpeded helix propagation. This process is directional, i.e. one of the two intermolecular helices (B) must form first to allow formation of the other (B'). A binding pathway, characterized by a hierarchy of intermediates leading to an irreversible and inhibitory RNA-RNA complex, is proposed.},
note = {0261-4189
Journal Article},
keywords = {Antisense/*chemistry/*genetics/metabolism RNA, Bacterial Models, Bacterial Proteins/genetics Base Sequence Binding, Bacterial/chemistry/genetics/metabolism Support, Competitive DNA Primers/genetics Escherichia coli/chemistry/genetics/metabolism Genes, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Dock-Bregeon A, Sankaranarayanan R, Romby P, Caillet J, Springer M, Rees B, Francklyn C S, Ehresmann C, Moras D
Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem Journal Article
In: Cell, vol. 103, no. 6, pp. 877-884, 2000, ISBN: 11136973, (0092-8674 Journal Article).
Abstract | Links | BibTeX | Tags: Acylation Amino Acid Activation Binding Sites Crystallography, Amino Acyl/chemistry/*metabolism Serine/metabolism Support, Molecular Mutation *Nucleic Acid Conformation Protein Structure, Non-U.S. Gov't Threonine/metabolism Threonine-tRNA Ligase/*chemistry/*genetics/metabolism Zinc/metabolism, ROMBY, Tertiary *RNA Editing RNA, Transfer, Unité ARN, X-Ray Kinetics Models
@article{,
title = {Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem},
author = {A Dock-Bregeon and R Sankaranarayanan and P Romby and J Caillet and M Springer and B Rees and C S Francklyn and C Ehresmann and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11136973},
isbn = {11136973},
year = {2000},
date = {2000-01-01},
journal = {Cell},
volume = {103},
number = {6},
pages = {877-884},
abstract = {Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot be fully discriminated at that step. We show that hydrolysis of the incorrectly formed ser-tRNA(Thr) is performed at a specific site in the N-terminal domain of the enzyme. The present study suggests that both classes of synthetases use effectively the ability of the CCA end of tRNA to switch between a hairpin and a helical conformation for aminoacylation and editing. As a consequence, the editing mechanism of both classes of synthetases can be described as mirror images, as already seen for tRNA binding and amino acid activation.},
note = {0092-8674
Journal Article},
keywords = {Acylation Amino Acid Activation Binding Sites Crystallography, Amino Acyl/chemistry/*metabolism Serine/metabolism Support, Molecular Mutation *Nucleic Acid Conformation Protein Structure, Non-U.S. Gov't Threonine/metabolism Threonine-tRNA Ligase/*chemistry/*genetics/metabolism Zinc/metabolism, ROMBY, Tertiary *RNA Editing RNA, Transfer, Unité ARN, X-Ray Kinetics Models},
pubstate = {published},
tppubtype = {article}
}
Brunel C, Romby P
Probing RNA structure and RNA-ligand complexes with chemical probes Journal Article
In: Methods Enzymol, vol. 318, pp. 3-21, 2000, ISBN: 10889976, (0076-6879 Journal Article Review Review, Tutorial).
Links | BibTeX | Tags: Crystallography, Genetic, ROMBY, Unité ARN, X-Ray *Ligands Nucleic Acid Conformation Nucleotides/chemistry/metabolism Proteins/chemistry RNA/*chemistry/drug effects/*metabolism Transcription
@article{,
title = {Probing RNA structure and RNA-ligand complexes with chemical probes},
author = {C Brunel and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10889976},
isbn = {10889976},
year = {2000},
date = {2000-01-01},
journal = {Methods Enzymol},
volume = {318},
pages = {3-21},
note = {0076-6879
Journal Article
Review
Review, Tutorial},
keywords = {Crystallography, Genetic, ROMBY, Unité ARN, X-Ray *Ligands Nucleic Acid Conformation Nucleotides/chemistry/metabolism Proteins/chemistry RNA/*chemistry/drug effects/*metabolism Transcription},
pubstate = {published},
tppubtype = {article}
}
Benito Y, Kolb F A, Romby P, Lina G, Etienne J, Vandenesch F
In: RNA, vol. 6, no. 5, pp. 668-679, 2000, ISBN: 10836788, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Antisense/*chemistry/genetics/metabolism RNA, Bacterial Models, Bacterial/*chemistry/genetics/metabolism Ribosomes/metabolism Staphylococcal Protein A/*genetics Staphylococcus aureus/*chemistry/*genetics/metabolism Support, Base Sequence Binding Sites/genetics DNA Primers/genetics Escherichia coli/metabolism Gene Expression Genes, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, ROMBY, Unité ARN
@article{,
title = {Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression},
author = {Y Benito and F A Kolb and P Romby and G Lina and J Etienne and F Vandenesch},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10836788},
isbn = {10836788},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {5},
pages = {668-679},
abstract = {RNAIII, a 514-nt RNA molecule, regulates the expression of many Staphylococcus aureus genes encoding exoproteins and cell-wall-associated proteins. We have studied the structure of RNAIII in solution, using a combination of chemical and enzymatic probes. A model of the secondary structure was derived from experimental data with the help of computer simulation of RNA folding. The model contains 14 hairpin structures connected by unpaired nucleotides. The data also point to three helices formed by distant nucleotides that close off structural domains. This model was generally compatible with the results of in vivo probing experiments with dimethylsulfate in late exponential-phase cultures. Toe-printing experiments revealed that the ribosome binding site of hld, which is encoded by RNAIII, was accessible to the Escherichia coli 30S ribosomal subunit, suggesting that the in vitro structure represented a translatable form of RNAIII. We also found that, within the 3' end of RNAIII, the conserved hairpin 13 and the terminator form an intrinsic structural domain that exerts specific regulatory activity on protein A gene expression.},
note = {1355-8382
Journal Article},
keywords = {Antisense/*chemistry/genetics/metabolism RNA, Bacterial Models, Bacterial/*chemistry/genetics/metabolism Ribosomes/metabolism Staphylococcal Protein A/*genetics Staphylococcus aureus/*chemistry/*genetics/metabolism Support, Base Sequence Binding Sites/genetics DNA Primers/genetics Escherichia coli/metabolism Gene Expression Genes, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Sankaranarayanan R, Dock-Bregeon A C, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D
In: Cell, vol. 97, no. 3, pp. 371-381, 1999, ISBN: 10319817, (0092-8674 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acyl/*chemistry/genetics/*metabolism Sequence Homology, Messenger/genetics RNA, Non-U.S. Gov't Zinc/*chemistry, ROMBY, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN
@article{,
title = {The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site},
author = {R Sankaranarayanan and A C Dock-Bregeon and P Romby and J Caillet and M Springer and B Rees and C Ehresmann and B Ehresmann and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10319817},
isbn = {10319817},
year = {1999},
date = {1999-01-01},
journal = {Cell},
volume = {97},
number = {3},
pages = {371-381},
abstract = {E. coli threonyl-tRNA synthetase (ThrRS) is a class II enzyme that represses the translation of its own mRNA. We report the crystal structure at 2.9 A resolution of the complex between tRNA(Thr) and ThrRS, whose structural features reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination.},
note = {0092-8674
Journal Article},
keywords = {Amino Acid Support, Amino Acyl/*chemistry/genetics/*metabolism Sequence Homology, Messenger/genetics RNA, Non-U.S. Gov't Zinc/*chemistry, ROMBY, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Perrin L, Romby P, Laurenti P, Berenger H, Kallenbach S, Bourbon H M, Pradel J
In: J Biol Chem, vol. 274, no. 10, pp. 6315-6323, 1999, ISBN: 10037720, (0021-9258 Journal Article).
Abstract | Links | BibTeX | Tags: Animals Base Sequence Binding Sites/genetics Chromatin/*genetics DNA/*genetics DNA-Binding Proteins/*genetics/metabolism Drosophila/*genetics *Drosophila Proteins *Genes, Insect Insect Proteins/*genetics/metabolism Molecular Sequence Data Phosphorylation RNA/*genetics RNA-Binding Proteins/*genetics/metabolism Support, Non-U.S. Gov't, ROMBY, Unité ARN
@article{,
title = {The Drosophila modifier of variegation modulo gene product binds specific RNA sequences at the nucleolus and interacts with DNA and chromatin in a phosphorylation-dependent manner},
author = {L Perrin and P Romby and P Laurenti and H Berenger and S Kallenbach and H M Bourbon and J Pradel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10037720},
isbn = {10037720},
year = {1999},
date = {1999-01-01},
journal = {J Biol Chem},
volume = {274},
number = {10},
pages = {6315-6323},
abstract = {modulo belongs to the modifier of Position Effect Variegation class of Drosophila genes, suggesting a role for its product in regulating chromatin structure. Genetics assigned a second function to the gene, in protein synthesis capacity. Bifunctionality is consistent with protein localization in two distinct subnuclear compartments, chromatin and nucleolus, and with its organization in modules potentially involved in DNA and RNA binding. In this study, we examine nucleic acid interactions established by Modulo at nucleolus and chromatin and the mechanism that controls the distribution and balances the function of the protein in the two compartments. Structure/function analysis and oligomer selection/amplification experiments indicate that, in vitro, two basic terminal domains independently contact DNA without sequence specificity, whereas a central RNA Recognition Motif (RRM)-containing domain allows recognition of a novel sequence-/motif-specific RNA class. Phosphorylation moreover is shown to down-regulate DNA binding. Evidence is provided that in vivo nucleolar Modulo is highly phosphorylated and belongs to a ribonucleoprotein particle, whereas chromatin-associated protein is not modified. A functional scheme is finally proposed in which modification by phosphorylation modulates Mod subnuclear distribution and balances its function at the nucleolus and chromatin.},
note = {0021-9258
Journal Article},
keywords = {Animals Base Sequence Binding Sites/genetics Chromatin/*genetics DNA/*genetics DNA-Binding Proteins/*genetics/metabolism Drosophila/*genetics *Drosophila Proteins *Genes, Insect Insect Proteins/*genetics/metabolism Molecular Sequence Data Phosphorylation RNA/*genetics RNA-Binding Proteins/*genetics/metabolism Support, Non-U.S. Gov't, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Schlegl J, Gegout V, Schlager B, Hentze M W, Westhof E, Ehresmann C, Ehresmann B, Romby P
Probing the structure of the regulatory region of human transferrin receptor messenger RNA and its interaction with iron regulatory protein-1 Journal Article
In: RNA, vol. 3, no. 10, pp. 1159-1172, 1997, ISBN: 9326491, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Base Composition Base Sequence Binding Sites Electrophoresis, Messenger/*chemistry/metabolism RNA-Binding Proteins/*metabolism Receptors, Molecular Molecular Sequence Data Mutation *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Polyacrylamide Gel Ethylnitrosourea/pharmacology Human Hydrolysis Hydroxyl Radical/metabolism Iron/metabolism Iron Regulatory Protein 1 Iron-Regulatory Proteins Iron-Sulfur Proteins/*metabolism Lead/pharmacology Models, ROMBY, Transferrin/*genetics Ribonuclease T1/metabolism Support, Unité ARN
@article{,
title = {Probing the structure of the regulatory region of human transferrin receptor messenger RNA and its interaction with iron regulatory protein-1},
author = {J Schlegl and V Gegout and B Schlager and M W Hentze and E Westhof and C Ehresmann and B Ehresmann and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9326491},
isbn = {9326491},
year = {1997},
date = {1997-01-01},
journal = {RNA},
volume = {3},
number = {10},
pages = {1159-1172},
abstract = {A portion of the 3'UTR of the human transferrin receptor mRNA mediates iron-dependent regulation of mRNA stability. The minimal RNA regulatory region contains three conserved hairpins, so-called iron responsive elements (IREs), that are recognized specifically by iron regulatory proteins (IRPs). The structure of this regulatory region and its complex with IRP-1 was probed using a combination of enzymes and chemicals. The data support the existence of an intrinsic IRE loop structure that is constrained by an internal C-G base pair. This particular structure is one of the determinants required for optimal IRP binding. IRP-1 covers one helical turn of the IRE and protects conserved residues in each of the three IREs: the bulged cytosine and nucleotides in the hairpin loops. Two essential IRP-phosphate contacts were identified by ethylation interference. Three-dimensional modeling of one IRE reveals that IRP-1 contacts several bases and the ribose-phosphate backbone located on one face in the deep groove, but contacts also exist with the shallow groove. A conformational change of the IRE loop mediated by IRP-1 binding was visualized by Pb2+-catalyzed hydrolysis. This effect is dependent on the loop structure and on the nature of the closing base pair. Within the regulatory region of transferrin receptor mRNA, IRP-1 induces reactivity changes in a U-rich hairpin loop that requires the presence of the stem-loop structure located just downstream the endonucleolytic cleavage site identified by Binder et al. (Binder R et al. 1994, EMBO J 13:1969-1980). These results provide indications of the mechanism by which IRP-1 stabilizes the transferrin receptor mRNA under iron depletion conditions.},
note = {1355-8382
Journal Article},
keywords = {Base Composition Base Sequence Binding Sites Electrophoresis, Messenger/*chemistry/metabolism RNA-Binding Proteins/*metabolism Receptors, Molecular Molecular Sequence Data Mutation *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Polyacrylamide Gel Ethylnitrosourea/pharmacology Human Hydrolysis Hydroxyl Radical/metabolism Iron/metabolism Iron Regulatory Protein 1 Iron-Regulatory Proteins Iron-Sulfur Proteins/*metabolism Lead/pharmacology Models, ROMBY, Transferrin/*genetics Ribonuclease T1/metabolism Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Malmgren C, Wagner E G, Ehresmann C, Ehresmann B, Romby P
Antisense RNA control of plasmid R1 replication. The dominant product of the antisense rna-mrna binding is not a full RNA duplex Journal Article
In: J Biol Chem, vol. 272, no. 19, pp. 12508-12512, 1997, ISBN: 9139701, (0021-9258 Journal Article).
Abstract | Links | BibTeX | Tags: Antisense/*metabolism RNA, Bacterial Proteins/genetics/metabolism Base Sequence Copper/metabolism Electrophoresis, Messenger/*metabolism Ribonuclease III Support, Non-U.S. Gov't, Polyacrylamide Gel Endoribonucleases/metabolism Escherichia coli Lead Molecular Sequence Data Nucleic Acid Conformation Plasmids/*metabolism Pseudomonas RNA, ROMBY, Unité ARN
@article{,
title = {Antisense RNA control of plasmid R1 replication. The dominant product of the antisense rna-mrna binding is not a full RNA duplex},
author = {C Malmgren and E G Wagner and C Ehresmann and B Ehresmann and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9139701},
isbn = {9139701},
year = {1997},
date = {1997-01-01},
journal = {J Biol Chem},
volume = {272},
number = {19},
pages = {12508-12512},
abstract = {The replication frequency of plasmid R1 is controlled by an antisense RNA (CopA) that binds to its target site (CopT) in the leader region of repA mRNA and inhibits the synthesis of the replication initiator protein RepA. Previous studies on CopA-CopT pairing in vitro revealed the existence of a primary loop-loop interaction (kissing complex) that is subsequently converted to an almost irreversible duplex. However, the structure of more stable binding intermediates that lead to the formation of a complete duplex was speculative. Here, we investigated the interaction between CopA and CopT by using Pb(II)-induced cleavages. The kissing complex was studied using a truncated antisense RNA (CopI) that is unable to form a full duplex with CopT. Furthermore, RNase III, which is known to process the CopA-CopT complex in vivo, was used to detect the existence of a full duplex. Our data indicate that the formation of a full CopA-CopT duplex appears to be a very slow process in vitro. Unexpectedly, we found that the loop-loop interaction persists in the predominant CopA-CopT complex and is stabilized by intermolecular base pairing involving the 5'-proximal 30 nucleotides of CopA and the complementary region of CopT. This almost irreversible complex suffices to inhibit ribosome binding at the tap ribosome binding site and may be the inhibitory complex in vivo.},
note = {0021-9258
Journal Article},
keywords = {Antisense/*metabolism RNA, Bacterial Proteins/genetics/metabolism Base Sequence Copper/metabolism Electrophoresis, Messenger/*metabolism Ribonuclease III Support, Non-U.S. Gov't, Polyacrylamide Gel Endoribonucleases/metabolism Escherichia coli Lead Molecular Sequence Data Nucleic Acid Conformation Plasmids/*metabolism Pseudomonas RNA, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Eckardt S, Romby P, Sczakiel G
Implications of RNA structure on the annealing of a potent antisense RNA directed against the human immunodeficiency virus type 1 Journal Article
In: Biochemistry, vol. 36, no. 42, pp. 12711-12721, 1997, ISBN: 9335527, (0006-2960 Journal Article).
Abstract | Links | BibTeX | Tags: Anti-HIV Agents/*chemistry/pharmacology Base Sequence Cells, Antisense/*chemistry/*pharmacology RNA, Calf Thymus Ribonuclease T1 Software Support, Cultured Electrophoresis, Genetic, Insertional Mutagenesis, Non-U.S. Gov't Thermodynamics Transcription, Polyacrylamide Gel HIV-1/*drug effects/genetics Human Kinetics Molecular Sequence Data Mutagenesis, ROMBY, Site-Directed *Nucleic Acid Conformation Oligodeoxyribonucleotides Oligoribonucleotides/*chemistry/pharmacology RNA, Unité ARN, Viral/*chemistry/drug effects Ribonuclease H
@article{,
title = {Implications of RNA structure on the annealing of a potent antisense RNA directed against the human immunodeficiency virus type 1},
author = {S Eckardt and P Romby and G Sczakiel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9335527},
isbn = {9335527},
year = {1997},
date = {1997-01-01},
journal = {Biochemistry},
volume = {36},
number = {42},
pages = {12711-12721},
abstract = {Antisense RNA-mediated regulation in bacterial systems is related to the kinetics of RNA-RNA annealing in vitro. Here, we investigated the secondary structure of alphaY69, an effective HIV-directed antisense RNA in human cells. Purified RNA preparations contain a single conformer. The global structure was identified by a cleavage experiment under native conditions using a short complementary oligonucleotide and RNase H. Structural analyses indicate a three-domain structure of alphaY69 consisting of two stem-loop elements connected by a seven-nucleotide single-stranded hinge region. Kinetic data suggest that the formation of base pairs between a CGC triplet of alphaY69 and its target RNA is essential for fast annealing. The complementary sequence stretch of the target folds into a high-energy secondary structure. The relationship between modifications in structural elements of alphaY69 and the annealing kinetics suggested that rate-limiting steps of the annealing involve a single site of alphaY69 and do not involve its 5' or 3'-end. Further, the data indicate that both initial base-specific interactions and duplex formation are dependent on the CGC triplet of the central region of alphaY69. This mechanism represents a specific and efficient way of RNA-RNA annealing that is initiated by the interaction of unstructured RNA regions.},
note = {0006-2960
Journal Article},
keywords = {Anti-HIV Agents/*chemistry/pharmacology Base Sequence Cells, Antisense/*chemistry/*pharmacology RNA, Calf Thymus Ribonuclease T1 Software Support, Cultured Electrophoresis, Genetic, Insertional Mutagenesis, Non-U.S. Gov't Thermodynamics Transcription, Polyacrylamide Gel HIV-1/*drug effects/genetics Human Kinetics Molecular Sequence Data Mutagenesis, ROMBY, Site-Directed *Nucleic Acid Conformation Oligodeoxyribonucleotides Oligoribonucleotides/*chemistry/pharmacology RNA, Unité ARN, Viral/*chemistry/drug effects Ribonuclease H},
pubstate = {published},
tppubtype = {article}
}
Yusupova G, Reinbolt J, Wakao H, Laalami S, Grunberg-Manago M, Romby P, Ehresmann B, Ehresmann C
Topography of the Escherichia coli initiation factor 2/fMet-tRNA(f)(Met) complex as studied by cross-linking Journal Article
In: Biochemistry, vol. 35, no. 9, pp. 2978-2984, 1996, ISBN: 8608135, (0006-2960 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Sequence Base Sequence Cisplatin/*pharmacology Cross-Linking Reagents Electrophoresis, Met/chemistry/isolation & purification/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Polyacrylamide Gel Escherichia coli/drug effects/*metabolism Eukaryotic Initiation Factor-2/chemistry/isolation & purification/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation Peptide Fragments/chemistry/isolation & purification Protein Conformation RNA, ROMBY, Transfer, Unité ARN
@article{,
title = {Topography of the Escherichia coli initiation factor 2/fMet-tRNA(f)(Met) complex as studied by cross-linking},
author = {G Yusupova and J Reinbolt and H Wakao and S Laalami and M Grunberg-Manago and P Romby and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8608135},
isbn = {8608135},
year = {1996},
date = {1996-01-01},
journal = {Biochemistry},
volume = {35},
number = {9},
pages = {2978-2984},
abstract = {trans-Diamminedichloroplatinum(II) was used to induce reversible cross-links between Escherichia coli initiation factor 2 (IF-2) and fMet-tRNA(f)(Met). Two distinct cross-links between IF-2 and the initiator tRNA were produced. Analysis of the cross-linking regions on both RNA and protein moieties reveals that the T arm of the tRNA is in the proximity of a region of the C-terminal domain of IF-2 (residues Asn611-Arg645). This cross-link is well-correlated with the fact that the C-domain of IF-2 contains the fMet-tRNA binding site and that the cross-linked RNA fragment precisely maps in a region which is protected by IF-2 from chemical modification and enzymatic digestion. Rather unexpectedly, a second cross-link was characterized which involves the anticodon arm of fMet-tRNA(f)(Met) and the N-terminal part of IF-2 (residues Trp215-Arg237).},
note = {0006-2960
Journal Article},
keywords = {Amino Acid Sequence Base Sequence Cisplatin/*pharmacology Cross-Linking Reagents Electrophoresis, Met/chemistry/isolation & purification/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Polyacrylamide Gel Escherichia coli/drug effects/*metabolism Eukaryotic Initiation Factor-2/chemistry/isolation & purification/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation Peptide Fragments/chemistry/isolation & purification Protein Conformation RNA, ROMBY, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Romby P, Caillet J, Ebel C, Sacerdot C, Graffe M, Eyermann F, Brunel C, Moine H, Ehresmann C, Ehresmann B, Springer M
The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions Journal Article
In: EMBO J, vol. 15, no. 21, pp. 5976-5987, 1996, ISBN: 8918475, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Anticodon Base Sequence Binding Sites Binding, Bacterial Gene Expression Regulation, Bacterial/chemistry/genetics/metabolism RNA, Biological Molecular Sequence Data Mutagenesis, Competitive Escherichia coli/*enzymology/*genetics/metabolism Gene Expression Regulation, Enzymologic Models, Genetic, Messenger/genetics/metabolism Repressor Proteins/genetics Support, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics Translation, ROMBY, Site-Directed Nucleic Acid Conformation Operator Regions (Genetics) RNA, Unité ARN
@article{,
title = {The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions},
author = {P Romby and J Caillet and C Ebel and C Sacerdot and M Graffe and F Eyermann and C Brunel and H Moine and C Ehresmann and B Ehresmann and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8918475},
isbn = {8918475},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {21},
pages = {5976-5987},
abstract = {Threonyl-tRNA synthetase from Escherichia coli represses the translation of its own mRNA by binding to the operator region located upstream from the ribosome binding site. The operator contains two stemloop structures which interact specifically with the homodimeric enzyme. Here, we provide in vitro and in vivo evidence that these two stem-loop structures are recognized by the enzyme in an analogous way and mimic the anticodon arm of E.coli tRNA(Thr). Determination of the stoichiometry of the different RNA-threonyl-tRNA synthetase complexes reveals that two tRNA(Thr) molecules bind to the enzyme whereas only one thrS operator interacts with the homodimeric enzyme. A model is presented in which the two anticodon-like domains of the operator bind symmetrically to the two tRNA(Thr) anticodon recognition sites (one per subunit) of the dimeric threonyl-tRNA synthetase. Although symmetrical operator-repressor interactions in transcriptional control are widespread, this report stresses the importance of such interactions in translational regulation of gene expression.},
note = {0261-4189
Journal Article},
keywords = {Anticodon Base Sequence Binding Sites Binding, Bacterial Gene Expression Regulation, Bacterial/chemistry/genetics/metabolism RNA, Biological Molecular Sequence Data Mutagenesis, Competitive Escherichia coli/*enzymology/*genetics/metabolism Gene Expression Regulation, Enzymologic Models, Genetic, Messenger/genetics/metabolism Repressor Proteins/genetics Support, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics Translation, ROMBY, Site-Directed Nucleic Acid Conformation Operator Regions (Genetics) RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Romby P, Caillet J, Ebel C, Sacerdot C, Graffe M, Eyermann F, Brunel C, Moine H, Ehresmann C, Ehresmann B, Springer M
The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions Journal Article
In: EMBO J, vol. 15, no. 21, pp. 5976-5987, 1996, ISBN: 8918475, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Anticodon Base Sequence Binding Sites Binding, Bacterial Gene Expression Regulation, Bacterial/chemistry/genetics/metabolism RNA, Biological Molecular Sequence Data Mutagenesis, Competitive Escherichia coli/*enzymology/*genetics/metabolism Gene Expression Regulation, Enzymologic Models, Genetic, Messenger/genetics/metabolism Repressor Proteins/genetics Support, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics Translation, ROMBY, Site-Directed Nucleic Acid Conformation Operator Regions (Genetics) RNA, Unité ARN
@article{,
title = {The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions},
author = {P Romby and J Caillet and C Ebel and C Sacerdot and M Graffe and F Eyermann and C Brunel and H Moine and C Ehresmann and B Ehresmann and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8918475},
isbn = {8918475},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {21},
pages = {5976-5987},
abstract = {Threonyl-tRNA synthetase from Escherichia coli represses the translation of its own mRNA by binding to the operator region located upstream from the ribosome binding site. The operator contains two stemloop structures which interact specifically with the homodimeric enzyme. Here, we provide in vitro and in vivo evidence that these two stem-loop structures are recognized by the enzyme in an analogous way and mimic the anticodon arm of E.coli tRNA(Thr). Determination of the stoichiometry of the different RNA-threonyl-tRNA synthetase complexes reveals that two tRNA(Thr) molecules bind to the enzyme whereas only one thrS operator interacts with the homodimeric enzyme. A model is presented in which the two anticodon-like domains of the operator bind symmetrically to the two tRNA(Thr) anticodon recognition sites (one per subunit) of the dimeric threonyl-tRNA synthetase. Although symmetrical operator-repressor interactions in transcriptional control are widespread, this report stresses the importance of such interactions in translational regulation of gene expression.},
note = {0261-4189
Journal Article},
keywords = {Anticodon Base Sequence Binding Sites Binding, Bacterial Gene Expression Regulation, Bacterial/chemistry/genetics/metabolism RNA, Biological Molecular Sequence Data Mutagenesis, Competitive Escherichia coli/*enzymology/*genetics/metabolism Gene Expression Regulation, Enzymologic Models, Genetic, Messenger/genetics/metabolism Repressor Proteins/genetics Support, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics Translation, ROMBY, Site-Directed Nucleic Acid Conformation Operator Regions (Genetics) RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Malmgren C, Engdahl H M, Romby P, Wagner E G
In: RNA, vol. 2, no. 10, pp. 1022-1032, 1996, ISBN: 8849778, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Antisense/chemistry/*metabolism RNA, Bacterial Proteins/genetics Base Sequence Escherichia coli/genetics Genetic Techniques Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation Peptide Chain Initiation/*genetics Protein Sorting Signals/genetics *Proteins R Factors/*chemistry/genetics RNA, Bacterial/chemistry/metabolism RNA, Messenger/chemistry/*metabolism Ribosomes/*metabolism Support, Non-U.S. Gov't, ROMBY, Unité ARN
@article{,
title = {An antisense/target RNA duplex or a strong intramolecular RNA structure 5' of a translation initiation signal blocks ribosome binding: the case of plasmid R1},
author = {C Malmgren and H M Engdahl and P Romby and E G Wagner},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8849778},
isbn = {8849778},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {10},
pages = {1022-1032},
abstract = {Antisense RNAs in prokaryotic systems often inhibit translation of mRNAs. In some cases, this involves sequestration of Shine-Dalgarno (SD) sequences and start codons. In other cases, antisense/target RNA duplexes do not overlap these signals, but form upstream. We have performed toeprinting analyses on repA mRNA of plasmid R1, both free and in duplex with the antisense RNA, CopA. An intermolecular RNA duplex 2 nt upstream of the tap SD prevents ribosome binding. An intrastrand stem-loop at this location yields the same inhibition. Thus, stable secondary structures immediately upstream of the tap SD sequence inhibit translation, as shown by toeprinting in vitro and repA-lacZ expression in vivo. Previous work showed that repA (initiator protein) expression requires tap (leader peptide) translation. Toeprinting data confirm that the tap ribosome binding site (RBS) is accessible, whereas the repA RBS, which is sequestered by a stable stem-loop, is weakly recognized by the ribosome. Truncated CopA RNA (CopI) is unable to pair completely with target RNA, but proceeds normally to a kissing intermediate. This mutant RNA species inhibits repA expression in vivo. By a kinetic toeprint inhibition protocol, we have shown that the structure of the kissing complex is sufficient to sterically prevent ribosome binding. These results are discussed in comparison with the effect of RNA structures elsewhere in the ribosome-binding region of an mRNA.},
note = {1355-8382
Journal Article},
keywords = {Antisense/chemistry/*metabolism RNA, Bacterial Proteins/genetics Base Sequence Escherichia coli/genetics Genetic Techniques Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation Peptide Chain Initiation/*genetics Protein Sorting Signals/genetics *Proteins R Factors/*chemistry/genetics RNA, Bacterial/chemistry/metabolism RNA, Messenger/chemistry/*metabolism Ribosomes/*metabolism Support, Non-U.S. Gov't, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Brunel C, Romby P, Sacerdot C, de Smit M, Graffe M, Dondon J, van Duin J, Ehresmann B, Ehresmann C, Springer M
Stabilised secondary structure at a ribosomal binding site enhances translational repression in E. coli Journal Article
In: J Mol Biol, vol. 253, no. 2, pp. 277-290, 1995, ISBN: 7563089, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Bacterial *Gene Expression Regulation, Base Composition Base Sequence Binding Sites Comparative Study Enzyme Repression Escherichia coli/genetics/*metabolism Gene Expression Regulation, Enzymologic Homeostasis Kinetics Mathematics Models, Genetic *Translation, Genetic beta-Galactosidase/biosynthesis, Messenger/biosynthesis/*chemistry/*metabolism Recombinant Proteins/biosynthesis Ribosomes/*metabolism Support, Non-U.S. Gov't Temperature Threonine-tRNA Ligase/*biosynthesis Transcription, ROMBY, Site-Directed *Nucleic Acid Conformation RNA, Theoretical Molecular Sequence Data Mutagenesis, Unité ARN
@article{,
title = {Stabilised secondary structure at a ribosomal binding site enhances translational repression in E. coli},
author = {C Brunel and P Romby and C Sacerdot and M de Smit and M Graffe and J Dondon and J van Duin and B Ehresmann and C Ehresmann and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7563089},
isbn = {7563089},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {253},
number = {2},
pages = {277-290},
abstract = {The expression of the gene encoding Escherichia coli threonyl-tRNA synthetase is negatively autoregulated at the translational level. The negative feedback is due to the binding of the synthetase to an operator site on its own mRNA located upstream of the initiation codon. The present work describes the characterisation of operator mutants that have the rare property of enhancing repression. These mutations cause (1) a low basal level of expression, (2) a temperature-dependent expression, and (3) an increased capacity of the synthetase to repress its own expression at low temperature. Surprisingly, this enhancement of repression is not explained by an increase of affinity of the mutant operators for the enzyme but by the formation, at low temperature, of a few supplementary base-pairs between the ribosomal binding site and a normally single-stranded domain of the operator. Although this additional base-pairing only slightly inhibits ribosome binding in the absence of repressor, simple thermodynamic considerations indicate that this is sufficient to increase repression. This increase is explained by the competition between the ribosome and repressor for overlapping regions of the mRNA. When the ribosomal binding site is base-paired, the ribosome cannot bind while the repressor can, giving the repressor the advantage in the competition. Thus, the existence of an open versus base-paired equilibrium in a ribosomal binding site of a translational operator amplifies the magnitude of control. This molecular amplification device might be an essential component of translational control considering the low free repressor/ribosome ratio of the low affinity of translational repressors for their target operators.},
note = {0022-2836
Journal Article},
keywords = {Bacterial *Gene Expression Regulation, Base Composition Base Sequence Binding Sites Comparative Study Enzyme Repression Escherichia coli/genetics/*metabolism Gene Expression Regulation, Enzymologic Homeostasis Kinetics Mathematics Models, Genetic *Translation, Genetic beta-Galactosidase/biosynthesis, Messenger/biosynthesis/*chemistry/*metabolism Recombinant Proteins/biosynthesis Ribosomes/*metabolism Support, Non-U.S. Gov't Temperature Threonine-tRNA Ligase/*biosynthesis Transcription, ROMBY, Site-Directed *Nucleic Acid Conformation RNA, Theoretical Molecular Sequence Data Mutagenesis, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Zenkova M, Ehresmann C, Caillet J, Springer M, Karpova G, Ehresmann B, Romby P
In: Eur J Biochem, vol. 231, no. 3, pp. 726-735, 1995, ISBN: 7544283, (0014-2956 Journal Article).
Abstract | Links | BibTeX | Tags: Alkylation Base Sequence Cross-Linking Reagents Escherichia coli/enzymology/*genetics Molecular Sequence Data Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/*chemistry/genetics RNA-Binding Proteins/*chemistry/genetics Support, Genetic, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics *Translation, ROMBY, Unité ARN
@article{,
title = {A novel approach to introduce site-directed specific cross-links within RNA-protein complexes. Application to the Escherichia coli threonyl-tRNA synthetase/translational operator complex},
author = {M Zenkova and C Ehresmann and J Caillet and M Springer and G Karpova and B Ehresmann and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7544283},
isbn = {7544283},
year = {1995},
date = {1995-01-01},
journal = {Eur J Biochem},
volume = {231},
number = {3},
pages = {726-735},
abstract = {We describe a methodology which allows the introduction of a photoactivatable azido group at specific internal positions of any RNA in order to identify the neighboring elements of an interacting protein. The first step involves site-directed modification of the target RNA with an antisense oligodeoxyribonucleotide bearing, at its 3' or 5' phosphate, a 4-[-N-(2-chloroethyl)-N-methylamino]benzylmethylamino group. Position N7 of a guanine residue located in the close vicinity of the hybrid is the main target for alkylation. The antisense oligodeoxyribonucleotide is then removed by acidic pH treatment and a photoreactive reagent (2,4-dinitro-5-fluorophenylazide) is condensed to the modified nucleotide. This method was used to induce specific cross-links between Escherichia coli threonyl-tRNA synthetase and the leader region of threonyl-tRNA synthetase mRNA, which is involved in translational feedback regulation. Control experiments revealed that the modification affects neither the structure of the mRNA nor the interaction with the enzyme. More than 50% of the modified mRNA complexed with threonyl-tRNA synthetase can be cross-linked to the enzyme, depending on the nucleotide modified.},
note = {0014-2956
Journal Article},
keywords = {Alkylation Base Sequence Cross-Linking Reagents Escherichia coli/enzymology/*genetics Molecular Sequence Data Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/*chemistry/genetics RNA-Binding Proteins/*chemistry/genetics Support, Genetic, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics *Translation, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Blomberg P, Engdahl H M, Malmgren C, Romby P, Wagner E G
In: Mol Microbiol, vol. 12, no. 1, pp. 49-60, 1994, ISBN: 7520116, (0950-382x Journal Article).
Abstract | Links | BibTeX | Tags: Antisense/chemistry/*physiology RNA, Bacterial Models, Bacterial Proteins/genetics/*metabolism Base Sequence Binding Sites *DNA Replication *Gene Expression Regulation, Bacterial/*genetics Reading Frames Ribosomes/*metabolism Sequence Alignment Support, Genetic, Genetic Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Peptides/*genetics/physiology *Proteins R Factors/*genetics RNA, Non-U.S. Gov't Translation, ROMBY, Unité ARN
@article{,
title = {Replication control of plasmid R1: disruption of an inhibitory RNA structure that sequesters the repA ribosome-binding site permits tap-independent RepA synthesis},
author = {P Blomberg and H M Engdahl and C Malmgren and P Romby and E G Wagner},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7520116},
isbn = {7520116},
year = {1994},
date = {1994-01-01},
journal = {Mol Microbiol},
volume = {12},
number = {1},
pages = {49-60},
abstract = {The replication frequency of plasmid R1 is controlled by an antisense RNA, CopA, that inhibits the synthesis of the replication initiator protein, RepA, at the post-transcriptional level. This inhibition is indirect and affects translation of a leader peptide reading frame (tap). Translation of tap is required for repA translation (Blomberg et al., 1992). Here we asked whether an RNA stem-loop sequestering the repA ribosome-binding site blocks tap translation-independent repA expression. Destabilization of this structure resulted in tap-independent RepA synthesis, concomitant with a loss of CopA-mediated inhibition; thus, CopA acts at the level of tap translation. Structure probing of RepA mRNAs confirmed that the introduced mutations induced a local destabilization in the repA ribosome-binding site stem-loop. An increased spacing between the repA Shine-Dalgarno region and the start codon permitted even higher repA expression. In Incl alpha/IncB plasmids, an RNA pseudoknot acts as an activator for rep translation. We suggest that the regulatory pathway in plasmid R1 does not involve an activator RNA pseudoknot.},
note = {0950-382x
Journal Article},
keywords = {Antisense/chemistry/*physiology RNA, Bacterial Models, Bacterial Proteins/genetics/*metabolism Base Sequence Binding Sites *DNA Replication *Gene Expression Regulation, Bacterial/*genetics Reading Frames Ribosomes/*metabolism Sequence Alignment Support, Genetic, Genetic Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Peptides/*genetics/physiology *Proteins R Factors/*genetics RNA, Non-U.S. Gov't Translation, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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 Journal Article
In: Eur J Biochem, vol. 215, no. 3, pp. 787-792, 1993, ISBN: 7689052, (0014-2956 Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
Brunel C, Romby P, Moine H, Caillet J, Grunberg-Manago M, Springer M, Ehresmann B, Ehresmann C
In: Biochimie, vol. 75, no. 12, pp. 1167-1179, 1993, ISBN: 8199252, (0300-9084 Journal Article).
Abstract | Links | BibTeX | Tags: Bacterial/*genetics Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) Point Mutation Protein Structure, Base Sequence Escherichia coli/*enzymology/genetics Gene Deletion Gene Expression Regulation, Genetic, Messenger/chemistry/metabolism RNA, Met/chemistry/metabolism Ribosomes/metabolism Structure-Activity Relationship Support, Non-U.S. Gov't Threonine-tRNA Ligase/chemistry/*genetics/metabolism Translation, ROMBY, Secondary RNA, Transfer, Unité ARN
@article{,
title = {Translational regulation of the Escherichia coli threonyl-tRNA synthetase gene: structural and functional importance of the thrS operator domains},
author = {C Brunel and P Romby and H Moine and J Caillet and M Grunberg-Manago and M Springer and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8199252},
isbn = {8199252},
year = {1993},
date = {1993-01-01},
journal = {Biochimie},
volume = {75},
number = {12},
pages = {1167-1179},
abstract = {Previous work showed that E coli threonyl-tRNA synthetase (ThrRS) binds to the leader region of its own mRNA and represses its translation by blocking ribosome binding. The operator consists of four distinct domains, one of them (domain 2) sharing structural analogies with the anticodon arm of the E coli tRNA(Thr). The regulation specificity can be switched by using tRNA identity rules, suggesting that the operator could be recognized by ThrRS as a tRNA-like structure. In the present paper, we investigated the relative contribution of the four domains to the regulation process by using deletions and point mutations. This was achieved by testing the effects of the mutations on RNA conformation (by probing experiments), on ThrRS recognition (by footprinting experiments and measure of the competition with tRNA(Thr) for aminoacylation), on ribosome binding and ribosome/ThrRS competition (by toeprinting experiments). It turns out that: i) the four domains are structurally and functionally independent; ii) domain 2 is essential for regulation and contains the major structural determinants for ThrRS binding; iii) domain 4 is involved in control and ThrRS recognition, but to a lesser degree than domain 2. However, the previously described analogies with the acceptor-like stem are not functionally significant. How it is recognized by ThrRS remains to be resolved; iv) domain 1, which contains the ribosome loading site, is not involved in ThrRS recognition. The binding of ThrRS probably masks the ribosome binding site by steric hindrance and not by direct contacts. This is only achieved when ThrRS interacts with both domains 2 and 4; and v) the unpaired domain 3, which connects domains 2 and 4, is not directly involved in ThrRS recognition. It should serve as an articulation to provide an appropriate spacing between domains 2 and 4. Furthermore, it is possibly involved in ribosome binding.},
note = {0300-9084
Journal Article},
keywords = {Bacterial/*genetics Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) Point Mutation Protein Structure, Base Sequence Escherichia coli/*enzymology/genetics Gene Deletion Gene Expression Regulation, Genetic, Messenger/chemistry/metabolism RNA, Met/chemistry/metabolism Ribosomes/metabolism Structure-Activity Relationship Support, Non-U.S. Gov't Threonine-tRNA Ligase/chemistry/*genetics/metabolism Translation, ROMBY, Secondary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Romby P, Brunel C, Caillet J, Springer M, Grunberg-Manago M, Westhof E, Ehresmann C, Ehresmann B
In: Nucleic Acids Res, vol. 20, no. 21, pp. 5633-5640, 1992, ISBN: 1280807, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Acylation Anticodon Base Sequence Binding, Bacterial Methionine-tRNA Ligase/metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/metabolism RNA, Competitive Escherichia coli/enzymology/*genetics *Gene Expression Regulation, Genetic, Met/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/antagonists & inhibitors/*genetics/metabolism Translation, ROMBY, Thr/metabolism Repressor Proteins/*metabolism Ribosomes/metabolism Support, Transfer, Transfer/*metabolism RNA, Unité ARN
@article{,
title = {Molecular mimicry in translational control of E. coli threonyl-tRNA synthetase gene. Competitive inhibition in tRNA aminoacylation and operator-repressor recognition switch using tRNA identity rules},
author = {P Romby and C Brunel and J Caillet and M Springer and M Grunberg-Manago and E Westhof and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1280807},
isbn = {1280807},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {21},
pages = {5633-5640},
abstract = {We previously showed that: (i) E.coli threonyl-tRNA synthetase (ThrRS) binds to the leader of its mRNA and represses translation by preventing ribosome binding to its loading site; (ii) the translational operator shares sequence and structure similarities with tRNA(Thr); (iii) it is possible to switch the specificity of the translational control from ThrRS to methionyl-tRNA synthetase (MetRS) by changing the CGU anticodon-like sequence to CAU, the tRNA(Met) anticodon. Here, we show that the wild type (CGU) and the mutated (CAU) operators act as competitive inhibitors of tRNA(Thr) and tRNA(fMet) for aminoacylation catalyzed by E.coli ThrRS and MetRS, respectively. The apparent Kd of the MetRS/CAU operator complex is one order magnitude higher than that of the ThrRS/CGU operator complex. Although ThrRS and MetRS shield the anticodon- and acceptor-like domains of their respective operators, the relative contribution of these two domains differs significantly. As in the threonine system, the interaction of MetRS with the CAU operator occludes ribosome binding to its loading site. The present data demonstrate that the anticodon-like sequence is one major determinant for the identity of the operator and the regulation specificity. It further shows that the tRNA-like operator obeys to tRNA identity rules.},
note = {0305-1048
Journal Article},
keywords = {Acylation Anticodon Base Sequence Binding, Bacterial Methionine-tRNA Ligase/metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/metabolism RNA, Competitive Escherichia coli/enzymology/*genetics *Gene Expression Regulation, Genetic, Met/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/antagonists & inhibitors/*genetics/metabolism Translation, ROMBY, Thr/metabolism Repressor Proteins/*metabolism Ribosomes/metabolism Support, Transfer, Transfer/*metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Graffe M, Dondon J, Caillet J, Romby P, Ehresmann C, Ehresmann B, Springer M
The specificity of translational control switched with transfer RNA identity rules Journal Article
In: Science, vol. 255, no. 5047, pp. 994-996, 1992, ISBN: 1372129, (0036-8075 Journal Article).
Abstract | Links | BibTeX | Tags: Bacterial Genes, Bacterial Molecular Sequence Data Nucleic Acid Conformation RNA, Bacterial Proteins/metabolism Base Sequence DNA Mutational Analysis *Gene Expression Regulation, Bacterial/metabolism RNA, Genetic, Messenger/*metabolism/ultrastructure RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics/metabolism *Translation, ROMBY, Structural, Thr/*metabolism Support, Transfer, Unité ARN
@article{,
title = {The specificity of translational control switched with transfer RNA identity rules},
author = {M Graffe and J Dondon and J Caillet and P Romby and C Ehresmann and B Ehresmann and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1372129},
isbn = {1372129},
year = {1992},
date = {1992-01-01},
journal = {Science},
volume = {255},
number = {5047},
pages = {994-996},
abstract = {The interaction of Escherichia coli threonyl-transfer RNA (tRNA) synthetase with the leader sequence of its own messenger RNA inhibits ribosome binding, resulting in negative translational feedback regulation. The leader sequence resembles the substrate (tRNA(Thr)) of the enzyme, and the nucleotides that mediate the correct recognition of the leader and the tRNA may be the same. A mutation suggested by tRNA identity rules that switches the resemblance of the leader sequence from tRNA(Thr) to tRNA(Met) causes the translation of the threonyl-tRNA synthetase messenger RNA to become regulated by methionyl-tRNA synthetase. This identity swap in the leader messenger RNA indicates that tRNA identity rules may be extended to interactions of synthetases with other RNAs.},
note = {0036-8075
Journal Article},
keywords = {Bacterial Genes, Bacterial Molecular Sequence Data Nucleic Acid Conformation RNA, Bacterial Proteins/metabolism Base Sequence DNA Mutational Analysis *Gene Expression Regulation, Bacterial/metabolism RNA, Genetic, Messenger/*metabolism/ultrastructure RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics/metabolism *Translation, ROMBY, Structural, Thr/*metabolism Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Brunel C, Caillet J, Lesage P, Graffe M, Dondon J, Moine H, Romby P, Ehresmann C, Ehresmann B, Grunberg-Manago M, Springer M
Domains of the Escherichia coli threonyl-tRNA synthetase translational operator and their relation to threonine tRNA isoacceptors Journal Article
In: J Mol Biol, vol. 227, no. 3, pp. 621-634, 1992, ISBN: 1383551, (0022-2836).
Abstract | Links | BibTeX | Tags: Bacterial/genetics Gene Expression Regulation, Bacterial/genetics RNA, Base Sequence Escherichia coli/genetics Gene Expression Regulation, Enzymologic/*genetics Molecular Sequence Data Mutagenesis, Genetic/*genetics, Messenger/*genetics/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics/metabolism Translation, ROMBY, Site-Directed/genetics Nucleic Acid Conformation RNA, Thr/*genetics/metabolism Recombinant Fusion Proteins/genetics Support, Transfer, Unité ARN
@article{,
title = {Domains of the Escherichia coli threonyl-tRNA synthetase translational operator and their relation to threonine tRNA isoacceptors},
author = {C Brunel and J Caillet and P Lesage and M Graffe and J Dondon and H Moine and P Romby and C Ehresmann and B Ehresmann and M Grunberg-Manago and M Springer},
url = {http://www.ncbi.nlm.nih.gov/pubmed/1383551},
doi = {10.1016/0022-2836(92)90212-3},
isbn = {1383551},
year = {1992},
date = {1992-01-01},
journal = {J Mol Biol},
volume = {227},
number = {3},
pages = {621-634},
abstract = {The expression of the gene for threonyl-tRNA synthetase (thrS) is negatively autoregulated at the translational level in Escherichia coli. The synthetase binds to a region of the thrS leader mRNA upstream from the ribosomal binding site inhibiting subsequent translation. The leader mRNA consists of four structural domains. The present work shows that mutations in these four domains affect expression and/or regulation in different ways. Domain 1, the 3' end of the leader, contains the ribosomal binding site, which appears not to be essential for synthetase binding. Mutations in this domain probably affect regulation by changing the competition between the ribosome and the synthetase for binding to the leader. Domain 2, 3' from the ribosomal binding site, is a stem and loop with structural similarities to the tRNA(Thr) anticodon arm. In tRNAs the anticodon loop is seven nucleotides long, mutations that increase or decrease the length of the anticodon-like loop of domain 2 from seven nucleotides abolish control. The nucleotides in the second and third positions of the anticodon-like sequence are essential for recognition and the nucleotide in the wobble position is not, again like tRNA(Thr). The effect of mutations in domain 3 indicate that it acts as an articulation between domains 2 and 4. Domain 4 is a stable arm that has similarities to the acceptor arm of tRNA(Thr) and is shown to be necessary for regulation. Based on this mutational analysis and previous footprinting experiments, it appears that domains 2 and 4, those analogous to tRNA(Thr), are involved in binding the synthetase which inhibits translation probably by interfering with ribosome loading at the nearby translation initiation site.},
note = {0022-2836},
keywords = {Bacterial/genetics Gene Expression Regulation, Bacterial/genetics RNA, Base Sequence Escherichia coli/genetics Gene Expression Regulation, Enzymologic/*genetics Molecular Sequence Data Mutagenesis, Genetic/*genetics, Messenger/*genetics/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics/metabolism Translation, ROMBY, Site-Directed/genetics Nucleic Acid Conformation RNA, Thr/*genetics/metabolism Recombinant Fusion Proteins/genetics Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}