Publications
2005
Vergara A, Lorber B, Sauter C, Giege R, Zagari A
Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology Article de journal
Dans: Biophys Chem, vol. 118, no. 2-3, p. 102-112, 2005, ISBN: 16150532, (0301-4622 (Print) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, GIEGE Animals *Biological Sciences Crystallization Equipment Design Humans Protein Conformation Proteins/*chemistry Research Support, Non-U.S. Gov't X-Ray Diffraction, SAUTER, Unité ARN
@article{,
title = {Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology},
author = {A Vergara and B Lorber and C Sauter and R Giege and A Zagari},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16150532},
isbn = {16150532},
year = {2005},
date = {2005-01-01},
journal = {Biophys Chem},
volume = {118},
number = {2-3},
pages = {102-112},
abstract = {The crystallographic quality of protein crystals that were grown in microgravity has been compared to that of crystals that were grown in parallel on earth gravity under otherwise identical conditions. A goal of this comparison was to assess if a more accurate 3D-structure can be derived from crystallographic analysis of the former crystals. Therefore, the properties of crystals prepared with the Advanced Protein Crystallisation Facility (APCF) on earth and in orbit during the last decade were evaluated. A statistical analysis reveals that about half of the crystals produced under microgravity had a superior X-ray diffraction limit with respect of terrestrial controls. Eleven protein structures could be determined at previously unachieved resolutions using crystals obtained in the APCF. Microgravity induced features of the most relevant structures are reported. A second goal of this study was to identify the cause of the crystal quality enhancement useful for structure determination. No correlations between the effect of microgravity and other system-dependent parameters, such as isoelectric point or crystal solvent content, were found except the reduced convection during the crystallisation process. Thus, crystal growth under diffusive regime appears to be the key parameter explaining the beneficial effect of microgravity on crystal quality. The mimicry of these effects on earth in gels or in capillary tubes is discussed and the practical consequences for structural biology highlighted.},
note = {0301-4622 (Print)
Journal Article
Review},
keywords = {FRUGIER, GIEGE Animals *Biological Sciences Crystallization Equipment Design Humans Protein Conformation Proteins/*chemistry Research Support, Non-U.S. Gov't X-Ray Diffraction, SAUTER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Bonnefond L, Fender A, Rudinger-Thirion J, Giege R, Florentz C, Sissler M
Toward the Full Set of Human Mitochondrial Aminoacyl-tRNA Synthetases: Characterization of AspRS and TyrRS Article de journal
Dans: Biochemistry, vol. 44, no. 12, p. 4805-4816, 2005, ISBN: 15779907, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: FLORENTZ, FRUGIER, SISSLER, Unité ARN
@article{,
title = {Toward the Full Set of Human Mitochondrial Aminoacyl-tRNA Synthetases: Characterization of AspRS and TyrRS},
author = {L Bonnefond and A Fender and J Rudinger-Thirion and R Giege and C Florentz and M Sissler},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15779907},
isbn = {15779907},
year = {2005},
date = {2005-01-01},
journal = {Biochemistry},
volume = {44},
number = {12},
pages = {4805-4816},
abstract = {The human mitochondrion possesses a translational machinery devoted to the synthesis of 13 proteins. While the required tRNAs and rRNAs are produced by transcription of the mitochondrial genome, all other factors needed for protein synthesis are synthesized in the cytosol and imported. This is the case for aminoacyl-tRNA synthetases, the enzymes which esterify their cognate tRNA with the specific amino acid. The genes for the full set of cytosolic aaRSs are well defined, but only nine genes for mitochondrial synthetases are known. Here we describe the genes for human mitochondrial aspartyl- and tyrosyl-tRNA synthetases and the initial characterization of the enzymes. Both belong to the expected class of synthetases, have a dimeric organization, and aminoacylate Escherichia coli tRNAs as well as in vitro transcribed human mitochondrial tRNAs. Genes for the remaining missing synthetases were also found with the exception of glutaminyl-tRNA synthetase. Their sequence analysis confirms and further extends the view that, except for lysyl- and glycyl-tRNA synthetases, human mitochondrial and cytosolic enzymes are coded by two different sets of genes.},
note = {0006-2960
Journal Article},
keywords = {FLORENTZ, FRUGIER, SISSLER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2004
Théobald-Dietrich A, Frugier M, Giege R, Rudinger-Thirion J
Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA Article de journal
Dans: Nucleic Acids Res, vol. 32, no. 3, p. 1091-1096, 2004, ISBN: 14872064, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/metabolism Base Sequence Lysine/*analogs & derivatives/*metabolism Lysine-tRNA Ligase/metabolism Methanosarcina barkeri/genetics Mitochondria/genetics Molecular Sequence Data Nucleic Acid Conformation Peptide Elongation Factor Tu/*metabolism RNA, Archaeal/chemistry/*metabolism RNA, FRUGIER, Non-U.S. Gov't Yeasts/enzymology, Ser/chemistry Selenocysteine/metabolism Support, Transfer, Transfer/chemistry/*metabolism RNA, Unité ARN
@article{,
title = {Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA},
author = {A Théobald-Dietrich and M Frugier and R Giege and J Rudinger-Thirion},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14872064},
isbn = {14872064},
year = {2004},
date = {2004-01-01},
journal = {Nucleic Acids Res},
volume = {32},
number = {3},
pages = {1091-1096},
abstract = {The newly discovered tRNA(Pyl) is involved in specific incorporation of pyrrolysine in the active site of methylamine methyltransferases in the archaeon Methanosarcina barkeri. In solution probing experiments, a transcript derived from tRNA(Pyl) displays a secondary fold slightly different from the canonical cloverleaf and interestingly similar to that of bovine mitochondrial tRNA(Ser)(uga). Aminoacylation of tRNA(Pyl) transcript by a typical class II synthetase, LysRS from yeast, was possible when its amber anticodon CUA was mutated into a lysine UUU anticodon. Hydrolysis protection assays show that lysylated tRNA(Pyl) can be recognized by bacterial elongation factor. This indicates that no antideterminant sequence is present in the body of the tRNA(Pyl) transcript to prevent it from interacting with EF-Tu, in contrast with the otherwise functionally similar tRNA(Sec) that mediates selenocysteine incorporation.},
note = {1362-4962
Journal Article},
keywords = {Anticodon/metabolism Base Sequence Lysine/*analogs & derivatives/*metabolism Lysine-tRNA Ligase/metabolism Methanosarcina barkeri/genetics Mitochondria/genetics Molecular Sequence Data Nucleic Acid Conformation Peptide Elongation Factor Tu/*metabolism RNA, Archaeal/chemistry/*metabolism RNA, FRUGIER, Non-U.S. Gov't Yeasts/enzymology, Ser/chemistry Selenocysteine/metabolism Support, Transfer, Transfer/chemistry/*metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Sissler M, Helm M, Frugier M, Giege R, Florentz C
Aminoacylation properties of pathology-related human mitochondrial tRNA(Lys) variants Article de journal
Dans: RNA, vol. 10, no. 5, p. 841-853, 2004, ISBN: 15100439, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ERIANI, FLORENTZ, FLORENTZ GIEGE Acylation Aminoacyltransferases/*genetics Human MERRF Syndrome/genetics Mitochondria/*genetics Mitochondrial Diseases/*genetics Mutation Nucleic Acid Conformation RNA, FRUGIER, Lys/*genetics Sequence Analysis, Non-U.S. Gov't Variation (Genetics), RNA Support, SISSLER, Transfer, Unité ARN
@article{,
title = {Aminoacylation properties of pathology-related human mitochondrial tRNA(Lys) variants},
author = {M Sissler and M Helm and M Frugier and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15100439},
isbn = {15100439},
year = {2004},
date = {2004-01-01},
journal = {RNA},
volume = {10},
number = {5},
pages = {841-853},
abstract = {In vitro transcription has proven to be a successful tool for preparation of functional RNAs, especially in the tRNA field, in which, despite the absence of post-transcriptional modifications, transcripts are correctly folded and functionally active. Human mitochondrial (mt) tRNA(Lys) deviates from this principle and folds into various inactive conformations, due to the absence of the post-transcriptional modification m(1)A9 which hinders base-pairing with U64 in the native tRNA. Unavailability of a functional transcript is a serious drawback for structure/function investigations as well as in deciphering the molecular mechanisms by which point mutations in the mt tRNA(Lys) gene cause severe human disorders. Here, we show that an engineered in vitro transcribed "pseudo-WT" tRNA(Lys) variant is efficiently recognized by lysyl-tRNA synthetase and can substitute for the WT tRNA as a valuable reference molecule. This has been exploited in a systematic analysis of the effects on aminoacylation of nine pathology-related mutations described so far. The sole mutation located in a loop of the tRNA secondary structure, A8344G, does not affect aminoacylation efficiency. Out of eight mutations located in helical domains converting canonical Watson-Crick pairs into G-U pairs or C.A mismatches, six have no effect on aminoacylation (A8296G, U8316C, G8342A, U8356C, U8362G, G8363A), and two lead to drastic decreases (5000- to 7000-fold) in lysylation efficiencies (G8313A and G8328A). This screening, allowing for analysis of the primary impact level of all mutations affecting one tRNA under comparable conditions, indicates distinct molecular origins for different disorders.},
note = {1355-8382
Journal Article},
keywords = {ERIANI, FLORENTZ, FLORENTZ GIEGE Acylation Aminoacyltransferases/*genetics Human MERRF Syndrome/genetics Mitochondria/*genetics Mitochondrial Diseases/*genetics Mutation Nucleic Acid Conformation RNA, FRUGIER, Lys/*genetics Sequence Analysis, Non-U.S. Gov't Variation (Genetics), RNA Support, SISSLER, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Deniziak M A, Sauter C, Becker H D, Giege R, Kern D
Crystallization and preliminary X-ray characterization of the atypical glutaminyl-tRNA synthetase from Deinococcus radiodurans Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 60, no. Pt 12 Pt 2, p. 2361-2363, 2004, ISBN: 15572799, (0907-4449 Journal article).
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, KERN GIEGE, SAUTER, Unité ARN
@article{,
title = {Crystallization and preliminary X-ray characterization of the atypical glutaminyl-tRNA synthetase from Deinococcus radiodurans},
author = {M A Deniziak and C Sauter and H D Becker and R Giege and D Kern},
url = {http://journals.iucr.org/d/issues/2004/12/02/za0130/za0130bdy.html},
isbn = {15572799},
year = {2004},
date = {2004-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {60},
number = {Pt 12 Pt 2},
pages = {2361-2363},
abstract = {The glutaminyl-tRNA synthetase (GlnRS) from the radiation-resistant bacterium Deinococcus radiodurans differs from known GlnRSs and other tRNA synthetases by the presence of an additional C-terminal domain resembling the C-terminal region of the GatB subunit of tRNA-dependent amidotransferase (AdT). This atypical synthetase was overexpressed in Escherichia coli, purified and crystallized in the presence of PEG 3350. Orthorhombic crystals were obtained that belong to space group P2(1)2(1)2(1) and diffract to 2.3 A resolution. The crystal structure was solved by molecular replacement using the structure of E. coli GlnRS as a search model.},
note = {0907-4449
Journal article},
keywords = {FRUGIER, KERN GIEGE, SAUTER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Barends S, Rudinger-Thirion J, Florentz C, Giege R, Pleij C W, Kraal B
tRNA-like structure regulates translation of Brome mosaic virus RNA Article de journal
Dans: J Virol, vol. 78, no. 8, p. 4003-4010, 2004, ISBN: 15047816, (0022-538x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ase Sequence Bromovirus/*genetics/metabolism Genetic Complementation Test Genome, FLORENTZ, FRUGIER, Genetic Triticum/virology Tyrosine/chemistry Tyrosine-tRNA Ligase/chemistry/genetics/metabolism Viral Proteins/chemistry/genetics, Non-U.S. Gov't Translation, Transfer/chemistry/genetics RNA, Unité ARN, Viral Molecular Sequence Data Nucleic Acid Conformation RNA, Viral/*chemistry/*genetics Support
@article{,
title = {tRNA-like structure regulates translation of Brome mosaic virus RNA},
author = {S Barends and J Rudinger-Thirion and C Florentz and R Giege and C W Pleij and B Kraal},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15047816},
isbn = {15047816},
year = {2004},
date = {2004-01-01},
journal = {J Virol},
volume = {78},
number = {8},
pages = {4003-4010},
abstract = {For various groups of plant viruses, the genomic RNAs end with a tRNA-like structure (TLS) instead of the 3' poly(A) tail of common mRNAs. The actual function of these TLSs has long been enigmatic. Recently, however, it became clear that for turnip yellow mosaic virus, a tymovirus, the valylated TLS(TYMV) of the single genomic RNA functions as a bait for host ribosomes and directs them to the internal initiation site of translation (with N-terminal valine) of the second open reading frame for the polyprotein. This discovery prompted us to investigate whether the much larger TLSs of a different genus of viruses have a comparable function in translation. Brome mosaic virus (BMV), a bromovirus, has a tripartite RNA genome with a subgenomic RNA4 for coat protein expression. All four RNAs carry a highly conserved and bulky 3' TLS(BMV) (about 200 nucleotides) with determinants for tyrosylation. We discovered TLS(BMV)-catalyzed self-tyrosylation of the tyrosyl-tRNA synthetase but could not clearly detect tyrosine incorporation into any virus-encoded protein. We established that BMV proteins do not need TLS(BMV) tyrosylation for their initiation. However, disruption of the TLSs strongly reduced the translation of genomic RNA1, RNA2, and less strongly, RNA3, whereas coat protein expression from RNA4 remained unaffected. This aberrant translation could be partially restored by providing the TLS(BMV) in trans. Intriguingly, a subdomain of the TLS(BMV) could even almost fully restore translation to the original pattern. We discuss here a model with a central and dominant role for the TLS(BMV) during the BMV infection cycle.},
note = {0022-538x
Journal Article},
keywords = {ase Sequence Bromovirus/*genetics/metabolism Genetic Complementation Test Genome, FLORENTZ, FRUGIER, Genetic Triticum/virology Tyrosine/chemistry Tyrosine-tRNA Ligase/chemistry/genetics/metabolism Viral Proteins/chemistry/genetics, Non-U.S. Gov't Translation, Transfer/chemistry/genetics RNA, Unité ARN, Viral Molecular Sequence Data Nucleic Acid Conformation RNA, Viral/*chemistry/*genetics Support},
pubstate = {published},
tppubtype = {article}
}
2003
Sohm B, Frugier M, Brule H, Olszak K, Przykorska A, Florentz C
Towards understanding human mitochondrial leucine aminoacylation identity Article de journal
Dans: J Mol Biol, vol. 328, no. 5, p. 995-1010, 2003, ISBN: 12729737, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Human In Vitro Leucine/*metabolism Leucine-tRNA Ligase/*metabolism Mitochondria/*metabolism Mitochondrial Diseases/genetics/metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, ERIANI, FLORENTZ, FRUGIER, Leu/chemistry/genetics/*metabolism Recombinant Proteins/genetics/metabolism Solutions Substrate Specificity Support, Non-U.S. Gov't Variation (Genetics), Transfer, Unité ARN
@article{,
title = {Towards understanding human mitochondrial leucine aminoacylation identity},
author = {B Sohm and M Frugier and H Brule and K Olszak and A Przykorska and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12729737},
isbn = {12729737},
year = {2003},
date = {2003-01-01},
journal = {J Mol Biol},
volume = {328},
number = {5},
pages = {995-1010},
abstract = {Specific recognition of tRNAs by aminoacyl-tRNA synthetases is governed by sets of aminoacylation identity elements, well defined for numerous prokaryotic systems and eukaryotic cytosolic systems. Only restricted information is available for aminoacylation of human mitochondrial tRNAs, despite their particularities linked to the non-classical structures of the tRNAs and their involvement in a growing number of human neurodegenerative disorders linked to mutations in the corresponding tRNA genes. A major difficulty to be overcome is the preparation of active in vitro transcripts enabling a rational mutagenic analysis, as is currently performed for classical tRNAs. Here, structural and aminoacylation properties of in vitro transcribed tRNA(Leu(UUR)) are presented. Solution probing using a combination of enzymatic and chemical tools revealed only partial folding into an L-shaped structure, with an acceptor branch but with a floppy anticodon branch. Optimization of aminoacylation conditions allowed charging of up to 75% of molecules, showing that, despite its partially relaxed structure, in vitro transcribed tRNA(Leu(UUR)) is able to adapt to the synthetase. In addition, mutational analysis demonstrates that the discriminator base as well as residue A14 are important leucine identity elements. Thus, human mitochondrial leucylation is dependent on rules similar to those that apply in Escherichia coli. The impact of a subset of pathology-related mutations on aminoacylation and on tRNA structure, has been explored. These variants do not show significant structural rearrangements and either do not affect aminoacylation (mutations T3250C, T3271C, C3303T) or lead to marked effects. Interestingly, two variants with a mutation at the same position (A3243G and A3243T) lead to markedly different losses in aminoacylation efficiencies (tenfold and 300-fold, respectively).},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Human In Vitro Leucine/*metabolism Leucine-tRNA Ligase/*metabolism Mitochondria/*metabolism Mitochondrial Diseases/genetics/metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, ERIANI, FLORENTZ, FRUGIER, Leu/chemistry/genetics/*metabolism Recombinant Proteins/genetics/metabolism Solutions Substrate Specificity Support, Non-U.S. Gov't Variation (Genetics), Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ryckelynck M, Giege R, Frugier M
Yeast tRNA(Asp) charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase Article de journal
Dans: J Biol Chem, vol. 278, no. 11, p. 9683-9690, 2003, ISBN: 12486031, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Motifs Aspartate-tRNA Ligase/*metabolism Aspartic Acid/chemistry Base Sequence Codon Escherichia coli/metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation Nucleic Acids/chemistry Protein Structure, Asp/*chemistry Support, FRUGIER, Messenger/metabolism RNA, Non-U.S. Gov't Yeasts/metabolism, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN
@article{,
title = {Yeast tRNA(Asp) charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase},
author = {M Ryckelynck and R Giege and M Frugier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12486031},
isbn = {12486031},
year = {2003},
date = {2003-01-01},
journal = {J Biol Chem},
volume = {278},
number = {11},
pages = {9683-9690},
abstract = {This study evaluates the role of the N-terminal extension from yeast aspartyl-tRNA synthetase in tRNA aspartylation. The presence of an RNA-binding motif in this extension, conserved in eukaryotic class IIb aminoacyl-tRNA synthetases, provides nonspecific tRNA binding properties to this enzyme. Here, it is assumed that the additional contacts the 70 amino acid-long appendix of aspartyl-tRNA synthetase makes with tRNA could be important in expression of aspartate identity in yeast. Using in vitro transcripts mutated at identity positions, it is demonstrated that the extension grants better aminoacylation efficiency but reduced specificity to the synthetase, increasing considerably the risk of noncognate tRNA mischarging. Yeast tRNA(Glu(UUC)) and tRNA(Asn(GUU)) were identified as the most easily mischarged tRNA species. Both have a G at the discriminator position, and their anticodon differs only by one change from the GUC aspartate anticodon.},
note = {0021-9258
Journal Article},
keywords = {Amino Acid Motifs Aspartate-tRNA Ligase/*metabolism Aspartic Acid/chemistry Base Sequence Codon Escherichia coli/metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation Nucleic Acids/chemistry Protein Structure, Asp/*chemistry Support, FRUGIER, Messenger/metabolism RNA, Non-U.S. Gov't Yeasts/metabolism, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giege R, Frugier M
Transfer RNA Structure and Identity Chapitre d'ouvrage
Dans: Lapointe, J; Brakier-Gringas, L (Ed.): Translation mechanisms, p. 1-24, Landes Bioscience, 2003.
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Unité ARN
@inbook{,
title = {Transfer RNA Structure and Identity},
author = {R Giege and M Frugier},
editor = {J Lapointe and L Brakier-Gringas},
url = {http://www.ncbi.nlm.nih.gov/books/NBK6236},
year = {2003},
date = {2003-01-01},
booktitle = {Translation mechanisms},
pages = {1-24},
publisher = {Landes Bioscience},
abstract = {The structure of tRNA and its relationship with the biological necessity of specific tRNA aminoacylation reactions, in other words with identity, is reviewed. New structural data show the typical L-shaped tRNA architecture in great detail and highlight how adequate rigidity and plasticity of the molecule is essential for interaction with its biological partners, in particular with aminoacyl-tRNA synthetases. Identity is ensured by a small number of nucleosides predominantly located at the two distal extremities of the tRNA molecule. In several crystallographic complexes, these residues have been shown in contact with amino acids from the synthetases. In most cases, the interaction is accompanied by a conformational change of the tRNA. Assuming that the structural framework of tRNA displays identity elements to synthetases implies that altered and/or simplified RNA architectures can fulfill this role provided they contain correctly located identity elements. This paradigm holds true in nature where atypical and tRNA-like domains have been selected by evolution. Rationale-based engineering or selection by artificial evolution of novel RNA molecules recognized and aminoacylated by synthetases also verified it.},
keywords = {FRUGIER, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Frugier M, Giege R, Schimmel P
RNA recognition by designed peptide fusion creates Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 100, no. 13, p. 7471-7475, 2003, ISBN: 12796515, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Motifs Amino Acid Sequence Amino Acyl-tRNA Ligases/*chemistry Base Sequence Binding Sites Catalytic Domain Escherichia coli/genetics/metabolism *Genetic Techniques Kinetics Models, FRUGIER, Genetic Molecular Sequence Data Mutation Nucleic Acid Conformation Peptides/*chemistry Protein Binding Protein Structure, Non-U.S. Gov't Support, P.H.S. Time Factors, Tertiary RNA/chemistry Recombinant Fusion Proteins/metabolism Support, U.S. Gov't, Unité ARN
@article{,
title = {RNA recognition by designed peptide fusion creates },
author = {M Frugier and R Giege and P Schimmel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12796515},
isbn = {12796515},
year = {2003},
date = {2003-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {100},
number = {13},
pages = {7471-7475},
abstract = {The genetic code was established through aminoacylations of RNA substrates that emerged as tRNAs. The 20 aminoacyl-tRNA synthetases (one for each amino acid) are ancient proteins, the active-site domain of which catalyzes formation of an aminoacyl adenylate that subsequently reacts with the 3' end of bound tRNA. Binding of tRNA depends on idiosyncratic (to the particular synthetase) domains and motifs that are fused to or inserted into the conserved active-site domain. Here we take the domain for synthesis of alanyl adenylate and fuse it to "artificial" peptide sequences (28 aa) that were shown previously to bind to the acceptor arm of tRNAAla. Certain fusions confer aminoacylation activity on tRNAAla and on hairpin microhelices modeled after its acceptor stem. Aminoacylation was sensitive to the presence of a specific G:U base pair known to be a major determinant of tRNAAla identity. Aminoacylation efficiency and specificity also depended on the specific peptide sequence. The results demonstrate that barriers to RNA-specific aminoacylations are low and can be achieved by relatively simple peptide fusions. They also suggest a paradigm for rationally designed specific aminoacylations based on peptide fusions.},
note = {0027-8424
Journal Article},
keywords = {Amino Acid Motifs Amino Acid Sequence Amino Acyl-tRNA Ligases/*chemistry Base Sequence Binding Sites Catalytic Domain Escherichia coli/genetics/metabolism *Genetic Techniques Kinetics Models, FRUGIER, Genetic Molecular Sequence Data Mutation Nucleic Acid Conformation Peptides/*chemistry Protein Binding Protein Structure, Non-U.S. Gov't Support, P.H.S. Time Factors, Tertiary RNA/chemistry Recombinant Fusion Proteins/metabolism Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Frugier M, Giege R
Yeast aspartyl-tRNA synthetase binds specifically its own mRNA Article de journal
Dans: J Mol Biol, vol. 331, no. 2, p. 375-383, 2003, ISBN: 12888345, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 5' Untranslated Regions Amino Acid Motifs Aspartate-tRNA Ligase/*chemistry/metabolism Binding, Competitive Blotting, Drug Gene Expression Regulation, Enzymologic Genes, FRUGIER, Fungal Kinetics Luminescent Proteins/metabolism Plasmids Protein Binding Protein Structure, Messenger/metabolism RNA, Non-U.S. Gov't, Tertiary RNA/metabolism RNA, Transfer/metabolism Saccharomyces cerevisiae/metabolism Support, Unité ARN, Western Dose-Response Relationship
@article{,
title = {Yeast aspartyl-tRNA synthetase binds specifically its own mRNA},
author = {M Frugier and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12888345},
isbn = {12888345},
year = {2003},
date = {2003-01-01},
journal = {J Mol Biol},
volume = {331},
number = {2},
pages = {375-383},
abstract = {Dimeric class II aspartyl-tRNA synthetase (AspRS) from yeast has a modular architecture and includes an N-terminal appendix of 70 amino acid residues that protrudes from the anticodon-binding module. This extension, of predicted helical structure, is not essential for aminoacylation but contains an RNA-binding motif that promotes non-specific interactions with tRNAs. As shown here, this protein extension can also interact with the 5' end of the AspRS mRNA. In vitro, optimal binding occurs on an mRNA domain comprising part of the 87 nucleotide long 5'UTR and the sequence encoding the N-terminal appendix. At the protein side, only the appendix and the anticodon-binding module participate in the interaction between AspRS and the mRNA domain. Binding is specific, since only tRNA(Asp) can dissociate the complex. In vivo, AspRS also binds specifically this mRNA domain and in doing so triggers a reduced translation of a fused GFP mRNA. From that, a mechanism for the regulation of this eukaryotic aminoacyl-tRNA synthetase is proposed. Implications for aspartylation accuracy in yeast are given.},
note = {0022-2836
Journal Article},
keywords = {5' Untranslated Regions Amino Acid Motifs Aspartate-tRNA Ligase/*chemistry/metabolism Binding, Competitive Blotting, Drug Gene Expression Regulation, Enzymologic Genes, FRUGIER, Fungal Kinetics Luminescent Proteins/metabolism Plasmids Protein Binding Protein Structure, Messenger/metabolism RNA, Non-U.S. Gov't, Tertiary RNA/metabolism RNA, Transfer/metabolism Saccharomyces cerevisiae/metabolism Support, Unité ARN, Western Dose-Response Relationship},
pubstate = {published},
tppubtype = {article}
}
Thore S, Mayer C, Sauter C, Weeks S, Suck D
Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in Archaea and Eucarya. Article de journal
Dans: J Biol Chem, vol. 278, no. 2, p. 1239-1247, 2003, ISBN: 12409299.
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, SAUTER, Unité ARN
@article{,
title = {Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in Archaea and Eucarya.},
author = {S Thore and C Mayer and C Sauter and S Weeks and D Suck},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12409299},
isbn = {12409299},
year = {2003},
date = {2003-01-01},
journal = {J Biol Chem},
volume = {278},
number = {2},
pages = {1239-1247},
abstract = {The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. Their proposed function is to mediate RNA-RNA interactions. We present here the crystal structures of Pyrococcus abyssi Sm protein (PA-Sm1) and its complex with a uridine heptamer. The overall structure of the protein complex, a heptameric ring with a central cavity, is similar to that proposed for the eukaryotic Sm core complex and found for other archaeal Sm proteins. RNA molecules bind to the protein at two different sites. They interact specifically inside the ring with three highly conserved residues, defining the uridine-binding pocket. In addition, nucleotides also interact on the surface formed by the N-terminal alpha-helix as well as a conserved aromatic residue in beta-strand 2 of the PA-Sm1 protein. The mutation of this conserved aromatic residue shows the importance of this second site for the discrimination between RNA sequences. Given the high structural homology between archaeal and eukaryotic Sm proteins, the PA-Sm1.RNA complex provides a model for how the small nuclear RNA contacts the Sm proteins in the Sm core. In addition, it suggests how Sm proteins might exert their function as modulators of RNA-RNA interactions.},
keywords = {FRUGIER, SAUTER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Sauter C, Basquin J, Suck D
Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli Article de journal
Dans: Nucleic Acids Res, vol. 31, no. 14, p. 4091-4098, 2003, ISBN: 12853626, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Amino Acid Sequence Bacteria/*genetics Crystallography, FRUGIER, Molecular Host Factor 1 Protein/chemistry/*genetics Molecular Sequence Data Protein Conformation Protein Structure, Non-U.S. Gov't, SAUTER, Secondary Ribonucleoproteins, Small Nuclear/chemistry/*genetics Sequence Alignment Sequence Homology, Unité ARN, X-Ray Dimerization Escherichia coli Proteins/chemistry/*genetics Evolution
@article{,
title = {Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli},
author = {C Sauter and J Basquin and D Suck},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12853626},
isbn = {12853626},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {14},
pages = {4091-4098},
abstract = {The Hfq protein was discovered in Escherichia coli in the early seventies as a host factor for the Qbeta phage RNA replication. During the last decade, it was shown to be involved in many RNA processing events and remote sequence homology indicated a link to spliceosomal Sm proteins. We report the crystal structure of the E.coli Hfq protein showing that its monomer displays a characteristic Sm-fold and forms a homo-hexamer, in agreement with former biochemical data. Overall, the structure of the E.coli Hfq ring is similar to the one recently described for Staphylococcus aureus. This confirms that bacteria contain a hexameric Sm-like protein which is likely to be an ancient and less specialized form characterized by a relaxed RNA binding specificity. In addition, we identified an Hfq ortholog in the archaeon Methanococcus jannaschii which lacks a classical Sm/Lsm gene. Finally, a detailed structural comparison shows that the Sm-fold is remarkably well conserved in bacteria, Archaea and Eukarya, and represents a universal and modular building unit for oligomeric RNA binding proteins.},
note = {1362-4962
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Bacteria/*genetics Crystallography, FRUGIER, Molecular Host Factor 1 Protein/chemistry/*genetics Molecular Sequence Data Protein Conformation Protein Structure, Non-U.S. Gov't, SAUTER, Secondary Ribonucleoproteins, Small Nuclear/chemistry/*genetics Sequence Alignment Sequence Homology, Unité ARN, X-Ray Dimerization Escherichia coli Proteins/chemistry/*genetics Evolution},
pubstate = {published},
tppubtype = {article}
}
2002
Ng J D, Sauter C, Lorber B, Kirkland N, Arnez J, Giege R
Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 58, no. Pt 4, p. 645-652, 2002, ISBN: 11914489, (0907-4449 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl-tRNA Ligases/*chemistry Comparative Study Crystallization Crystallography, FRUGIER, Molecular Support, Non-U.S. Gov't Thermus thermophilus/chemistry Water/chemistry Weightlessness, SAUTER, Unité ARN, X-Ray Models
@article{,
title = {Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination},
author = {J D Ng and C Sauter and B Lorber and N Kirkland and J Arnez and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11914489},
isbn = {11914489},
year = {2002},
date = {2002-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {58},
number = {Pt 4},
pages = {645-652},
abstract = {Protein crystallization under microgravity aims at benefiting from the quasi-absence of convection and sedimentation to favor well ordered crystal nucleation and growth. The dimeric multidomain enzyme aspartyl-tRNA synthetase from Thermus thermophilus has been crystallized within dialysis reactors of the Advanced Protein Crystallization Facility in the laboratory on earth and under microgravity aboard the US Space Shuttle. A strictly comparative crystallographic analysis reveals that the crystals grown in space are superior in every respect to control crystals prepared in otherwise identical conditions on earth. They diffract X-rays more intensely and have a lower mosaicity, facilitating the process of protein structure determination. Indeed, the electron-density map calculated from diffraction data of space-grown crystals contains considerably more detail. The resulting three-dimensional structure model at 2.0 A resolution is more accurate than that produced in parallel using the data originating from earth-grown crystals. The major differences between the structures, including the better defined amino-acid side chains and the higher order of bound water molecules, are emphasized.},
note = {0907-4449
Journal Article},
keywords = {Amino Acyl-tRNA Ligases/*chemistry Comparative Study Crystallization Crystallography, FRUGIER, Molecular Support, Non-U.S. Gov't Thermus thermophilus/chemistry Water/chemistry Weightlessness, SAUTER, Unité ARN, X-Ray Models},
pubstate = {published},
tppubtype = {article}
}
Biertümpfel C, Basquin J, Suck D, Sauter C
Crystallization of biological macromolecules using agarose gel. Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 58, no. 10, p. 1657-1659, 2002, ISBN: 10.1107/S0907444902012738.
Résumé | Liens | BibTeX | Étiquettes: Agarose gel Crystallization Biological macromolecule Counter-diffusion., FRUGIER, SAUTER, Unité ARN
@article{,
title = {Crystallization of biological macromolecules using agarose gel.},
author = {C Biertümpfel and J Basquin and D Suck and C Sauter},
url = {http://scripts.iucr.org/cgi-bin/paper?ic0008},
isbn = {10.1107/S0907444902012738},
year = {2002},
date = {2002-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {58},
number = {10},
pages = {1657-1659},
abstract = {Gellified media prevent convection and crystal sedimentation, and provide an attractive growth environment for optimising biological crystals. Agarose gels are particularly easy to use and they are compatible with most of the common crystallization methods. They also offer new possibilities like counter-diffusion techniques. This paper gives a brief overview of their general properties and presents an application of a counter-diffusion setup combining agarose gel and capillaries to the crystallization of proteins and protein / nucleic acid complexes.},
keywords = {Agarose gel Crystallization Biological macromolecule Counter-diffusion., FRUGIER, SAUTER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Sauter C, Lorber B, Giege R
Towards atomic resolution with crystals grown in gel: the case of thaumatin seen at room temperature Article de journal
Dans: Proteins, vol. 48, no. 2, p. 146-150, 2002, ISBN: 12112683, (1097-0134 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Crystallization *Crystallography, FRUGIER, Molecular Plant Proteins/*chemistry Support, Non-U.S. Gov't *Sweetening Agents Temperature Weightlessness, SAUTER, Unité ARN, X-Ray Hydrogels/*chemistry *Models
@article{,
title = {Towards atomic resolution with crystals grown in gel: the case of thaumatin seen at room temperature},
author = {C Sauter and B Lorber and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12112683},
isbn = {12112683},
year = {2002},
date = {2002-01-01},
journal = {Proteins},
volume = {48},
number = {2},
pages = {146-150},
abstract = {One reason for introducing a gel in the crystallization medium of proteins is its ability to reduce convection in solution. This can lead to better nucleation and growth conditions, and to crystals having enhanced diffraction properties. We report here the X-ray characterization at room temperature of high-quality crystals of the intensely sweet thaumatin prepared in a sodium tartrate solution gelified with 0.15% (m/v) agarose. Using a synchrotron radiation, these crystals diffracted to a previously unachieved resolution. A diffraction dataset was collected from four crystals at a resolution of 1.2 A with a R(sym) of 3.6% and a completeness of 99%. Refinement was carried out to a final crystallographic R-factor of 12.0%. The quality of the electron density map allowed for the observation of fine structural details in the protein and its solvation shell. Crystallization in gel might be used more generally to improve the quality of macromolecular crystals. Advantages provided by the gelified medium in the frame of structural studies are emphasized.},
note = {1097-0134
Journal Article},
keywords = {Crystallization *Crystallography, FRUGIER, Molecular Plant Proteins/*chemistry Support, Non-U.S. Gov't *Sweetening Agents Temperature Weightlessness, SAUTER, Unité ARN, X-Ray Hydrogels/*chemistry *Models},
pubstate = {published},
tppubtype = {article}
}
2000
Frugier M, Moulinier L, Giege R
A domain in the N-terminal extension of class IIb eukaryotic aminoacyl-tRNA synthetases is important for tRNA binding Article de journal
Dans: EMBO J, vol. 19, no. 10, p. 2371-2380, 2000, ISBN: 10811628, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Amino Acyl-tRNA Ligases/chemistry/*metabolism Aspartate-tRNA Ligase/chemistry/metabolism Molecular Sequence Data RNA, ERIANI, FRUGIER, Fungal/metabolism RNA, Non-U.S. Gov't, Transfer/*metabolism Saccharomyces cerevisiae/*metabolism Sequence Alignment Support, Unité ARN
@article{,
title = {A domain in the N-terminal extension of class IIb eukaryotic aminoacyl-tRNA synthetases is important for tRNA binding},
author = {M Frugier and L Moulinier and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10811628},
isbn = {10811628},
year = {2000},
date = {2000-01-01},
journal = {EMBO J},
volume = {19},
number = {10},
pages = {2371-2380},
abstract = {Cytoplasmic aspartyl-tRNA synthetase (AspRS) from Saccharomyces cerevisiae is a homodimer of 64 kDa subunits. Previous studies have emphasized the high sensitivity of the N-terminal region to proteolytic cleavage, leading to truncated species that have lost the first 20-70 residues but that retain enzymatic activity and dimeric structure. In this work, we demonstrate that the N-terminal extension in yeast AspRS participates in tRNA binding and we generalize this finding to eukaryotic class IIb aminoacyl-tRNA synthetases. By gel retardation studies and footprinting experiments on yeast tRNA(Asp), we show that the extension, connected to the anticodon-binding module of the synthetase, contacts tRNA on the minor groove side of its anticodon stem. Sequence comparison of eukaryotic class IIb synthetases identifies a lysine-rich 11 residue sequence ((29)LSKKALKKLQK(39) in yeast AspRS with the consensus xSKxxLKKxxK in class IIb synthetases) that is important for this binding. Direct proof of the role of this sequence comes from a mutagenesis analysis and from binding studies using the isolated peptide.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid Sequence Amino Acyl-tRNA Ligases/chemistry/*metabolism Aspartate-tRNA Ligase/chemistry/metabolism Molecular Sequence Data RNA, ERIANI, FRUGIER, Fungal/metabolism RNA, Non-U.S. Gov't, Transfer/*metabolism Saccharomyces cerevisiae/*metabolism Sequence Alignment Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1994
Frugier M, Soll D, Giege R, Florentz C
Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases Article de journal
Dans: Biochemistry, vol. 33, no. 33, p. 9912-9921, 1994, ISBN: 8060999, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Crystallization Escherichia coli/*enzymology/genetics Glutamate-tRNA Ligase/chemistry/*metabolism Kinetics Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism RNA, ERIANI, FLORENTZ, FRUGIER, Gln/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases},
author = {M Frugier and D Soll and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8060999},
isbn = {8060999},
year = {1994},
date = {1994-01-01},
journal = {Biochemistry},
volume = {33},
number = {33},
pages = {9912-9921},
abstract = {High-resolution X-ray structures for the tRNA/aminoacyl-tRNA synthetase complexes between Escherichia coli tRNAGln/GlnRS and yeast tRNAAsp/AspRS have been determined. Positive identity nucleotides that direct aminoacylation specificity have been defined in both cases; E. coli tRNAGln identity is governed by 10 elements scattered in the tRNA structure, while specific aminoacylation of yeast tRNAAsp is dependent on 5 positions. Both identity sets are partially overlapping and share 3 nucleotides. Interestingly, the two enzymes belong to two different classes described for aminoacyl-tRNA synthetases. The class I glutaminyl-tRNA synthetase and the class II aspartyl-tRNA synthetase recognize their cognate tRNA from opposite sides. Mutants derived from glutamine and aspartate tRNAs have been created by progressively introducing identity elements from one tRNA into the other one. Glutaminylation and aspartylation assays of the transplanted tRNAs show that identity nucleotides from a tRNA originally aminoacylated by a synthetase from one class are still recognized if they are presented to the enzyme in a structural framework corresponding to a tRNA aminoacylated by a synthetase belonging to the other class. The simple transplantation of the glutamine identity set into tRNAAsp is sufficient to obtain glutaminylatable tRNA, but additional subtle features seem to be important for the complete conversion of tRNAGln in an aspartylatable substrate. This study defines C38 in yeast tRNAAsp as a new identity nucleotide for aspartylation. We show also in this paper that, during the complex formation, aminoacyl-tRNA synthetases are at least partially responsible for conformational changes which involve structural constraints in tRNA molecules.},
note = {0006-2960
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Crystallization Escherichia coli/*enzymology/genetics Glutamate-tRNA Ligase/chemistry/*metabolism Kinetics Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism RNA, ERIANI, FLORENTZ, FRUGIER, Gln/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Frugier M, Florentz C, Hosseini M W, Lehn J M, Giege R
Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 14, p. 2784-2790, 1994, ISBN: 8052534, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacteriophage T7/enzymology Base Sequence Comparative Study DNA-Directed RNA Polymerases/drug effects/*metabolism Kinetics Molecular Sequence Data Molecular Structure Nucleic Acid Conformation Oligodeoxyribonucleotides Polyamines/chemistry/*pharmacology Promoter Regions (Genetics) RNA, ERIANI, FLORENTZ, FRUGIER, Genetic Transcription, Genetic/*drug effects, Non-U.S. Gov't Templates, Transfer, Unité ARN, Val/*biosynthesis/chemistry Structure-Activity Relationship Support
@article{,
title = {Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase},
author = {M Frugier and C Florentz and M W Hosseini and J M Lehn and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8052534},
isbn = {8052534},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {14},
pages = {2784-2790},
abstract = {The influence of nine synthetic polyamines on in vitro transcription with T7 RNA polymerase has been studied. The compounds used were linear or macrocyclic tetra- and hexaamine, varying in their size, shape and number of protonated groups. Their effect was tested on different types of templates, all presenting the T7 RNA promoter in a double-stranded form followed by sequences encoding short transcripts (25 to 35-mers) either on single- or double-stranded synthetic oligodeoxyribonucleotides. All polyamines used stimulate transcription of both types of templates at levels dependent on their size, shape, protonation degree, and concentration. For each compound, an optimal concentration could be defined; above this concentration, transcription inhibition occurred. Highest stimulation (up to 12-fold) was obtained by the largest cyclic compound called [38]N6C10.},
note = {0305-1048
Journal Article},
keywords = {Bacteriophage T7/enzymology Base Sequence Comparative Study DNA-Directed RNA Polymerases/drug effects/*metabolism Kinetics Molecular Sequence Data Molecular Structure Nucleic Acid Conformation Oligodeoxyribonucleotides Polyamines/chemistry/*pharmacology Promoter Regions (Genetics) RNA, ERIANI, FLORENTZ, FRUGIER, Genetic Transcription, Genetic/*drug effects, Non-U.S. Gov't Templates, Transfer, Unité ARN, Val/*biosynthesis/chemistry Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
Frugier M, Florentz C, Giege R
Efficient aminoacylation of resected RNA helices by class II aspartyl-tRNA synthetase dependent on a single nucleotide Article de journal
Dans: EMBO J, vol. 13, no. 9, p. 2218-2226, 1994, ISBN: 8187774, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Anticodon Aspartate-tRNA Ligase/*metabolism Aspartic Acid/metabolism Base Sequence Evolution Molecular Sequence Data Nucleic Acid Conformation RNA, ERIANI, FLORENTZ, FRUGIER, Fungal/chemistry/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Unité ARN
@article{,
title = {Efficient aminoacylation of resected RNA helices by class II aspartyl-tRNA synthetase dependent on a single nucleotide},
author = {M Frugier and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8187774},
isbn = {8187774},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {9},
pages = {2218-2226},
abstract = {We show here that small RNA helices which recapitulate part or all of the acceptor stem of yeast aspartate tRNA are efficiently aminoacylated by cognate class II aspartyl-tRNA synthetase. Aminoacylation is strongly dependent on the presence of the single-stranded G73 'discriminator' identity nucleotide and is essentially insensitive to the sequence of the helical region. Substrates which contain as few as 3 bp fused to G73CCAOH are aspartylated. Their charging is insensitive to the sequence of the loop closing the short helical domains. Aminoacylation of the aspartate mini-helix is not stimulated by a hairpin helix mimicking the anticodon domain and containing the three major anticodon identity nucleotides. A thermodynamic analysis demonstrates that enzyme interactions with G73 in the resected RNA substrates and in the whole tRNA are the same. Thus, if the resected RNA molecules resemble in some way the earliest substrates for aminoacylation with aspartate, then the contemporary tRNA(Asp) has quantitatively retained the influence of the major signal for aminoacylation in these substrates.},
note = {0261-4189
Journal Article},
keywords = {Acylation Anticodon Aspartate-tRNA Ligase/*metabolism Aspartic Acid/metabolism Base Sequence Evolution Molecular Sequence Data Nucleic Acid Conformation RNA, ERIANI, FLORENTZ, FRUGIER, Fungal/chemistry/*metabolism Substrate Specificity Support, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1993
Frugier M, Florentz C, Schimmel P, Giege R
Triple aminoacylation specificity of a chimerized transfer RNA Article de journal
Dans: Biochemistry, vol. 32, no. 50, p. 14053-14061, 1993, ISBN: 8268184, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Alanine/metabolism Base Sequence Chimera Escherichia coli/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation Phenylalanine/metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/genetics Support, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Support, P.H.S. Valine/metabolism, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Triple aminoacylation specificity of a chimerized transfer RNA},
author = {M Frugier and C Florentz and P Schimmel and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8268184},
isbn = {8268184},
year = {1993},
date = {1993-01-01},
journal = {Biochemistry},
volume = {32},
number = {50},
pages = {14053-14061},
abstract = {We report here the rational design and construction of a chimerized transfer RNA with tripartite aminoacylation specificity. A yeast aspartic acid specific tRNA was transformed into a highly efficient acceptor of alanine and phenylalanine and a moderate acceptor of valine. The transformation was guided by available knowledge of the requirements for aminoacylation by each of the three amino acids and was achieved by iterative changes in the local sequence context and the structural framework of the variable loop and the two variable regions of the dihydrouridine loop. The changes introduced to confer efficient acceptance of the three amino acids eliminate aminoacylation with aspartate. The interplay of determinants and antideterminants for different specific aminoacylations, and the constraints imposed by the structural framework, suggest that a tRNA with an appreciable capacity for more than three efficient aminoacylations may be inherently difficult to achieve.},
note = {0006-2960
Journal Article},
keywords = {Acylation Alanine/metabolism Base Sequence Chimera Escherichia coli/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation Phenylalanine/metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/genetics Support, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Support, P.H.S. Valine/metabolism, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1992
Frugier M, Florentz C, Giege R
Anticodon-independent aminoacylation of an RNA minihelix with valine Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 89, no. 9, p. 3990-3994, 1992, ISBN: 1570324, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Amino Acid Activation Anticodon Base Sequence Hydrogen Bonding In Vitro Molecular Sequence Data RNA, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Valine-tRNA Ligase/*metabolism, Transfer, Unité ARN, Val/chemistry/*metabolism Saccharomyces cerevisiae Structure-Activity Relationship Support
@article{,
title = {Anticodon-independent aminoacylation of an RNA minihelix with valine},
author = {M Frugier and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1570324},
isbn = {1570324},
year = {1992},
date = {1992-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {89},
number = {9},
pages = {3990-3994},
abstract = {Minihelices mimicking the amino acid acceptor and anticodon branches of yeast tRNA(Val) have been synthesized by in vitro transcription of synthetic templates. It is shown that a minihelix corresponding to the amino acid acceptor branch and containing solely a valine-specific identity nucleotide can be aminoacylated by yeast valyl-tRNA synthetase. Its charging ability is lost after mutating this nucleotide. This ability is stimulated somewhat by the addition of a second hairpin helix that mimicks the anticodon arm, which suggests that information originating from the anticodon stem-loop can be transmitted to the active site of the enzyme by the core of the protein.},
note = {0027-8424
Journal Article},
keywords = {*Amino Acid Activation Anticodon Base Sequence Hydrogen Bonding In Vitro Molecular Sequence Data RNA, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Valine-tRNA Ligase/*metabolism, Transfer, Unité ARN, Val/chemistry/*metabolism Saccharomyces cerevisiae Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
Lorber B, Giege R
A versatile reactor for temperature controlled crystallization of biological macromolecules. Article de journal
Dans: J Crystal Growth, vol. 122, no. 1-4, p. 168-175, 1992, ISBN: 10.1016/0022-0248(92)90240-J.
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Unité ARN
@article{,
title = {A versatile reactor for temperature controlled crystallization of biological macromolecules.},
author = {B Lorber and R Giege},
url = {http://www.sciencedirect.com/science/article/pii/002202489290240J},
isbn = {10.1016/0022-0248(92)90240-J},
year = {1992},
date = {1992-01-01},
journal = {J Crystal Growth},
volume = {122},
number = {1-4},
pages = {168-175},
abstract = {Accurate control of crystallization conditions, and accordingly reproducibility of experiments, is often hampered by the lack of adequate instrumentation in the laboratory. A versatile and inexpensive crystallization reactor allowing crystal growth by vapor phase equilibration (sitting, hanging or sandwiched drops) or by the batch technique is described here. In this reactor, temperature is controlled accurately by a Peltier device and the crystallization process monitored by a time-lapse video recorder. An application for evaluating the growth kinetics of tetragonal lysozyme crystals as a function of temperature is given. It was observed that the apparent growth rate decreased when temperature was lowered, although under such conditions supersaturation was increased and crystals appeared sooner.},
keywords = {FRUGIER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}