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2006
Leontis N B, Lescoute A, Westhof E
The building blocks and motifs of RNA architecture Article de journal
Dans: Curr Opin Struct Biol, vol. 16, no. 3, p. 279-287, 2006, ISBN: 16713707, (0959-440X (Print) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: ase Pairing Base Sequence Computational Biology/methods Conserved Sequence *Models, Extramural Research Support, Molecular Nucleic Acid Conformation RNA/*chemistry Research Support, N.I.H., Non-U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {The building blocks and motifs of RNA architecture},
author = {N B Leontis and A Lescoute and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16713707},
isbn = {16713707},
year = {2006},
date = {2006-01-01},
journal = {Curr Opin Struct Biol},
volume = {16},
number = {3},
pages = {279-287},
abstract = {RNA motifs can be defined broadly as recurrent structural elements containing multiple intramolecular RNA-RNA interactions, as observed in atomic-resolution RNA structures. They constitute the modular building blocks of RNA architecture, which is organized hierarchically. Recent work has focused on analyzing RNA backbone conformations to identify, define and search for new instances of recurrent motifs in X-ray structures. One current view asserts that recurrent RNA strand segments with characteristic backbone configurations qualify as independent motifs. Other considerations indicate that, to characterize modular motifs, one must take into account the larger structural context of such strand segments. This follows the biologically relevant motivation, which is to identify RNA structural characteristics that are subject to sequence constraints and that thus relate RNA architectures to sequences.},
note = {0959-440X (Print)
Journal Article
Review},
keywords = {ase Pairing Base Sequence Computational Biology/methods Conserved Sequence *Models, Extramural Research Support, Molecular Nucleic Acid Conformation RNA/*chemistry Research Support, N.I.H., Non-U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
RNA motifs can be defined broadly as recurrent structural elements containing multiple intramolecular RNA-RNA interactions, as observed in atomic-resolution RNA structures. They constitute the modular building blocks of RNA architecture, which is organized hierarchically. Recent work has focused on analyzing RNA backbone conformations to identify, define and search for new instances of recurrent motifs in X-ray structures. One current view asserts that recurrent RNA strand segments with characteristic backbone configurations qualify as independent motifs. Other considerations indicate that, to characterize modular motifs, one must take into account the larger structural context of such strand segments. This follows the biologically relevant motivation, which is to identify RNA structural characteristics that are subject to sequence constraints and that thus relate RNA architectures to sequences.
Fender A, Sauter C, Messmer M, Putz J, Giege R, Florentz C, Sissler M
Loss of a primordial identity element for a mammalian mitochondrial aminoacylation system Article de journal
Dans: J Biol Chem, vol. 281, no. 23, p. 15980-15986, 2006, ISBN: 16597625, (0021-9258 (Print) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Base Sequence Humans Kinetics Mutagenesis Nucleic Acid Conformation Plasmids RNA | Non-U.S. Gov't, Asp/chemistry/genetics/*metabolism Research Support, FLORENTZ, FRUGIER, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN
@article{,
title = {Loss of a primordial identity element for a mammalian mitochondrial aminoacylation system},
author = {A Fender and C Sauter and M Messmer and J Putz 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=16597625},
isbn = {16597625},
year = {2006},
date = {2006-01-01},
journal = {J Biol Chem},
volume = {281},
number = {23},
pages = {15980-15986},
abstract = {In mammalian mitochondria the translational machinery is of dual origin with tRNAs encoded by a simplified and rapidly evolving mitochondrial (mt) genome and aminoacyl-tRNA synthetases (aaRS) coded by the nuclear genome, and imported. Mt-tRNAs are atypical with biased sequences, size variations in loops and stems, and absence of residues forming classical tertiary interactions, whereas synthetases appear typical. This raises questions about identity elements in mt-tRNAs and adaptation of their cognate mt-aaRSs. We have explored here the human mt-aspartate system in which a prokaryotic-type AspRS, highly similar to the Escherichia coli enzyme, recognizes a bizarre tRNA(Asp). Analysis of human mt-tRNA(Asp) transcripts confirms the identity role of the GUC anticodon as in other aspartylation systems but reveals the non-involvement of position 73. This position is otherwise known as the site of a universally conserved major aspartate identity element, G73, also known as a primordial identity signal. In mt-tRNA(Asp), position 73 can be occupied by any of the four nucleotides without affecting aspartylation. Sequence alignments of various AspRSs allowed placing Gly-269 at a position occupied by Asp-220, the residue contacting G73 in the crystallographic structure of E. coli AspRS-tRNA(Asp) complex. Replacing this glycine by an aspartate renders human mt-AspRS more discriminative to G73. Restriction in the aspartylation identity set, driven by a rapid mutagenic rate of the mt-genome, suggests a reverse evolution of the mt-tRNA(Asp) identity elements in regard to its bacterial ancestor.},
note = {0021-9258 (Print)
Journal Article},
keywords = {Acylation Base Sequence Humans Kinetics Mutagenesis Nucleic Acid Conformation Plasmids RNA | Non-U.S. Gov't, Asp/chemistry/genetics/*metabolism Research Support, FLORENTZ, FRUGIER, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In mammalian mitochondria the translational machinery is of dual origin with tRNAs encoded by a simplified and rapidly evolving mitochondrial (mt) genome and aminoacyl-tRNA synthetases (aaRS) coded by the nuclear genome, and imported. Mt-tRNAs are atypical with biased sequences, size variations in loops and stems, and absence of residues forming classical tertiary interactions, whereas synthetases appear typical. This raises questions about identity elements in mt-tRNAs and adaptation of their cognate mt-aaRSs. We have explored here the human mt-aspartate system in which a prokaryotic-type AspRS, highly similar to the Escherichia coli enzyme, recognizes a bizarre tRNA(Asp). Analysis of human mt-tRNA(Asp) transcripts confirms the identity role of the GUC anticodon as in other aspartylation systems but reveals the non-involvement of position 73. This position is otherwise known as the site of a universally conserved major aspartate identity element, G73, also known as a primordial identity signal. In mt-tRNA(Asp), position 73 can be occupied by any of the four nucleotides without affecting aspartylation. Sequence alignments of various AspRSs allowed placing Gly-269 at a position occupied by Asp-220, the residue contacting G73 in the crystallographic structure of E. coli AspRS-tRNA(Asp) complex. Replacing this glycine by an aspartate renders human mt-AspRS more discriminative to G73. Restriction in the aspartylation identity set, driven by a rapid mutagenic rate of the mt-genome, suggests a reverse evolution of the mt-tRNA(Asp) identity elements in regard to its bacterial ancestor.
2005
Nielsen H, Westhof E, Johansen S
An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme Article de journal
Dans: Science, vol. 309, no. 5740, p. 1584-1587, 2005, ISBN: 16141078, (1095-9203 (Electronic) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ase Sequence Catalysis Endonucleases/biosynthesis/*genetics Esterification *Introns Molecular Sequence Data RNA Caps/*chemistry *RNA Splicing RNA, Catalytic/chemistry/*metabolism Research Support, Non-U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme},
author = {H Nielsen and E Westhof and S Johansen},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16141078},
isbn = {16141078},
year = {2005},
date = {2005-01-01},
journal = {Science},
volume = {309},
number = {5740},
pages = {1584-1587},
abstract = {Twin-ribozyme introns are formed by two ribozymes belonging to the group I family and occur in some ribosomal RNA transcripts. The group I-like ribozyme, GIR1, liberates the 5' end of a homing endonuclease messenger RNA in the slime mold Didymium iridis. We demonstrate that this cleavage occurs by a transesterification reaction with the joining of the first and the third nucleotide of the messenger by a 2',5'-phosphodiester linkage. Thus, a group I-like ribozyme catalyzes an RNA branching reaction similar to the first step of splicing in group II introns and spliceosomal introns. The resulting short lariat, by forming a protective 5' cap, might have been useful in a primitive RNA world.},
note = {1095-9203 (Electronic)
Journal Article},
keywords = {ase Sequence Catalysis Endonucleases/biosynthesis/*genetics Esterification *Introns Molecular Sequence Data RNA Caps/*chemistry *RNA Splicing RNA, Catalytic/chemistry/*metabolism Research Support, Non-U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Twin-ribozyme introns are formed by two ribozymes belonging to the group I family and occur in some ribosomal RNA transcripts. The group I-like ribozyme, GIR1, liberates the 5' end of a homing endonuclease messenger RNA in the slime mold Didymium iridis. We demonstrate that this cleavage occurs by a transesterification reaction with the joining of the first and the third nucleotide of the messenger by a 2',5'-phosphodiester linkage. Thus, a group I-like ribozyme catalyzes an RNA branching reaction similar to the first step of splicing in group II introns and spliceosomal introns. The resulting short lariat, by forming a protective 5' cap, might have been useful in a primitive RNA world.
Kisseleva N, Khvorova A, Westhof E, Schiemann O
Binding of manganese(II) to a tertiary stabilized hammerhead ribozyme as studied by electron paramagnetic resonance spectroscopy Article de journal
Dans: RNA, vol. 11, no. 1, p. 1-6, 2005, ISBN: 15611296, (1355-8382 Letter).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites Electron Spin Resonance Spectroscopy Framycetin/chemistry/metabolism Kinetics Manganese/*metabolism Nucleic Acid Conformation RNA, Catalytic/*chemistry/*metabolism Research Support, Non-U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Binding of manganese(II) to a tertiary stabilized hammerhead ribozyme as studied by electron paramagnetic resonance spectroscopy},
author = {N Kisseleva and A Khvorova and E Westhof and O Schiemann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15611296},
isbn = {15611296},
year = {2005},
date = {2005-01-01},
journal = {RNA},
volume = {11},
number = {1},
pages = {1-6},
abstract = {Electron paramagnetic resonance (EPR) spectroscopy is used to study the binding of MnII ions to a tertiary stabilized hammer-head ribozyme (tsHHRz) and to compare it with the binding to the minimal hammerhead ribozyme (mHHRz). Continuous wave EPR measurements show that the tsHHRz possesses a single high-affinity MnII binding site with a KD of < or =10 nM at an NaCl concentration of 0.1 M. This dissociation constant is at least two orders of magnitude smaller than the KD determined previously for the single high-affinity MnII site in the mHHRz. In addition, whereas the high-affinity MnII is displaced from the mHHRz upon binding of the aminoglycoside antibiotic neomycin B, it is not from the tsHHRz. Despite these pronounced differences in binding, a comparison between the electron spin echo envelope modulation and hyperfine sublevel correlation spectra of the minimal and tertiary stabilized HHRz demonstrates that the structure of both binding sites is very similar. This suggests that the MnII is located in both ribozymes between the bases A9 and G10.1 of the sheared G. A tandem base pair, as shown previously and in detail for the mHHRz. Thus, the much stronger MnII binding in the tsHHRz is attributed to the interaction between the two external loops, which locks in the RNA fold, trapping the MnII in the tightly bound conformation, whereas the absence of long-range loop-loop interactions in the mHHRz leads to more dynamical and open conformations, decreasing MnII binding.},
note = {1355-8382
Letter},
keywords = {Base Sequence Binding Sites Electron Spin Resonance Spectroscopy Framycetin/chemistry/metabolism Kinetics Manganese/*metabolism Nucleic Acid Conformation RNA, Catalytic/*chemistry/*metabolism Research Support, Non-U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Electron paramagnetic resonance (EPR) spectroscopy is used to study the binding of MnII ions to a tertiary stabilized hammer-head ribozyme (tsHHRz) and to compare it with the binding to the minimal hammerhead ribozyme (mHHRz). Continuous wave EPR measurements show that the tsHHRz possesses a single high-affinity MnII binding site with a KD of < or =10 nM at an NaCl concentration of 0.1 M. This dissociation constant is at least two orders of magnitude smaller than the KD determined previously for the single high-affinity MnII site in the mHHRz. In addition, whereas the high-affinity MnII is displaced from the mHHRz upon binding of the aminoglycoside antibiotic neomycin B, it is not from the tsHHRz. Despite these pronounced differences in binding, a comparison between the electron spin echo envelope modulation and hyperfine sublevel correlation spectra of the minimal and tertiary stabilized HHRz demonstrates that the structure of both binding sites is very similar. This suggests that the MnII is located in both ribozymes between the bases A9 and G10.1 of the sheared G. A tandem base pair, as shown previously and in detail for the mHHRz. Thus, the much stronger MnII binding in the tsHHRz is attributed to the interaction between the two external loops, which locks in the RNA fold, trapping the MnII in the tightly bound conformation, whereas the absence of long-range loop-loop interactions in the mHHRz leads to more dynamical and open conformations, decreasing MnII binding.
Henriet S, Richer D, Bernacchi S, Decroly E, Vigne R, Ehresmann B, Ehresmann C, Paillart J C, Marquet R
Cooperative and specific binding of Vif to the 5' region of HIV-1 genomic RNA Article de journal
Dans: J Mol Biol, vol. 354, no. 1, p. 55-72, 2005, ISBN: 16236319, (0022-2836 (Print) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 5' Untranslated Regions/chemistry/*metabolism Base Sequence Electrophoretic Mobility Shift Assay Gene Products, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, vif/*metabolism HIV Long Terminal Repeat HIV-1/*genetics/*metabolism Hela Cells Humans Molecular Sequence Data Nucleic Acid Conformation Protein Binding RNA, Viral/chemistry/*metabolism RNA-Binding Proteins/metabolism Recombinant Proteins/metabolism Research Support
@article{,
title = {Cooperative and specific binding of Vif to the 5' region of HIV-1 genomic RNA},
author = {S Henriet and D Richer and S Bernacchi and E Decroly and R Vigne and B Ehresmann and C Ehresmann and J C Paillart and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16236319},
isbn = {16236319},
year = {2005},
date = {2005-01-01},
journal = {J Mol Biol},
volume = {354},
number = {1},
pages = {55-72},
abstract = {The viral infectivity factor (Vif) protein of human immunodeficiency virus type 1 (HIV-1) is essential for viral replication in vivo. Packaging of Vif into viral particles is mediated by an interaction with viral genomic RNA and association with viral nucleoprotein complexes. Despite recent findings on the RNA-binding properties of Vif suggesting that Vif could be involved in retroviral assembly, no RNA sequence or structure specificity has been determined so far. To gain further insight into the mechanisms by which Vif might regulate viral replication, we studied the interactions of Vif with HIV-1 genomic RNA in vitro. Using extensive biochemical analysis, we have measured the affinity of recombinant Vif proteins for synthetic RNAs corresponding to various regions of the HIV-1 genome. We found that recombinant Vif proteins bind specifically to HIV-1 viral RNA fragments corresponding to the 5'-untranslated region (5'-UTR), gag and the 5' part of pol (K(d) between 45 nM and 65 nM). RNA encompassing nucleotides 1-497 or 499-996 of the HIV-1 genomic RNA bind 9+/-2 and 21+/-3 Vif molecules, respectively, and at least some of these proteins bind in a cooperative manner (Hill constant alpha(H) = 2.3). In contrast, RNAs corresponding to other parts of the HIV-1 genome or heterologous RNAs showed poor binding capacity and weak cooperativity (K(d) > 200 nM). Moreover, RNase T1 footprinting revealed a hierarchical binding of Vif, pointing to TAR and the poly(A) stem-loop structures as primary strong affinity targets, and downstream structures as secondary sites with moderate affinity. Taken together, our findings suggest that Vif may assist other proteins to maintain a correct folding of the genomic RNA in order to facilitate its packaging and further steps such as reverse transcription. Interestingly, our results suggest also that Vif could bind the viral RNA in order to protect it from the action of the antiviral factor APOBEC-3G/3F.},
note = {0022-2836 (Print)
Journal Article},
keywords = {5' Untranslated Regions/chemistry/*metabolism Base Sequence Electrophoretic Mobility Shift Assay Gene Products, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, vif/*metabolism HIV Long Terminal Repeat HIV-1/*genetics/*metabolism Hela Cells Humans Molecular Sequence Data Nucleic Acid Conformation Protein Binding RNA, Viral/chemistry/*metabolism RNA-Binding Proteins/metabolism Recombinant Proteins/metabolism Research Support},
pubstate = {published},
tppubtype = {article}
}
The viral infectivity factor (Vif) protein of human immunodeficiency virus type 1 (HIV-1) is essential for viral replication in vivo. Packaging of Vif into viral particles is mediated by an interaction with viral genomic RNA and association with viral nucleoprotein complexes. Despite recent findings on the RNA-binding properties of Vif suggesting that Vif could be involved in retroviral assembly, no RNA sequence or structure specificity has been determined so far. To gain further insight into the mechanisms by which Vif might regulate viral replication, we studied the interactions of Vif with HIV-1 genomic RNA in vitro. Using extensive biochemical analysis, we have measured the affinity of recombinant Vif proteins for synthetic RNAs corresponding to various regions of the HIV-1 genome. We found that recombinant Vif proteins bind specifically to HIV-1 viral RNA fragments corresponding to the 5'-untranslated region (5'-UTR), gag and the 5' part of pol (K(d) between 45 nM and 65 nM). RNA encompassing nucleotides 1-497 or 499-996 of the HIV-1 genomic RNA bind 9+/-2 and 21+/-3 Vif molecules, respectively, and at least some of these proteins bind in a cooperative manner (Hill constant alpha(H) = 2.3). In contrast, RNAs corresponding to other parts of the HIV-1 genome or heterologous RNAs showed poor binding capacity and weak cooperativity (K(d) > 200 nM). Moreover, RNase T1 footprinting revealed a hierarchical binding of Vif, pointing to TAR and the poly(A) stem-loop structures as primary strong affinity targets, and downstream structures as secondary sites with moderate affinity. Taken together, our findings suggest that Vif may assist other proteins to maintain a correct folding of the genomic RNA in order to facilitate its packaging and further steps such as reverse transcription. Interestingly, our results suggest also that Vif could bind the viral RNA in order to protect it from the action of the antiviral factor APOBEC-3G/3F.
2004
Ferrandon Dominique, Imler Jean-Luc, Hoffmann Jules A
Sensing infection in Drosophila: Toll and beyond Article de journal
Dans: Semin Immunol, vol. 16, p. 43–53, 2004, ISSN: 1044-5323.
Résumé | BibTeX | Étiquettes: Animals, Carrier Proteins/chemistry/immunology/physiology, Cell Surface/immunology/*physiology, Drosophila Proteins/chemistry/immunology/*physiology, Drosophila/genetics/*immunology/microbiology, ferrandon, Fungi/immunology, Gene Expression Regulation, Gram-Negative Bacterial Infections/immunology, Gram-Positive Bacterial Infections/immunology, hoffmann, imler, Immunological, Insect Proteins/chemistry/immunology/physiology, M3i, Models, Non-U.S. Gov't, Receptors, Signal Transduction/immunology/physiology, Support
@article{ferrandon_sensing_2004b,
title = {Sensing infection in Drosophila: Toll and beyond},
author = {Dominique Ferrandon and Jean-Luc Imler and Jules A Hoffmann},
issn = {1044-5323},
year = {2004},
date = {2004-01-01},
journal = {Semin Immunol},
volume = {16},
pages = {43--53},
abstract = {Drosophila has evolved a potent immune system that is somewhat adapted to the nature of infections through the selective activation of either one of two NF-kappa B-like signalling pathways, the Toll and IMD (Immune deficiency) pathways. In contrast to the mammalian system, the Toll receptor does not act as a pattern recognition receptor (PRR) but as a cytokine receptor. The sensing of microbial infections is achieved by at least four PRRs that belong to two distinct families: the peptidoglycan recognition proteins (PGRPs) and the Gram-negative binding proteins (GNBPs)/beta-glucan recognition proteins (beta GRPs).},
keywords = {Animals, Carrier Proteins/chemistry/immunology/physiology, Cell Surface/immunology/*physiology, Drosophila Proteins/chemistry/immunology/*physiology, Drosophila/genetics/*immunology/microbiology, ferrandon, Fungi/immunology, Gene Expression Regulation, Gram-Negative Bacterial Infections/immunology, Gram-Positive Bacterial Infections/immunology, hoffmann, imler, Immunological, Insect Proteins/chemistry/immunology/physiology, M3i, Models, Non-U.S. Gov't, Receptors, Signal Transduction/immunology/physiology, Support},
pubstate = {published},
tppubtype = {article}
}
Drosophila has evolved a potent immune system that is somewhat adapted to the nature of infections through the selective activation of either one of two NF-kappa B-like signalling pathways, the Toll and IMD (Immune deficiency) pathways. In contrast to the mammalian system, the Toll receptor does not act as a pattern recognition receptor (PRR) but as a cytokine receptor. The sensing of microbial infections is achieved by at least four PRRs that belong to two distinct families: the peptidoglycan recognition proteins (PGRPs) and the Gram-negative binding proteins (GNBPs)/beta-glucan recognition proteins (beta GRPs).
Grosjean H, Keith G, Droogmans L
Detection and quantification of modified nucleotides in RNA using thin-layer chromatography Book Section
Dans: Gott, J M (Ed.): RNA Interference, Editing, and Modification: Methods and Protocols, vol. 265, p. 357-91, Springer Protocols, Humana Press, 2004.
Résumé | BibTeX | Étiquettes: KEITH 5' Untranslated Regions/chemistry Base Composition Chromatography, Non-U.S. Gov't
@incollection{,
title = {Detection and quantification of modified nucleotides in RNA using thin-layer chromatography},
author = {H Grosjean and G Keith and L Droogmans},
editor = {J M Gott},
year = {2004},
date = {2004-01-01},
booktitle = {RNA Interference, Editing, and Modification: Methods and Protocols},
volume = {265},
pages = {357-91},
publisher = {Springer Protocols, Humana Press},
series = {Methods in Molecular Biology},
abstract = {Identification of a modified nucleotide and its localization within an RNA molecule is a difficult task. Only direct sequencing of purified RNA molecules and high-performance liquid chromatography mass spectrometry analysis of purified RNA fragments allow determination of both the type and location of a given modified nucleotide within an RNA of 50-150 nt in length. The objective of this chapter is to describe in detail a few simple procedures that we have found particularly suited for the detection, localization, and quantification of modified nucleotides within an RNA of known sequence. The methods can also be used to reveal the enzymatic activity of a particular RNA-modifying enzyme in vitro or in vivo. The procedures are based on the use of radiolabeled RNA (with [32P], [14C], or [3H]) or [32P]-postlabeled oligonucleotides and two-dimensional thin-layer chromatography of labeled nucleotides on cellulose plates. This chapter provides useful maps of the migration characteristics of 70 modified nucleotides on thin-layer cellulose plates.},
keywords = {KEITH 5' Untranslated Regions/chemistry Base Composition Chromatography, Non-U.S. Gov't},
pubstate = {published},
tppubtype = {incollection}
}
Identification of a modified nucleotide and its localization within an RNA molecule is a difficult task. Only direct sequencing of purified RNA molecules and high-performance liquid chromatography mass spectrometry analysis of purified RNA fragments allow determination of both the type and location of a given modified nucleotide within an RNA of 50-150 nt in length. The objective of this chapter is to describe in detail a few simple procedures that we have found particularly suited for the detection, localization, and quantification of modified nucleotides within an RNA of known sequence. The methods can also be used to reveal the enzymatic activity of a particular RNA-modifying enzyme in vitro or in vivo. The procedures are based on the use of radiolabeled RNA (with [32P], [14C], or [3H]) or [32P]-postlabeled oligonucleotides and two-dimensional thin-layer chromatography of labeled nucleotides on cellulose plates. This chapter provides useful maps of the migration characteristics of 70 modified nucleotides on thin-layer cellulose plates.
Zukiel R, Nowak S, Barciszewska A M, Gawronska I, Keith G, Barciszewska M Z
A simple epigenetic method for the diagnosis and classification of brain tumors Article de journal
Dans: Mol Cancer Res, vol. 2, no. 3, p. 196-202, 2004, ISBN: 15037658, (1541-7786 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Genetic Female Human Male Middle Aged Oxidative Stress Reactive Oxygen Species/metabolism Sensitivity and Specificity Support, KEITH 5-Methylcytosine/*analysis Adult Aged Brain Neoplasms/*classification/*diagnosis/genetics/pathology Chromatography, Neoplasm/*chemistry/*metabolism *Epigenesis, Non-U.S. Gov't, Thin Layer *DNA Methylation DNA, Unité ARN
@article{,
title = {A simple epigenetic method for the diagnosis and classification of brain tumors},
author = {R Zukiel and S Nowak and A M Barciszewska and I Gawronska and G Keith and M Z Barciszewska},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15037658},
isbn = {15037658},
year = {2004},
date = {2004-01-01},
journal = {Mol Cancer Res},
volume = {2},
number = {3},
pages = {196-202},
abstract = {The new, simple, and reliable method for the diagnosis of brain tumors is described. It is based on a TLC quantitative determination of 5-methylcytosine (m(5)C) in relation to its damage products of DNA from tumor tissue. Currently, there is evidence that oxidative stress through reactive oxygen species (ROS) plays an important role in the etiology and progression of several human diseases. Oxidative damage of DNA, lipids, and proteins is deleterious for the cell. m(5)C, along with other basic components of DNA, is the target for ROS, which results in the appearance of new modified nucleic acid bases. If so, m(5)C residue constitutes a mutational hotspot position, whether it occurs within a nucleotide sequence of a structural gene or a regulatory region. Here, we show the results of the analysis of 82 DNA samples taken from brain tumor tissues. DNA was isolated and hydrolyzed into nucleotides, which, after labeling with [gamma-(32)P]ATP, were separated on TLC. Chromatograms were evaluated using PhosphorImager and the amounts of 5-methyldeoxycytosine (m(5)dC) were calculated as a ratio (R) of m(5)dC to m(5)dC + deoxycytosine + deoxythymidine spot intensities. The R value could not only be a good diagnostic marker for brain tumors but also a factor differentiating low-grade and high-grade gliomas. Therefore, DNA methylation pattern might be a useful tool to give a primary diagnosis of a brain tumor or as a marker for the early detection of the relapse of the disease. This method has several advantages over those existing nowadays.},
note = {1541-7786
Journal Article},
keywords = {Genetic Female Human Male Middle Aged Oxidative Stress Reactive Oxygen Species/metabolism Sensitivity and Specificity Support, KEITH 5-Methylcytosine/*analysis Adult Aged Brain Neoplasms/*classification/*diagnosis/genetics/pathology Chromatography, Neoplasm/*chemistry/*metabolism *Epigenesis, Non-U.S. Gov't, Thin Layer *DNA Methylation DNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The new, simple, and reliable method for the diagnosis of brain tumors is described. It is based on a TLC quantitative determination of 5-methylcytosine (m(5)C) in relation to its damage products of DNA from tumor tissue. Currently, there is evidence that oxidative stress through reactive oxygen species (ROS) plays an important role in the etiology and progression of several human diseases. Oxidative damage of DNA, lipids, and proteins is deleterious for the cell. m(5)C, along with other basic components of DNA, is the target for ROS, which results in the appearance of new modified nucleic acid bases. If so, m(5)C residue constitutes a mutational hotspot position, whether it occurs within a nucleotide sequence of a structural gene or a regulatory region. Here, we show the results of the analysis of 82 DNA samples taken from brain tumor tissues. DNA was isolated and hydrolyzed into nucleotides, which, after labeling with [gamma-(32)P]ATP, were separated on TLC. Chromatograms were evaluated using PhosphorImager and the amounts of 5-methyldeoxycytosine (m(5)dC) were calculated as a ratio (R) of m(5)dC to m(5)dC + deoxycytosine + deoxythymidine spot intensities. The R value could not only be a good diagnostic marker for brain tumors but also a factor differentiating low-grade and high-grade gliomas. Therefore, DNA methylation pattern might be a useful tool to give a primary diagnosis of a brain tumor or as a marker for the early detection of the relapse of the disease. This method has several advantages over those existing nowadays.
Zhang H, Kolb F A, Jaskiewicz L, Westhof E, Filipowicz W
Single processing center models for human Dicer and bacterial RNase III Article de journal
Dans: Cell, vol. 118, no. 1, p. 57-68, 2004, ISBN: 15242644, (0092-8674 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Amino Acid Sequence Base Sequence Comparative Study Conserved Sequence Dimerization Endoribonucleases/*chemistry/genetics/isolation & purification/*metabolism Escherichia coli/enzymology Human Manganese/metabolism MicroRNAs/metabolism Models, Double-Stranded/chemistry/*metabolism RNA, Molecular Molecular Sequence Data Molecular Weight Mutagenesis, Non-U.S. Gov't, Post-Transcriptional RNA, Secondary Protein Structure, Site-Directed Mutation Protein Structure, Small Interfering/metabolism Recombinant Proteins/metabolism Ribonuclease III/*chemistry/genetics/isolation & purification/*metabolism Sequence Homology, Tertiary RNA Helicases/*chemistry/genetics/isolation & purification/*metabolism *RNA Processing, Unité ARN, WESTHOF
@article{,
title = {Single processing center models for human Dicer and bacterial RNase III},
author = {H Zhang and F A Kolb and L Jaskiewicz and E Westhof and W Filipowicz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15242644},
isbn = {15242644},
year = {2004},
date = {2004-01-01},
journal = {Cell},
volume = {118},
number = {1},
pages = {57-68},
abstract = {Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21 nt small interfering RNAs (siRNAs) during RNA interference, and excises microRNAs from precursor hairpins. Dicer contains two domains related to the bacterial dsRNA-specific endonuclease, RNase III, which is known to function as a homodimer. Based on an X-ray structure of the Aquifex aeolicus RNase III, models of the enzyme interaction with dsRNA, and its cleavage at two composite catalytic centers, have been proposed. We have generated mutations in human Dicer and Escherichia coli RNase III residues implicated in the catalysis, and studied their effect on RNA processing. Our results indicate that both enzymes have only one processing center, containing two RNA cleavage sites and generating products with 2 nt 3' overhangs. Based on these and other data, we propose that Dicer functions through intramolecular dimerization of its two RNase III domains, assisted by the flanking RNA binding domains, PAZ and dsRBD.},
note = {0092-8674
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Base Sequence Comparative Study Conserved Sequence Dimerization Endoribonucleases/*chemistry/genetics/isolation & purification/*metabolism Escherichia coli/enzymology Human Manganese/metabolism MicroRNAs/metabolism Models, Double-Stranded/chemistry/*metabolism RNA, Molecular Molecular Sequence Data Molecular Weight Mutagenesis, Non-U.S. Gov't, Post-Transcriptional RNA, Secondary Protein Structure, Site-Directed Mutation Protein Structure, Small Interfering/metabolism Recombinant Proteins/metabolism Ribonuclease III/*chemistry/genetics/isolation & purification/*metabolism Sequence Homology, Tertiary RNA Helicases/*chemistry/genetics/isolation & purification/*metabolism *RNA Processing, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21 nt small interfering RNAs (siRNAs) during RNA interference, and excises microRNAs from precursor hairpins. Dicer contains two domains related to the bacterial dsRNA-specific endonuclease, RNase III, which is known to function as a homodimer. Based on an X-ray structure of the Aquifex aeolicus RNase III, models of the enzyme interaction with dsRNA, and its cleavage at two composite catalytic centers, have been proposed. We have generated mutations in human Dicer and Escherichia coli RNase III residues implicated in the catalysis, and studied their effect on RNA processing. Our results indicate that both enzymes have only one processing center, containing two RNA cleavage sites and generating products with 2 nt 3' overhangs. Based on these and other data, we propose that Dicer functions through intramolecular dimerization of its two RNase III domains, assisted by the flanking RNA binding domains, PAZ and dsRBD.
Martineau Y, Bec C Le, Monbrun L, Allo V, Chiu I M, Danos O, Moine H, Prats H, Prats A C
Internal ribosome entry site structural motifs conserved among mammalian fibroblast growth factor 1 alternatively spliced mRNAs Article de journal
Dans: Mol Cell Biol, vol. 24, no. 17, p. 7622-7635, 2004, ISBN: 15314170, (0270-7306 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: EHRESMANN *5' Untranslated Regions *Alternative Splicing Animals Base Sequence Cell Line Fibroblast Growth Factor 1/*genetics Gene Transfer Techniques Genes, Messenger/chemistry/*genetics/metabolism Ribosomes/*metabolism Sequence Alignment Support, Non-U.S. Gov't, Site-Directed *Nucleic Acid Conformation *Promoter Regions (Genetics) RNA, Skeletal/cytology/physiology Mutagenesis, Structural/genetics Genetic Vectors Human Mice Molecular Sequence Data Muscle, Unité ARN
@article{,
title = {Internal ribosome entry site structural motifs conserved among mammalian fibroblast growth factor 1 alternatively spliced mRNAs},
author = {Y Martineau and C Le Bec and L Monbrun and V Allo and I M Chiu and O Danos and H Moine and H Prats and A C Prats},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15314170},
isbn = {15314170},
year = {2004},
date = {2004-01-01},
journal = {Mol Cell Biol},
volume = {24},
number = {17},
pages = {7622-7635},
abstract = {Fibroblast growth factor 1 (FGF-1) is a powerful angiogenic factor whose gene structure contains four promoters, giving rise to a process of alternative splicing resulting in four mRNAs with alternative 5' untranslated regions (5' UTRs). Here we have identified, by using double luciferase bicistronic vectors, the presence of internal ribosome entry sites (IRESs) in the human FGF-1 5' UTRs, particularly in leaders A and C, with distinct activities in mammalian cells. DNA electrotransfer in mouse muscle revealed that the IRES present in the FGF-1 leader A has a high activity in vivo. We have developed a new regulatable TET OFF bicistronic system, which allowed us to rule out the possibility of any cryptic promoter in the FGF-1 leaders. FGF-1 IRESs A and C, which were mapped in fragments of 118 and 103 nucleotides, respectively, are flexible in regard to the position of the initiation codon, making them interesting from a biotechnological point of view. Furthermore, we show that FGF-1 IRESs A of murine and human origins show similar IRES activity profiles. Enzymatic and chemical probing of the FGF-1 IRES A RNA revealed a structural domain conserved among mammals at both the nucleotide sequence and RNA structure levels. The functional role of this structural motif has been demonstrated by point mutagenesis, including compensatory mutations. These data favor an important role of IRESs in the control of FGF-1 expression and provide a new IRES structural motif that could help IRES prediction in 5' UTR databases.},
note = {0270-7306
Journal Article},
keywords = {EHRESMANN *5' Untranslated Regions *Alternative Splicing Animals Base Sequence Cell Line Fibroblast Growth Factor 1/*genetics Gene Transfer Techniques Genes, Messenger/chemistry/*genetics/metabolism Ribosomes/*metabolism Sequence Alignment Support, Non-U.S. Gov't, Site-Directed *Nucleic Acid Conformation *Promoter Regions (Genetics) RNA, Skeletal/cytology/physiology Mutagenesis, Structural/genetics Genetic Vectors Human Mice Molecular Sequence Data Muscle, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Fibroblast growth factor 1 (FGF-1) is a powerful angiogenic factor whose gene structure contains four promoters, giving rise to a process of alternative splicing resulting in four mRNAs with alternative 5' untranslated regions (5' UTRs). Here we have identified, by using double luciferase bicistronic vectors, the presence of internal ribosome entry sites (IRESs) in the human FGF-1 5' UTRs, particularly in leaders A and C, with distinct activities in mammalian cells. DNA electrotransfer in mouse muscle revealed that the IRES present in the FGF-1 leader A has a high activity in vivo. We have developed a new regulatable TET OFF bicistronic system, which allowed us to rule out the possibility of any cryptic promoter in the FGF-1 leaders. FGF-1 IRESs A and C, which were mapped in fragments of 118 and 103 nucleotides, respectively, are flexible in regard to the position of the initiation codon, making them interesting from a biotechnological point of view. Furthermore, we show that FGF-1 IRESs A of murine and human origins show similar IRES activity profiles. Enzymatic and chemical probing of the FGF-1 IRES A RNA revealed a structural domain conserved among mammals at both the nucleotide sequence and RNA structure levels. The functional role of this structural motif has been demonstrated by point mutagenesis, including compensatory mutations. These data favor an important role of IRESs in the control of FGF-1 expression and provide a new IRES structural motif that could help IRES prediction in 5' UTR databases.
Martin F, Barends S, Eriani G
Single amino acid changes in AspRS reveal alternative routes for expanding its tRNA repertoire in vivo Article de journal
Dans: Nucleic Acids Res, vol. 32, no. 13, p. 4081-4089, 2004, ISBN: 15289581, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Substitution Anticodon/metabolism Aspartate-tRNA Ligase/*chemistry/genetics/*metabolism Aspartic Acid/metabolism Binding Sites Models, Amino Acyl/chemistry/*metabolism Support, ERIANI, Molecular Mutation Phenotype Protein Engineering Protein Structure, Non-U.S. Gov't, Tertiary RNA, Transfer, Unité ARN
@article{,
title = {Single amino acid changes in AspRS reveal alternative routes for expanding its tRNA repertoire in vivo},
author = {F Martin and S Barends and G Eriani},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15289581},
isbn = {15289581},
year = {2004},
date = {2004-01-01},
journal = {Nucleic Acids Res},
volume = {32},
number = {13},
pages = {4081-4089},
abstract = {Aminoacyl-tRNA synthetases (aaRSs) are enzymes that are highly specific for their tRNA substrates. Here, we describe the expansion of a class IIb aaRS-tRNA specificity by a genetic selection that involves the use of a modified tRNA displaying an amber anticodon and the argE(amber) and lacZ(amber) reporters. The study was performed on Escherichia coli aspartyl-tRNA synthetase (AspRS) and amber tRNA(Asp). Nine AspRS mutants able to charge the amber tRNA(Asp) and to suppress the reporter genes were selected from a randomly mutated library. All the mutants exhibited a new amber tRNA(Asp) specificity in addition to the initial native tRNA(Asp). Six mutations were found in the anticodon-binding site located in the N-terminal OB-fold. The strongest suppressor was a mutation of residue Glu-93 that contacts specifically the anticodon nucleotide 34 in the crystal structure. The other mutations in the OB-fold were found at close distance from the anticodon in the so-called loop L45 and strand S1. They concern residues that do not contact tRNA(Asp) in the native complex. In addition, this study shows that suppressors can carry mutations located far from the anticodon-binding site. One such mutation was found in the synthetase hinge-module where it increases the tRNA(Asp)-charging rate, and two other mutations were found in the prokaryotic-specific insertion domain and the catalytic core. These mutants seem to act by indirect effects on the tRNA acceptor stem binding and on the conformation of the active site of the enzyme. Altogether, these data suggest the existence of various ways for modifying the mechanism of tRNA discrimination.},
note = {1362-4962
Journal Article},
keywords = {Amino Acid Substitution Anticodon/metabolism Aspartate-tRNA Ligase/*chemistry/genetics/*metabolism Aspartic Acid/metabolism Binding Sites Models, Amino Acyl/chemistry/*metabolism Support, ERIANI, Molecular Mutation Phenotype Protein Engineering Protein Structure, Non-U.S. Gov't, Tertiary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that are highly specific for their tRNA substrates. Here, we describe the expansion of a class IIb aaRS-tRNA specificity by a genetic selection that involves the use of a modified tRNA displaying an amber anticodon and the argE(amber) and lacZ(amber) reporters. The study was performed on Escherichia coli aspartyl-tRNA synthetase (AspRS) and amber tRNA(Asp). Nine AspRS mutants able to charge the amber tRNA(Asp) and to suppress the reporter genes were selected from a randomly mutated library. All the mutants exhibited a new amber tRNA(Asp) specificity in addition to the initial native tRNA(Asp). Six mutations were found in the anticodon-binding site located in the N-terminal OB-fold. The strongest suppressor was a mutation of residue Glu-93 that contacts specifically the anticodon nucleotide 34 in the crystal structure. The other mutations in the OB-fold were found at close distance from the anticodon in the so-called loop L45 and strand S1. They concern residues that do not contact tRNA(Asp) in the native complex. In addition, this study shows that suppressors can carry mutations located far from the anticodon-binding site. One such mutation was found in the synthetase hinge-module where it increases the tRNA(Asp)-charging rate, and two other mutations were found in the prokaryotic-specific insertion domain and the catalytic core. These mutants seem to act by indirect effects on the tRNA acceptor stem binding and on the conformation of the active site of the enzyme. Altogether, these data suggest the existence of various ways for modifying the mechanism of tRNA discrimination.
Grosjean H, Keith G, Droogmans L
Detection and quantification of modified nucleotides in RNA using thin-layer chromatography Chapitre d'ouvrage
Dans: Gott, J M (Ed.): RNA Interference, Editing, and Modification: Methods and Protocols, vol. 265, p. 357-391, Springer Protocols, Humana Press, 2004, ISBN: 15103084.
Résumé | Liens | BibTeX | Étiquettes: KEITH 5' Untranslated Regions/chemistry Base Composition Chromatography, Non-U.S. Gov't, Unité ARN
@inbook{,
title = {Detection and quantification of modified nucleotides in RNA using thin-layer chromatography},
author = {H Grosjean and G Keith and L Droogmans},
editor = {J M Gott},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15103084},
doi = {10.1385/1-59259-775-0:357},
isbn = {15103084},
year = {2004},
date = {2004-01-01},
booktitle = {RNA Interference, Editing, and Modification: Methods and Protocols},
volume = {265},
pages = {357-391},
publisher = {Springer Protocols, Humana Press},
series = {Methods in Molecular Biology},
abstract = {Identification of a modified nucleotide and its localization within an RNA molecule is a difficult task. Only direct sequencing of purified RNA molecules and high-performance liquid chromatography mass spectrometry analysis of purified RNA fragments allow determination of both the type and location of a given modified nucleotide within an RNA of 50-150 nt in length. The objective of this chapter is to describe in detail a few simple procedures that we have found particularly suited for the detection, localization, and quantification of modified nucleotides within an RNA of known sequence. The methods can also be used to reveal the enzymatic activity of a particular RNA-modifying enzyme in vitro or in vivo. The procedures are based on the use of radiolabeled RNA (with [32P], [14C], or [3H]) or [32P]-postlabeled oligonucleotides and two-dimensional thin-layer chromatography of labeled nucleotides on cellulose plates. This chapter provides useful maps of the migration characteristics of 70 modified nucleotides on thin-layer cellulose plates.},
keywords = {KEITH 5' Untranslated Regions/chemistry Base Composition Chromatography, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Identification of a modified nucleotide and its localization within an RNA molecule is a difficult task. Only direct sequencing of purified RNA molecules and high-performance liquid chromatography mass spectrometry analysis of purified RNA fragments allow determination of both the type and location of a given modified nucleotide within an RNA of 50-150 nt in length. The objective of this chapter is to describe in detail a few simple procedures that we have found particularly suited for the detection, localization, and quantification of modified nucleotides within an RNA of known sequence. The methods can also be used to reveal the enzymatic activity of a particular RNA-modifying enzyme in vitro or in vivo. The procedures are based on the use of radiolabeled RNA (with [32P], [14C], or [3H]) or [32P]-postlabeled oligonucleotides and two-dimensional thin-layer chromatography of labeled nucleotides on cellulose plates. This chapter provides useful maps of the migration characteristics of 70 modified nucleotides on thin-layer cellulose plates.
de la Pena-Lefebvre P Garcia, Chanseaud Y, Tamby M C, Reinbolt J, Batteux F, Allanore Y, Kahan A, Meyer O, Benveniste O, Boyer O, Guillevin L, Boissier M C, Mouthon L
IgG reactivity with a 100-kDa tissue and endothelial cell antigen identified as topoisomerase 1 distinguishes between limited and diffuse systemic sclerosis patients Article de journal
Dans: Clin Immunol, vol. 111, no. 3, p. 241-251, 2004, ISBN: 15183145, (1521-6616 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: EHRESMANN Autoantibodies/*analysis Blotting, Non-U.S. Gov't, Polyacrylamide Gel Endothelial Cells/*immunology Enzyme-Linked Immunosorbent Assay Female Human Immunoglobulin G/analysis Immunoglobulin M/analysis Male Middle Aged Scleroderma, Systemic/*immunology Support, Type I/*immunology Electrophoresis, Unité ARN, Western Centromere/immunology DNA Topoisomerases
@article{,
title = {IgG reactivity with a 100-kDa tissue and endothelial cell antigen identified as topoisomerase 1 distinguishes between limited and diffuse systemic sclerosis patients},
author = {P Garcia de la Pena-Lefebvre and Y Chanseaud and M C Tamby and J Reinbolt and F Batteux and Y Allanore and A Kahan and O Meyer and O Benveniste and O Boyer and L Guillevin and M C Boissier and L Mouthon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15183145},
isbn = {15183145},
year = {2004},
date = {2004-01-01},
journal = {Clin Immunol},
volume = {111},
number = {3},
pages = {241-251},
abstract = {We have analyzed antibody (Ab) reactivities of patients with limited systemic sclerosis (SSc) and anti-centromere Ab, patients with diffuse SSc and anti-topoisomerase 1 (anti-topo 1) Ab, patients with diffuse SSc without anti-topo 1 or anti-centromere Ab and age- and gender-matched healthy controls with normal human tissue and endothelial cell (EC) antigens. IgG reactivities with tissue antigens differed significantly between patients with anti-topo 1 Ab and patients with anti-centromere Ab. One 100-kDa band identified as topoisomerase 1 in macrovascular and microvascular EC extracts was recognized by IgG from patients with anti-topo 1 Ab and 50% of patients without specific Ab. IgG from patients with limited SSc and anti-centromere Ab, but not those of other patients or controls specifically recognized a 80-kDa band only in microvascular EC. Our results indicate that Ab from patients with limited or diffuse SSc with or without anti-topo 1 Ab exhibit specific and mutually exclusive reactivity patterns.},
note = {1521-6616
Journal Article},
keywords = {EHRESMANN Autoantibodies/*analysis Blotting, Non-U.S. Gov't, Polyacrylamide Gel Endothelial Cells/*immunology Enzyme-Linked Immunosorbent Assay Female Human Immunoglobulin G/analysis Immunoglobulin M/analysis Male Middle Aged Scleroderma, Systemic/*immunology Support, Type I/*immunology Electrophoresis, Unité ARN, Western Centromere/immunology DNA Topoisomerases},
pubstate = {published},
tppubtype = {article}
}
We have analyzed antibody (Ab) reactivities of patients with limited systemic sclerosis (SSc) and anti-centromere Ab, patients with diffuse SSc and anti-topoisomerase 1 (anti-topo 1) Ab, patients with diffuse SSc without anti-topo 1 or anti-centromere Ab and age- and gender-matched healthy controls with normal human tissue and endothelial cell (EC) antigens. IgG reactivities with tissue antigens differed significantly between patients with anti-topo 1 Ab and patients with anti-centromere Ab. One 100-kDa band identified as topoisomerase 1 in macrovascular and microvascular EC extracts was recognized by IgG from patients with anti-topo 1 Ab and 50% of patients without specific Ab. IgG from patients with limited SSc and anti-centromere Ab, but not those of other patients or controls specifically recognized a 80-kDa band only in microvascular EC. Our results indicate that Ab from patients with limited or diffuse SSc with or without anti-topo 1 Ab exhibit specific and mutually exclusive reactivity patterns.
Fender A, Geslain R, Eriani G, Giege R, Sissler M, Florentz C
A yeast arginine specific tRNA is a remnant aspartate acceptor Article de journal
Dans: Nucleic Acids Res, vol. 32, no. 17, p. 5076-5086, 2004, ISBN: 15452274, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Arg/*chemistry/genetics/metabolism RNA, Asp/*chemistry/genetics/metabolism Saccharomyces cerevisiae/*genetics Sequence Alignment Support, ERIANI, ERIANI FLORENTZ GIEGE Aspartic Acid/metabolism Base Sequence *Evolution, FLORENTZ, Fungal/*chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Point Mutation RNA, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN
@article{,
title = {A yeast arginine specific tRNA is a remnant aspartate acceptor},
author = {A Fender and R Geslain and G Eriani and R Giege and M Sissler and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15452274},
isbn = {15452274},
year = {2004},
date = {2004-01-01},
journal = {Nucleic Acids Res},
volume = {32},
number = {17},
pages = {5076-5086},
abstract = {High specificity in aminoacylation of transfer RNAs (tRNAs) with the help of their cognate aminoacyl-tRNA synthetases (aaRSs) is a guarantee for accurate genetic translation. Structural and mechanistic peculiarities between the different tRNA/aaRS couples, suggest that aminoacylation systems are unrelated. However, occurrence of tRNA mischarging by non-cognate aaRSs reflects the relationship between such systems. In Saccharomyces cerevisiae, functional links between arginylation and aspartylation systems have been reported. In particular, it was found that an in vitro transcribed tRNAAsp is a very efficient substrate for ArgRS. In this study, the relationship of arginine and aspartate systems is further explored, based on the discovery of a fourth isoacceptor in the yeast genome, tRNA4Arg. This tRNA has a sequence strikingly similar to that of tRNAAsp but distinct from those of the other three arginine isoacceptors. After transplantation of the full set of aspartate identity elements into the four arginine isoacceptors, tRNA4Arg gains the highest aspartylation efficiency. Moreover, it is possible to convert tRNA4Arg into an aspartate acceptor, as efficient as tRNAAsp, by only two point mutations, C38 and G73, despite the absence of the major anticodon aspartate identity elements. Thus, cryptic aspartate identity elements are embedded within tRNA4Arg. The latent aspartate acceptor capacity in a contemporary tRNAArg leads to the proposal of an evolutionary link between tRNA4Arg and tRNAAsp genes.},
note = {1362-4962
Journal Article},
keywords = {Arg/*chemistry/genetics/metabolism RNA, Asp/*chemistry/genetics/metabolism Saccharomyces cerevisiae/*genetics Sequence Alignment Support, ERIANI, ERIANI FLORENTZ GIEGE Aspartic Acid/metabolism Base Sequence *Evolution, FLORENTZ, Fungal/*chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Point Mutation RNA, Non-U.S. Gov't, SISSLER, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
High specificity in aminoacylation of transfer RNAs (tRNAs) with the help of their cognate aminoacyl-tRNA synthetases (aaRSs) is a guarantee for accurate genetic translation. Structural and mechanistic peculiarities between the different tRNA/aaRS couples, suggest that aminoacylation systems are unrelated. However, occurrence of tRNA mischarging by non-cognate aaRSs reflects the relationship between such systems. In Saccharomyces cerevisiae, functional links between arginylation and aspartylation systems have been reported. In particular, it was found that an in vitro transcribed tRNAAsp is a very efficient substrate for ArgRS. In this study, the relationship of arginine and aspartate systems is further explored, based on the discovery of a fourth isoacceptor in the yeast genome, tRNA4Arg. This tRNA has a sequence strikingly similar to that of tRNAAsp but distinct from those of the other three arginine isoacceptors. After transplantation of the full set of aspartate identity elements into the four arginine isoacceptors, tRNA4Arg gains the highest aspartylation efficiency. Moreover, it is possible to convert tRNA4Arg into an aspartate acceptor, as efficient as tRNAAsp, by only two point mutations, C38 and G73, despite the absence of the major anticodon aspartate identity elements. Thus, cryptic aspartate identity elements are embedded within tRNA4Arg. The latent aspartate acceptor capacity in a contemporary tRNAArg leads to the proposal of an evolutionary link between tRNA4Arg and tRNAAsp genes.
Dubois D Y, Blaise M, Becker H D, Campanacci V, Keith G, Giege R, Cambillau C, Lapointe J, Kern D
An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 101, no. 20, p. 7530-7535, 2004, ISBN: 15096594, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/*metabolism Support, KERN GIEGE Amino Acyl-tRNA Ligases/chemistry/genetics/*metabolism Crystallography, Messenger/metabolism RNA, Non-U.S. Gov't, Tertiary RNA, Transfer, Unité ARN, X-Ray Escherichia coli/enzymology/genetics/*metabolism Escherichia coli Proteins/chemistry/genetics/*metabolism Glutamic Acid/*metabolism Peptide Elongation Factor 2/metabolism Phylogeny Protein Structure
@article{,
title = {An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp},
author = {D Y Dubois and M Blaise and H D Becker and V Campanacci and G Keith and R Giege and C Cambillau and J Lapointe and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15096594},
isbn = {15096594},
year = {2004},
date = {2004-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {101},
number = {20},
pages = {7530-7535},
abstract = {The product of the Escherichia coli yadB gene is homologous to the N-terminal part of bacterial glutamyl-tRNA synthetases (GluRSs), including the Rossmann fold with the acceptor-binding domain and the stem-contact fold. This GluRS-like protein, which lacks the anticodon-binding domain, does not use tRNA(Glu) as substrate in vitro nor in vivo, but aminoacylates tRNA(Asp) with glutamate. The yadB gene is expressed in wild-type E. coli as an operon with the dksA gene, which encodes a protein involved in the general stress response by means of its action at the translational level. The fate of the glutamylated tRNA(Asp) is not known, but its incapacity to bind elongation factor Tu suggests that it is not involved in ribosomal protein synthesis. Genes homologous to yadB are present only in bacteria, mostly in Proteobacteria. Sequence alignments and phylogenetic analyses show that the YadB proteins form a distinct monophyletic group related to the bacterial and organellar GluRSs (alpha-type GlxRSs superfamily) with ubiquitous function as suggested by the similar functional properties of the YadB homologue from Neisseria meningitidis.},
note = {0027-8424
Journal Article},
keywords = {Asp/*metabolism Support, KERN GIEGE Amino Acyl-tRNA Ligases/chemistry/genetics/*metabolism Crystallography, Messenger/metabolism RNA, Non-U.S. Gov't, Tertiary RNA, Transfer, Unité ARN, X-Ray Escherichia coli/enzymology/genetics/*metabolism Escherichia coli Proteins/chemistry/genetics/*metabolism Glutamic Acid/*metabolism Peptide Elongation Factor 2/metabolism Phylogeny Protein Structure},
pubstate = {published},
tppubtype = {article}
}
The product of the Escherichia coli yadB gene is homologous to the N-terminal part of bacterial glutamyl-tRNA synthetases (GluRSs), including the Rossmann fold with the acceptor-binding domain and the stem-contact fold. This GluRS-like protein, which lacks the anticodon-binding domain, does not use tRNA(Glu) as substrate in vitro nor in vivo, but aminoacylates tRNA(Asp) with glutamate. The yadB gene is expressed in wild-type E. coli as an operon with the dksA gene, which encodes a protein involved in the general stress response by means of its action at the translational level. The fate of the glutamylated tRNA(Asp) is not known, but its incapacity to bind elongation factor Tu suggests that it is not involved in ribosomal protein synthesis. Genes homologous to yadB are present only in bacteria, mostly in Proteobacteria. Sequence alignments and phylogenetic analyses show that the YadB proteins form a distinct monophyletic group related to the bacterial and organellar GluRSs (alpha-type GlxRSs superfamily) with ubiquitous function as suggested by the similar functional properties of the YadB homologue from Neisseria meningitidis.
Charron C, Giege R, Lorber B
Structure of thaumatin in a hexagonal space group: comparison of packing contacts in four crystal lattices Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 60, no. Pt 1, p. 83-89, 2004, ISBN: 14684896, (0907-4449 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: GIEGE Comparative Study Crystallization Crystallography, Molecular Plant Proteins/*chemistry Support, Non-U.S. Gov't, Unité ARN, X-Ray Hydrogen Bonding Models
@article{,
title = {Structure of thaumatin in a hexagonal space group: comparison of packing contacts in four crystal lattices},
author = {C Charron and R Giege and B Lorber},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14684896},
isbn = {14684896},
year = {2004},
date = {2004-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {60},
number = {Pt 1},
pages = {83-89},
abstract = {The intensely sweet protein thaumatin has been crystallized in a hexagonal lattice after a temperature shift from 293 to 277 K. The structure of the protein in the new crystal was solved at 1.6 A resolution. The protein fold is identical to that found in three other crystal forms grown in the presence of crystallizing agents of differing chemical natures. The proportions of lattice interactions involving hydrogen bonds, hydrophobic or ionic groups differ greatly from one form to another. Moreover, the distribution of acidic and basic residues taking part in contacts also varies. The hexagonal packing is characterized by the presence of channels parallel to the c axis that are so wide that protein molecules can diffuse through them.},
note = {0907-4449
Journal Article},
keywords = {GIEGE Comparative Study Crystallization Crystallography, Molecular Plant Proteins/*chemistry Support, Non-U.S. Gov't, Unité ARN, X-Ray Hydrogen Bonding Models},
pubstate = {published},
tppubtype = {article}
}
The intensely sweet protein thaumatin has been crystallized in a hexagonal lattice after a temperature shift from 293 to 277 K. The structure of the protein in the new crystal was solved at 1.6 A resolution. The protein fold is identical to that found in three other crystal forms grown in the presence of crystallizing agents of differing chemical natures. The proportions of lattice interactions involving hydrogen bonds, hydrophobic or ionic groups differ greatly from one form to another. Moreover, the distribution of acidic and basic residues taking part in contacts also varies. The hexagonal packing is characterized by the presence of channels parallel to the c axis that are so wide that protein molecules can diffuse through them.
Blaise M, Becker H D, Keith G, Cambillau C, Lapointe J, Giege R, Kern D
A minimalist glutamyl-tRNA synthetase dedicated to aminoacylation of the tRNAAsp QUC anticodon Article de journal
Dans: Nucleic Acids Res, vol. 32, no. 9, p. 2768-2775, 2004, ISBN: 15150343, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/*metabolism RNA, Bacterial/chemistry/genetics/metabolism RNA, Glu/chemistry/genetics/metabolism Support, KERN Acylation Anticodon/chemistry/genetics/*metabolism Base Sequence Conserved Sequence Escherichia coli/*enzymology/*genetics Evolution Glutamate-tRNA Ligase/*chemistry/genetics/*metabolism Molecular Mimicry Nucleoside Q/genetics/*metabolism Periodic Acid/pharmacology RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {A minimalist glutamyl-tRNA synthetase dedicated to aminoacylation of the tRNAAsp QUC anticodon},
author = {M Blaise and H D Becker and G Keith and C Cambillau and J Lapointe and R Giege and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15150343},
isbn = {15150343},
year = {2004},
date = {2004-01-01},
journal = {Nucleic Acids Res},
volume = {32},
number = {9},
pages = {2768-2775},
abstract = {Escherichia coli encodes YadB, a protein displaying 34% identity with the catalytic core of glutamyl-tRNA synthetase but lacking the anticodon-binding domain. We show that YadB is a tRNA modifying enzyme that evidently glutamylates the queuosine residue, a modified nucleoside at the wobble position of the tRNA(Asp) QUC anticodon. This conclusion is supported by a variety of biochemical data and by the inability of the enzyme to glutamylate tRNA(Asp) isolated from an E.coli tRNA-guanosine transglycosylase minus strain deprived of the capacity to exchange guanosine 34 with queuosine. Structural mimicry between the tRNA(Asp) anticodon stem and the tRNA(Glu) amino acid acceptor stem in prokaryotes encoding YadB proteins indicates that the function of these tRNA modifying enzymes, which we rename glutamyl-Q tRNA(Asp) synthetases, is conserved among prokaryotes.},
note = {1362-4962
Journal Article},
keywords = {Asp/chemistry/genetics/*metabolism RNA, Bacterial/chemistry/genetics/metabolism RNA, Glu/chemistry/genetics/metabolism Support, KERN Acylation Anticodon/chemistry/genetics/*metabolism Base Sequence Conserved Sequence Escherichia coli/*enzymology/*genetics Evolution Glutamate-tRNA Ligase/*chemistry/genetics/*metabolism Molecular Mimicry Nucleoside Q/genetics/*metabolism Periodic Acid/pharmacology RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Escherichia coli encodes YadB, a protein displaying 34% identity with the catalytic core of glutamyl-tRNA synthetase but lacking the anticodon-binding domain. We show that YadB is a tRNA modifying enzyme that evidently glutamylates the queuosine residue, a modified nucleoside at the wobble position of the tRNA(Asp) QUC anticodon. This conclusion is supported by a variety of biochemical data and by the inability of the enzyme to glutamylate tRNA(Asp) isolated from an E.coli tRNA-guanosine transglycosylase minus strain deprived of the capacity to exchange guanosine 34 with queuosine. Structural mimicry between the tRNA(Asp) anticodon stem and the tRNA(Glu) amino acid acceptor stem in prokaryotes encoding YadB proteins indicates that the function of these tRNA modifying enzymes, which we rename glutamyl-Q tRNA(Asp) synthetases, is conserved among prokaryotes.
2003
Kurz Léopold C, Chauvet Sophie, Andrès Emmanuel, Aurouze Marianne, Vallet Isabelle, Michel Gérard P F, Uh Mitch, Celli Jean, Filloux Alain, Bentzmann Sophie De, Steinmetz Ivo, Hoffmann Jules A, Finlay Brett B, Gorvel Jean-Pierre, Ferrandon Dominique, Ewbank Jonathan J
Virulence factors of the human opportunistic pathogen Serratia marcescens identified by in vivo screening Article de journal
Dans: Embo J, vol. 22, p. 1451–60, 2003, ISBN: 0261-4189.
Résumé | Liens | BibTeX | Étiquettes: *Virulence, Animal, Caenorhabditis elegans/*microbiology, ferrandon, hoffmann, M3i, Mutation, Non-U.S. Gov't, Serratia marcescens/genetics/*pathogenicity, Support
@article{kurz_virulence_2003b,
title = {Virulence factors of the human opportunistic pathogen Serratia marcescens identified by in vivo screening},
author = {Léopold C Kurz and Sophie Chauvet and Emmanuel Andrès and Marianne Aurouze and Isabelle Vallet and Gérard P F Michel and Mitch Uh and Jean Celli and Alain Filloux and Sophie De Bentzmann and Ivo Steinmetz and Jules A Hoffmann and Brett B Finlay and Jean-Pierre Gorvel and Dominique Ferrandon and Jonathan J Ewbank},
doi = {10.1093/emboj/cdg159},
isbn = {0261-4189},
year = {2003},
date = {2003-04-01},
journal = {Embo J},
volume = {22},
pages = {1451--60},
abstract = {The human opportunistic pathogen Serratia marcescens is a bacterium with a broad host range, and represents a growing problem for public health. Serratia marcescens kills Caenorhabditis elegans after colonizing the nematode's intestine. We used C.elegans to screen a bank of transposon-induced S.marcescens mutants and isolated 23 clones with an attenuated virulence. Nine of the selected bacterial clones also showed a reduced virulence in an insect model of infection. Of these, three exhibited a reduced cytotoxicity in vitro, and among them one was also markedly attenuated in its virulence in a murine lung infection model. For 21 of the 23 mutants, the transposon insertion site was identified. This revealed that among the genes necessary for full in vivo virulence are those that function in lipopolysaccharide (LPS) biosynthesis, iron uptake and hemolysin production. Using this system we also identified novel conserved virulence factors required for Pseudomonas aeruginosa pathogenicity. This study extends the utility of C.elegans as an in vivo model for the study of bacterial virulence and advances the molecular understanding of S.marcescens pathogenicity.},
keywords = {*Virulence, Animal, Caenorhabditis elegans/*microbiology, ferrandon, hoffmann, M3i, Mutation, Non-U.S. Gov't, Serratia marcescens/genetics/*pathogenicity, Support},
pubstate = {published},
tppubtype = {article}
}
The human opportunistic pathogen Serratia marcescens is a bacterium with a broad host range, and represents a growing problem for public health. Serratia marcescens kills Caenorhabditis elegans after colonizing the nematode's intestine. We used C.elegans to screen a bank of transposon-induced S.marcescens mutants and isolated 23 clones with an attenuated virulence. Nine of the selected bacterial clones also showed a reduced virulence in an insect model of infection. Of these, three exhibited a reduced cytotoxicity in vitro, and among them one was also markedly attenuated in its virulence in a murine lung infection model. For 21 of the 23 mutants, the transposon insertion site was identified. This revealed that among the genes necessary for full in vivo virulence are those that function in lipopolysaccharide (LPS) biosynthesis, iron uptake and hemolysin production. Using this system we also identified novel conserved virulence factors required for Pseudomonas aeruginosa pathogenicity. This study extends the utility of C.elegans as an in vivo model for the study of bacterial virulence and advances the molecular understanding of S.marcescens pathogenicity.
Zhao M W, Hao R, Chen J F, Martin F, Eriani G, Wang E D
Enzymes assembled from Aquifex aeolicus and Escherichia coli leucyl-tRNA synthetases Article de journal
Dans: Biochemistry, vol. 42, no. 25, p. 7694-7700, 2003, ISBN: 12820878, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl-tRNA Ligases/genetics/*metabolism Escherichia coli/*enzymology Evolution, ERIANI, Horizontal Heat Kinetics Mutation RNA, Leu/*metabolism Structure-Activity Relationship Support, Molecular Gene Transfer, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Enzymes assembled from Aquifex aeolicus and Escherichia coli leucyl-tRNA synthetases},
author = {M W Zhao and R Hao and J F Chen and F Martin and G Eriani and E D Wang},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12820878},
isbn = {12820878},
year = {2003},
date = {2003-01-01},
journal = {Biochemistry},
volume = {42},
number = {25},
pages = {7694-7700},
abstract = {Aquifex aeolicus alphabeta-LeuRS is the only known heterodimeric LeuRS, while Escherichia coli LeuRS is a canonical monomeric enzyme. By using the genes encoding A. aeolicus and E. coli LeuRS as PCR templates, the genes encoding the alpha and beta subunits from A. aeolicus alphabeta-LeuRS and the equivalent amino- and carboxy-terminal parts of E. coli LeuRS (identified as alpha' and beta') were amplified and recombined using suitable plasmids. These recombinant plasmids were transformed or cotransformed into E. coli to produce five monomeric and five heterodimeric LeuRS mutants. Seven of these were successfully overexpressed in vivo and purified, while three dimeric mutants with the beta' part of E. coli LeuRS were not successfully expressed. The seven purified mutants catalyzed amino acid activation, although several exhibited reduced aminoacylation properties. Removal of the last 36 residues of the alpha subunit of the A. aeolicus enzyme was determined to be deleterious for tRNA charging. Indeed, subunit exchange showed that the cross-species-specific recognition of A. aeolicus tRNA(Leu) occurs at the alpha subunit. None of the mixed E. coli-A. aeolicus enzymes were as thermostable as the native alphabeta-LeuRS. However, the fusion of the two alpha and beta peptides from A. aeolicus as a single chain analogous to canonical LeuRS resulted in a product more resistant to heat denaturation than the original enzyme.},
note = {0006-2960
Journal Article},
keywords = {Amino Acyl-tRNA Ligases/genetics/*metabolism Escherichia coli/*enzymology Evolution, ERIANI, Horizontal Heat Kinetics Mutation RNA, Leu/*metabolism Structure-Activity Relationship Support, Molecular Gene Transfer, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Aquifex aeolicus alphabeta-LeuRS is the only known heterodimeric LeuRS, while Escherichia coli LeuRS is a canonical monomeric enzyme. By using the genes encoding A. aeolicus and E. coli LeuRS as PCR templates, the genes encoding the alpha and beta subunits from A. aeolicus alphabeta-LeuRS and the equivalent amino- and carboxy-terminal parts of E. coli LeuRS (identified as alpha' and beta') were amplified and recombined using suitable plasmids. These recombinant plasmids were transformed or cotransformed into E. coli to produce five monomeric and five heterodimeric LeuRS mutants. Seven of these were successfully overexpressed in vivo and purified, while three dimeric mutants with the beta' part of E. coli LeuRS were not successfully expressed. The seven purified mutants catalyzed amino acid activation, although several exhibited reduced aminoacylation properties. Removal of the last 36 residues of the alpha subunit of the A. aeolicus enzyme was determined to be deleterious for tRNA charging. Indeed, subunit exchange showed that the cross-species-specific recognition of A. aeolicus tRNA(Leu) occurs at the alpha subunit. None of the mixed E. coli-A. aeolicus enzymes were as thermostable as the native alphabeta-LeuRS. However, the fusion of the two alpha and beta peptides from A. aeolicus as a single chain analogous to canonical LeuRS resulted in a product more resistant to heat denaturation than the original enzyme.
Vicens Q, Westhof E
Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide Article de journal
Dans: J Mol Biol, vol. 326, no. 4, p. 1175-1188, 2003, ISBN: 12589761, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*chemistry/genetics/metabolism Support, Anti-Bacterial Agents/*chemistry/metabolism Binding Sites Crystallography, Bacterial Gentamicins/*chemistry/metabolism Human Models, Molecular Molecular Structure *Nucleic Acid Conformation Oligonucleotides/*chemistry/genetics/metabolism Protein Binding *Protein Conformation RNA, Non-U.S. Gov't, Ribosomal, Unité ARN, WESTHOF, X-Ray Drug Design Genes
@article{,
title = {Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide},
author = {Q Vicens and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12589761},
isbn = {12589761},
year = {2003},
date = {2003-01-01},
journal = {J Mol Biol},
volume = {326},
number = {4},
pages = {1175-1188},
abstract = {Aminoglycosides are antibacterial molecules that decrease translation accuracy by binding to the decoding aminoacyl-tRNA site (A site) on 16S ribosomal RNA. We have solved the crystal structure of an RNA fragment containing the A site bound to geneticin at 2.40A resolution. Geneticin, also known as G418, is a gentamicin-related aminoglycoside: it contains three rings that are functionalized by hydroxyl, ammonium and methyl groups. The detailed comparison of the distinctive behaviour of geneticin (binding to pro- and eukaryotic A sites) with the crystallographic, biochemical and microbiological results obtained so far for aminoglycoside-A site complexes offers new insights on the system. The two sugar rings constituting the neamine part common to most of the aminoglycosides bind to the A site, as already observed in the crystal structures solved previously with paromomycin and tobramycin. The essential hydrogen bonds involving ring I (to A1408) and ring II (to the phosphate oxygen atoms of the bulged adenine bases 1492 and 1493 and to G1494) are conserved and additional contacts are observed from ring III (to phosphate oxygen atoms of G1405 and U1406). The present work illustrates a molecular basis of the range in sensitiveness exhibited by geneticin towards common point A site mutations associated to resistance phenotypes. In addition, analysis and comparisons of the structures cast light on the role played by the conserved U1406.U1495 pair in the recognition of the A site by aminoglycosides.},
note = {0022-2836
Journal Article},
keywords = {16S/*chemistry/genetics/metabolism Support, Anti-Bacterial Agents/*chemistry/metabolism Binding Sites Crystallography, Bacterial Gentamicins/*chemistry/metabolism Human Models, Molecular Molecular Structure *Nucleic Acid Conformation Oligonucleotides/*chemistry/genetics/metabolism Protein Binding *Protein Conformation RNA, Non-U.S. Gov't, Ribosomal, Unité ARN, WESTHOF, X-Ray Drug Design Genes},
pubstate = {published},
tppubtype = {article}
}
Aminoglycosides are antibacterial molecules that decrease translation accuracy by binding to the decoding aminoacyl-tRNA site (A site) on 16S ribosomal RNA. We have solved the crystal structure of an RNA fragment containing the A site bound to geneticin at 2.40A resolution. Geneticin, also known as G418, is a gentamicin-related aminoglycoside: it contains three rings that are functionalized by hydroxyl, ammonium and methyl groups. The detailed comparison of the distinctive behaviour of geneticin (binding to pro- and eukaryotic A sites) with the crystallographic, biochemical and microbiological results obtained so far for aminoglycoside-A site complexes offers new insights on the system. The two sugar rings constituting the neamine part common to most of the aminoglycosides bind to the A site, as already observed in the crystal structures solved previously with paromomycin and tobramycin. The essential hydrogen bonds involving ring I (to A1408) and ring II (to the phosphate oxygen atoms of the bulged adenine bases 1492 and 1493 and to G1494) are conserved and additional contacts are observed from ring III (to phosphate oxygen atoms of G1405 and U1406). The present work illustrates a molecular basis of the range in sensitiveness exhibited by geneticin towards common point A site mutations associated to resistance phenotypes. In addition, analysis and comparisons of the structures cast light on the role played by the conserved U1406.U1495 pair in the recognition of the A site by aminoglycosides.
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, 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, 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}
}
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.
Roy H, Becker H D, Reinbolt J, Kern D
When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 100, no. 17, p. 9837-9842, 2003, ISBN: 12874385, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Substrate Specificity Support, Amino Acid Sequence Amino Acids/*metabolism Amino Acyl-tRNA Ligases/chemistry/genetics/*metabolism Catalytic Domain/genetics Cloning, Archaeal Genes, Bacterial Models, Molecular Escherichia coli/genetics/metabolism Genes, Molecular Molecular Sequence Data Phylogeny Protein Conformation Pyrococcus/enzymology/genetics Sequence Homology, Non-U.S. Gov't, Unité ARN
@article{,
title = {When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism},
author = {H Roy and H D Becker and J Reinbolt and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12874385},
isbn = {12874385},
year = {2003},
date = {2003-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {100},
number = {17},
pages = {9837-9842},
abstract = {Faithful protein synthesis relies on a family of essential enzymes called aminoacyl-tRNA synthetases, assembled in a piecewise fashion. Analysis of the completed archaeal genomes reveals that all archaea that possess asparaginyl-tRNA synthetase (AsnRS) also display a second ORF encoding an AsnRS truncated from its anticodon binding-domain (AsnRS2). We show herein that Pyrococcus abyssi AsnRS2, in contrast to AsnRS, does not sustain asparaginyl-tRNAAsn synthesis but is instead capable of converting aspartic acid into asparagine. Functional analysis and complementation of an Escherichia coli asparagine auxotrophic strain show that AsnRS2 constitutes the archaeal homologue of the bacterial ammonia-dependent asparagine synthetase A (AS-A), therefore named archaeal asparagine synthetase A (AS-AR). Primary sequence- and 3D-based phylogeny shows that an archaeal AspRS ancestor originated AS-AR, which was subsequently transferred into bacteria by lateral gene transfer in which it underwent structural changes producing AS-A. This study provides evidence that a contemporary aminoacyl-tRNA synthetase can be recruited to sustain amino acid metabolism.},
note = {0027-8424
Journal Article},
keywords = {Amino Acid Substrate Specificity Support, Amino Acid Sequence Amino Acids/*metabolism Amino Acyl-tRNA Ligases/chemistry/genetics/*metabolism Catalytic Domain/genetics Cloning, Archaeal Genes, Bacterial Models, Molecular Escherichia coli/genetics/metabolism Genes, Molecular Molecular Sequence Data Phylogeny Protein Conformation Pyrococcus/enzymology/genetics Sequence Homology, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Faithful protein synthesis relies on a family of essential enzymes called aminoacyl-tRNA synthetases, assembled in a piecewise fashion. Analysis of the completed archaeal genomes reveals that all archaea that possess asparaginyl-tRNA synthetase (AsnRS) also display a second ORF encoding an AsnRS truncated from its anticodon binding-domain (AsnRS2). We show herein that Pyrococcus abyssi AsnRS2, in contrast to AsnRS, does not sustain asparaginyl-tRNAAsn synthesis but is instead capable of converting aspartic acid into asparagine. Functional analysis and complementation of an Escherichia coli asparagine auxotrophic strain show that AsnRS2 constitutes the archaeal homologue of the bacterial ammonia-dependent asparagine synthetase A (AS-A), therefore named archaeal asparagine synthetase A (AS-AR). Primary sequence- and 3D-based phylogeny shows that an archaeal AspRS ancestor originated AS-AR, which was subsequently transferred into bacteria by lateral gene transfer in which it underwent structural changes producing AS-A. This study provides evidence that a contemporary aminoacyl-tRNA synthetase can be recruited to sustain amino acid metabolism.
Pfister P, Hobbie S, Vicens Q, Bottger E C, Westhof E
The molecular basis for A-site mutations conferring aminoglycoside resistance: relationship between ribosomal susceptibility and X-ray crystal structures Article de journal
Dans: Chembiochem, vol. 4, no. 10, p. 1078-1088, 2003, ISBN: 14523926, (1439-4227 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Aminoglycosides/*pharmacology Anti-Bacterial Agents/*pharmacology Binding Sites Comparative Study Crystallography, Bacterial/genetics Ribosomes/*chemistry/drug effects/metabolism Species Specificity Structure-Activity Relationship Support, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Nucleic Acid Conformation Oligonucleotides/chemistry/metabolism Plasmids Point Mutation/drug effects RNA, Unité ARN, WESTHOF, X-Ray Drug Design Drug Resistance Escherichia coli/genetics/metabolism Hemagglutinins Models
@article{,
title = {The molecular basis for A-site mutations conferring aminoglycoside resistance: relationship between ribosomal susceptibility and X-ray crystal structures},
author = {P Pfister and S Hobbie and Q Vicens and E C Bottger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14523926},
isbn = {14523926},
year = {2003},
date = {2003-01-01},
journal = {Chembiochem},
volume = {4},
number = {10},
pages = {1078-1088},
abstract = {Aminoglycoside antibiotics target the 16S ribosomal RNA (rRNA) bacterial A site and induce misreading of the genetic code. Point mutations of the ribosomal A site may confer resistance to aminoglycoside antibiotics. The influence of bacterial mutations (introduced by site-directed mutagenesis) on ribosomal drug susceptibility was investigated in vivo by determination of minimal inhibitory concentrations. To determine the origin of the various resistance phenotypes at a molecular level, the in vivo results were compared with the previously published crystal structures of paromomycin, tobramycin, and geneticin bound to oligonucleotides containing the minimal A site. Two regions appear crucial for binding in the A site: the single adenine residue at position 1408 and the non-Watson-Crick U1406.U1495 pair. The effects of mutations at those positions are modulated by the nature of the substituent at position 6' (either hydroxy or ammonium group) on ring I, by the number of positive charges on the antibiotic, and by the linkage between rings I and III (either 4,5 or 4,6). In particular, the analysis demonstrates: 1) that the C1409-G1491 to A1409-U1491 polymorphism (observed in 15 % of bacteria) is not associated with resistance, which indicates that it does not affect the stacking of ring I on residue 1491, 2) that the high-level resistance to 6'-NH3+ aminoglycosides exhibited by the A1408G mutation most probably results from the inability of ring I forming a pseudo base pair with G1408, which prevents its insertion inside the A site helix, and 3) that mutations of the uracil residues forming the U1406.U1495 pair either to cytosine or to adenine residues mostly confer low to moderate levels of drug resistance, whereas the U1406C/U1495A double mutation confers high-level resistance (except for neomycin), which suggests that aminoglycoside binding to the wild-type A site and its functional consequences strongly depend on a particular geometry of the U1406.U1495 pair. The relationships between the resistance phenotypes observed in vivo and the interactions described at the molecular level define the biological importance of the different structural interactions observed by X-ray crystallography studies.},
note = {1439-4227
Journal Article},
keywords = {Aminoglycosides/*pharmacology Anti-Bacterial Agents/*pharmacology Binding Sites Comparative Study Crystallography, Bacterial/genetics Ribosomes/*chemistry/drug effects/metabolism Species Specificity Structure-Activity Relationship Support, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Nucleic Acid Conformation Oligonucleotides/chemistry/metabolism Plasmids Point Mutation/drug effects RNA, Unité ARN, WESTHOF, X-Ray Drug Design Drug Resistance Escherichia coli/genetics/metabolism Hemagglutinins Models},
pubstate = {published},
tppubtype = {article}
}
Aminoglycoside antibiotics target the 16S ribosomal RNA (rRNA) bacterial A site and induce misreading of the genetic code. Point mutations of the ribosomal A site may confer resistance to aminoglycoside antibiotics. The influence of bacterial mutations (introduced by site-directed mutagenesis) on ribosomal drug susceptibility was investigated in vivo by determination of minimal inhibitory concentrations. To determine the origin of the various resistance phenotypes at a molecular level, the in vivo results were compared with the previously published crystal structures of paromomycin, tobramycin, and geneticin bound to oligonucleotides containing the minimal A site. Two regions appear crucial for binding in the A site: the single adenine residue at position 1408 and the non-Watson-Crick U1406.U1495 pair. The effects of mutations at those positions are modulated by the nature of the substituent at position 6' (either hydroxy or ammonium group) on ring I, by the number of positive charges on the antibiotic, and by the linkage between rings I and III (either 4,5 or 4,6). In particular, the analysis demonstrates: 1) that the C1409-G1491 to A1409-U1491 polymorphism (observed in 15 % of bacteria) is not associated with resistance, which indicates that it does not affect the stacking of ring I on residue 1491, 2) that the high-level resistance to 6'-NH3+ aminoglycosides exhibited by the A1408G mutation most probably results from the inability of ring I forming a pseudo base pair with G1408, which prevents its insertion inside the A site helix, and 3) that mutations of the uracil residues forming the U1406.U1495 pair either to cytosine or to adenine residues mostly confer low to moderate levels of drug resistance, whereas the U1406C/U1495A double mutation confers high-level resistance (except for neomycin), which suggests that aminoglycoside binding to the wild-type A site and its functional consequences strongly depend on a particular geometry of the U1406.U1495 pair. The relationships between the resistance phenotypes observed in vivo and the interactions described at the molecular level define the biological importance of the different structural interactions observed by X-ray crystallography studies.
Petit N, Lescure A, Rederstorff M, Krol A, Moghadaszadeh B, Wewer U M, Guicheney P
Selenoprotein N: an endoplasmic reticulum glycoprotein with an early developmental expression pattern Article de journal
Dans: Hum Mol Genet, vol. 12, no. 9, p. 1045-1053, 2003, ISBN: 12700173, (0964-6906 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Cell Division/physiology Endoplasmic Reticulum/*metabolism Fetus/metabolism Fibroblasts/metabolism Human Muscle Proteins/*metabolism Protein Sorting Signals Support, LESCURE, Non-U.S. Gov't, Unité ARN
@article{,
title = {Selenoprotein N: an endoplasmic reticulum glycoprotein with an early developmental expression pattern},
author = {N Petit and A Lescure and M Rederstorff and A Krol and B Moghadaszadeh and U M Wewer and P Guicheney},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12700173},
isbn = {12700173},
year = {2003},
date = {2003-01-01},
journal = {Hum Mol Genet},
volume = {12},
number = {9},
pages = {1045-1053},
abstract = {Rigid spine muscular dystrophy and the classical form of multiminicore disease are caused by mutations in SEPN1 gene, leading to a new clinical entity referred to as SEPN1-related myopathy. SEPN1 codes for selenoprotein N, a new member of the selenoprotein family, the function of which is still unknown. In a previous study, two isoforms were deduced from SEPN1 transcript analyses. Using polyclonal antibodies directed against SEPN1 and cDNA constructs encoding for the two isoforms, we show that the main SEPN1 gene product corresponds to a 70 kDa protein, containing a single selenocysteine residue. Subcellular fractionation experiments and endoglycosidase H sensitivity indicate that SEPN1 is a glycoprotein-localized within the endoplasmic reticulum. Immunofluorescence analyses confirm this subcellular localization and green fluorescent protein fusion experiments demonstrate the presence of an endoplasmic reticulum-addressing and -retention signal within the N-terminus. SEPN1 is present at a high level in several human fetal tissues and at a lower level in adult ones, including skeletal muscle. Its high expression in cultured myoblasts is also down-regulated in differentiating myotubes, suggesting a role for SEPN1 in early development and in cell proliferation or regeneration.},
note = {0964-6906
Journal Article},
keywords = {Cell Division/physiology Endoplasmic Reticulum/*metabolism Fetus/metabolism Fibroblasts/metabolism Human Muscle Proteins/*metabolism Protein Sorting Signals Support, LESCURE, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rigid spine muscular dystrophy and the classical form of multiminicore disease are caused by mutations in SEPN1 gene, leading to a new clinical entity referred to as SEPN1-related myopathy. SEPN1 codes for selenoprotein N, a new member of the selenoprotein family, the function of which is still unknown. In a previous study, two isoforms were deduced from SEPN1 transcript analyses. Using polyclonal antibodies directed against SEPN1 and cDNA constructs encoding for the two isoforms, we show that the main SEPN1 gene product corresponds to a 70 kDa protein, containing a single selenocysteine residue. Subcellular fractionation experiments and endoglycosidase H sensitivity indicate that SEPN1 is a glycoprotein-localized within the endoplasmic reticulum. Immunofluorescence analyses confirm this subcellular localization and green fluorescent protein fusion experiments demonstrate the presence of an endoplasmic reticulum-addressing and -retention signal within the N-terminus. SEPN1 is present at a high level in several human fetal tissues and at a lower level in adult ones, including skeletal muscle. Its high expression in cultured myoblasts is also down-regulated in differentiating myotubes, suggesting a role for SEPN1 in early development and in cell proliferation or regeneration.
Miturski R, Postawski K, Semczuk A, Bogusiewicz M, Baranowski W, Jakowicki J A, Keith G
Global DNA methylation in relation to hMLH1 and hMSH2 protein immunoreactivity in sporadic human endometrial carcinomas Article de journal
Dans: Int J Mol Med, vol. 11, no. 5, p. 569-574, 2003, ISBN: 12684691, (1107-3756 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Pair Mismatch Carcinoma/genetics/*metabolism/pathology *DNA Methylation DNA Repair Endometrial Neoplasms/genetics/*metabolism/pathology Female Human Immunohistochemistry Neoplasm Proteins/*metabolism Proto-Oncogene Proteins/*metabolism Support, Non-U.S. Gov't, Unité ARN
@article{,
title = {Global DNA methylation in relation to hMLH1 and hMSH2 protein immunoreactivity in sporadic human endometrial carcinomas},
author = {R Miturski and K Postawski and A Semczuk and M Bogusiewicz and W Baranowski and J A Jakowicki and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12684691},
isbn = {12684691},
year = {2003},
date = {2003-01-01},
journal = {Int J Mol Med},
volume = {11},
number = {5},
pages = {569-574},
abstract = {Overall DNA methylation status was studied in a group of 28 sporadic human endometrial carcinomas (ECs) using the [32P]-postlabeling technique. Moreover, expression of the DNA mismatch repair proteins (hMLH1 and hMSH2) was investigated in ECs using immunohistochemistry. Mean 5-methyldeoxycytosine (m5dC) content in the studied group was 3.48+/-0.37% (range, 2.89-4.12%). The mean m5dC scores were significantly different between early (3.35+/-0.33%) and advanced (3.66+/-0.36%) endometrial neoplasms (chi2-test; p=0.03). There was a markedly increased overall DNA methylation with the degree of histological differentiation and with the infiltration of the myometrium (p<0.05). Loss of hMLH1 and hMSH2 expression was reported in 7 (25%) and 5 (18%) tumors, respectively, but the immunoreactivity did not correlate with the known clinicopathological variables of cancer. In addition, no obvious correlation was found between global m5dC content and the lack of hMLH1 and hMSH2 protein expression in human uterine tumors (p=0.97 and p=0.19 for hMLH1 and hMSH2, respectively; Spearman's rank correlation test). Our results clearly show that alterations in global DNA methylation may influence tumor progression, but they are not directly associated with the inactivation of the mismatch-repair machinery in sporadic human ECs.},
note = {1107-3756
Journal Article},
keywords = {Base Pair Mismatch Carcinoma/genetics/*metabolism/pathology *DNA Methylation DNA Repair Endometrial Neoplasms/genetics/*metabolism/pathology Female Human Immunohistochemistry Neoplasm Proteins/*metabolism Proto-Oncogene Proteins/*metabolism Support, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Overall DNA methylation status was studied in a group of 28 sporadic human endometrial carcinomas (ECs) using the [32P]-postlabeling technique. Moreover, expression of the DNA mismatch repair proteins (hMLH1 and hMSH2) was investigated in ECs using immunohistochemistry. Mean 5-methyldeoxycytosine (m5dC) content in the studied group was 3.48+/-0.37% (range, 2.89-4.12%). The mean m5dC scores were significantly different between early (3.35+/-0.33%) and advanced (3.66+/-0.36%) endometrial neoplasms (chi2-test; p=0.03). There was a markedly increased overall DNA methylation with the degree of histological differentiation and with the infiltration of the myometrium (p<0.05). Loss of hMLH1 and hMSH2 expression was reported in 7 (25%) and 5 (18%) tumors, respectively, but the immunoreactivity did not correlate with the known clinicopathological variables of cancer. In addition, no obvious correlation was found between global m5dC content and the lack of hMLH1 and hMSH2 protein expression in human uterine tumors (p=0.97 and p=0.19 for hMLH1 and hMSH2, respectively; Spearman's rank correlation test). Our results clearly show that alterations in global DNA methylation may influence tumor progression, but they are not directly associated with the inactivation of the mismatch-repair machinery in sporadic human ECs.
Heyman T, Wilhelm M, Wilhelm F X
The central PPT of the yeast retrotransposon Ty1 is not essential for transposition Article de journal
Dans: J Mol Biol, vol. 331, no. 2, p. 315-320, 2003, ISBN: 12888340, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA/*biosynthesis Models, Genetic Molecular Sequence Data Mutation Purines/*chemistry Retroelements/*genetics Saccharomyces cerevisiae/genetics Support, Non-U.S. Gov't, Unité ARN
@article{,
title = {The central PPT of the yeast retrotransposon Ty1 is not essential for transposition},
author = {T Heyman and M Wilhelm and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12888340},
isbn = {12888340},
year = {2003},
date = {2003-01-01},
journal = {J Mol Biol},
volume = {331},
number = {2},
pages = {315-320},
abstract = {The yeast retrotransposon Ty1 has structural and functional similarities to retroviruses. We report here that, as in retroviruses, the plus-strand DNA of Ty1 is synthesized as two segments. A central DNA flap is formed during reverse transcription consecutive to elongation (with strand displacement) of the upstream segment beyond the central polypurine tract (cPPT) until the replication machinery is stopped at the central termination sequence. Comparison of wild-type and cPPT-mutant Ty1 elements shows that the mutant element lacking the central DNA flap is only twofold defective in transposition.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence DNA/*biosynthesis Models, Genetic Molecular Sequence Data Mutation Purines/*chemistry Retroelements/*genetics Saccharomyces cerevisiae/genetics Support, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The yeast retrotransposon Ty1 has structural and functional similarities to retroviruses. We report here that, as in retroviruses, the plus-strand DNA of Ty1 is synthesized as two segments. A central DNA flap is formed during reverse transcription consecutive to elongation (with strand displacement) of the upstream segment beyond the central polypurine tract (cPPT) until the replication machinery is stopped at the central termination sequence. Comparison of wild-type and cPPT-mutant Ty1 elements shows that the mutant element lacking the central DNA flap is only twofold defective in transposition.
Geslain R, Martin F, Camasses A, Eriani G
A yeast knockout strain to discriminate between active and inactive tRNA molecules Article de journal
Dans: Nucleic Acids Res, vol. 31, no. 16, p. 4729-4737, 2003, ISBN: 12907713, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl-tRNA Ligases/metabolism Arginine/genetics/metabolism Base Sequence Blotting, Arg/chemistry/*genetics/metabolism Saccharomyces cerevisiae/*genetics Support, ERIANI, Molecular Hydrogen-Ion Concentration Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Northern Cloning, Site-Directed Mutation Nucleic Acid Conformation RNA, Transfer, Unité ARN
@article{,
title = {A yeast knockout strain to discriminate between active and inactive tRNA molecules},
author = {R Geslain and F Martin and A Camasses and G Eriani},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12907713},
isbn = {12907713},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {16},
pages = {4729-4737},
abstract = {Here we report the construction of a yeast genetic screen designed to identify essential residues in tRNA(Arg). The system consists of a tRNA(Arg) knockout strain and a set of vectors designed to rescue and select for variants of tRNA(Arg). By plasmid shuffling we selected inactive tRNA mutants that were further analyzed by northern blotting. The mutational analysis focused on the tRNA D and anticodon loops that contact the aminoacyl-tRNA synthetase. The anticodon triplet was excluded from the analysis because of its role in decoding the Arg codons. Most of the inactivating mutations are residues involved in tertiary interactions. These mutations had dramatic effects on tRNA(Arg) abundance. Other inactivating mutations were located in the anticodon loop, where they did not affect transcription and aminoacylation but probably altered interaction with the translation machinery. No lethal effects were observed when residues 16, 20 and 38 were individually mutated, despite the fact that they are involved in sequence-specific interactions with the aminoacyl-tRNA synthetase. However, the steady-state levels of the aminoacylated forms of U20A and U20G were decreased by a factor of 3.5-fold in vivo. This suggests that, unlike in the Escherichia coli tRNA(Arg):ArgRS system where residue 20 (A) is a major identity element, in yeast this position is of limited consequence.},
note = {1362-4962
Journal Article},
keywords = {Amino Acyl-tRNA Ligases/metabolism Arginine/genetics/metabolism Base Sequence Blotting, Arg/chemistry/*genetics/metabolism Saccharomyces cerevisiae/*genetics Support, ERIANI, Molecular Hydrogen-Ion Concentration Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Northern Cloning, Site-Directed Mutation Nucleic Acid Conformation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Here we report the construction of a yeast genetic screen designed to identify essential residues in tRNA(Arg). The system consists of a tRNA(Arg) knockout strain and a set of vectors designed to rescue and select for variants of tRNA(Arg). By plasmid shuffling we selected inactive tRNA mutants that were further analyzed by northern blotting. The mutational analysis focused on the tRNA D and anticodon loops that contact the aminoacyl-tRNA synthetase. The anticodon triplet was excluded from the analysis because of its role in decoding the Arg codons. Most of the inactivating mutations are residues involved in tertiary interactions. These mutations had dramatic effects on tRNA(Arg) abundance. Other inactivating mutations were located in the anticodon loop, where they did not affect transcription and aminoacylation but probably altered interaction with the translation machinery. No lethal effects were observed when residues 16, 20 and 38 were individually mutated, despite the fact that they are involved in sequence-specific interactions with the aminoacyl-tRNA synthetase. However, the steady-state levels of the aminoacylated forms of U20A and U20G were decreased by a factor of 3.5-fold in vivo. This suggests that, unlike in the Escherichia coli tRNA(Arg):ArgRS system where residue 20 (A) is a major identity element, in yeast this position is of limited consequence.
Geslain R, Bey G, Cavarelli J, Eriani G
Limited set of amino acid residues in a class Ia aminoacyl-tRNA synthetase is crucial for tRNA binding Article de journal
Dans: Biochemistry, vol. 42, no. 51, p. 15092-15101, 2003, ISBN: 14690419, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Alanine/genetics Amino Acids/*chemistry/genetics Anticodon/chemistry/genetics Arginine-tRNA Ligase/*chemistry/classification/genetics Binding Sites/genetics Genes, Arg/*chemistry Saccharomyces cerevisiae/enzymology/genetics/growth & development Saccharomyces cerevisiae Proteins/*chemistry/*genetics Support, ERIANI, Lethal Mutagenesis, Non-U.S. Gov't, Site-Directed Protein Binding/genetics Protein Structure, Tertiary/genetics RNA, Transfer, Unité ARN
@article{,
title = {Limited set of amino acid residues in a class Ia aminoacyl-tRNA synthetase is crucial for tRNA binding},
author = {R Geslain and G Bey and J Cavarelli and G Eriani},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14690419},
isbn = {14690419},
year = {2003},
date = {2003-01-01},
journal = {Biochemistry},
volume = {42},
number = {51},
pages = {15092-15101},
abstract = {The aim of this work was to characterize crucial amino acids for the aminoacylation of tRNA(Arg) by yeast arginyl-tRNA synthetase. Alanine mutagenesis was used to probe all the side chain mediated interactions that occur between tRNA(Arg2)(ICG) and ArgRS. The effects of the substitutions were analyzed in vivo in an ArgRS-knockout strain and in vitro by measuring the aminoacylation efficiencies for two distinct tRNA(Arg) isoacceptors. Nine mutants that generate lethal phenotypes were identified, suggesting that only a limited set of side chain mediated interactions is essential for tRNA recognition. The majority of the lethal mutants was mapped to the anticodon binding domain of ArgRS, a helix bundle that is characteristic for class Ia synthetases. The alanine mutations induce drastic decreases in the tRNA charging rates, which is correlated with a loss in affinity in the catalytic site for ATP. One of those lethal mutations corresponds to an Arg residue that is strictly conserved in all class Ia synthetases. In the known crystallographic structures of complexes of tRNAs and class Ia synthetases, this invariant Arg residue stabilizes the idiosyncratic conformation of the anticodon loop. This paper also highlights the crucial role of the tRNA and enzyme plasticity upon binding. Divalent ions are also shown to contribute to the induced fit process as they may stabilize the local tRNA-enzyme interface. Furthermore, one lethal phenotype can be reverted in the presence of high Mg(2+) concentrations. In contrast with the bacterial system, in yeast arginyl-tRNA synthetase, no lethal mutation has been found in the ArgRS specific domain recognizing the Dhu-loop of the tRNA(Arg). Mutations in this domain have no effects on tRNA(Arg) aminoacylation, thus confirming that Saccharomyces cerevisiae and other fungi belong to a distinct class of ArgRS.},
note = {0006-2960
Journal Article},
keywords = {Acylation Alanine/genetics Amino Acids/*chemistry/genetics Anticodon/chemistry/genetics Arginine-tRNA Ligase/*chemistry/classification/genetics Binding Sites/genetics Genes, Arg/*chemistry Saccharomyces cerevisiae/enzymology/genetics/growth & development Saccharomyces cerevisiae Proteins/*chemistry/*genetics Support, ERIANI, Lethal Mutagenesis, Non-U.S. Gov't, Site-Directed Protein Binding/genetics Protein Structure, Tertiary/genetics RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The aim of this work was to characterize crucial amino acids for the aminoacylation of tRNA(Arg) by yeast arginyl-tRNA synthetase. Alanine mutagenesis was used to probe all the side chain mediated interactions that occur between tRNA(Arg2)(ICG) and ArgRS. The effects of the substitutions were analyzed in vivo in an ArgRS-knockout strain and in vitro by measuring the aminoacylation efficiencies for two distinct tRNA(Arg) isoacceptors. Nine mutants that generate lethal phenotypes were identified, suggesting that only a limited set of side chain mediated interactions is essential for tRNA recognition. The majority of the lethal mutants was mapped to the anticodon binding domain of ArgRS, a helix bundle that is characteristic for class Ia synthetases. The alanine mutations induce drastic decreases in the tRNA charging rates, which is correlated with a loss in affinity in the catalytic site for ATP. One of those lethal mutations corresponds to an Arg residue that is strictly conserved in all class Ia synthetases. In the known crystallographic structures of complexes of tRNAs and class Ia synthetases, this invariant Arg residue stabilizes the idiosyncratic conformation of the anticodon loop. This paper also highlights the crucial role of the tRNA and enzyme plasticity upon binding. Divalent ions are also shown to contribute to the induced fit process as they may stabilize the local tRNA-enzyme interface. Furthermore, one lethal phenotype can be reverted in the presence of high Mg(2+) concentrations. In contrast with the bacterial system, in yeast arginyl-tRNA synthetase, no lethal mutation has been found in the ArgRS specific domain recognizing the Dhu-loop of the tRNA(Arg). Mutations in this domain have no effects on tRNA(Arg) aminoacylation, thus confirming that Saccharomyces cerevisiae and other fungi belong to a distinct class of ArgRS.
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}
}
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.
Ennifar E, Walter P, Dumas P
A crystallographic study of the binding of 13 metal ions to two related RNA duplexes Article de journal
Dans: Nucleic Acids Res, vol. 31, no. 10, p. 2671-2682, 2003, ISBN: 12736317, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites/genetics Binding, Competitive Cations, Divalent/chemistry/metabolism Cobalt/chemistry/metabolism Comparative Study Crystallization Crystallography, ENNIFAR, Molecular Nucleic Acid Heteroduplexes/*chemistry/genetics/metabolism Oligoribonucleotides/chemistry/genetics/metabolism Platinum Compounds/chemistry/metabolism RNA/*chemistry/genetics/metabolism Ruthenium Compounds/chemistry/metabolism Support, Non-U.S. Gov't, Unité ARN, X-Ray Gold Compounds/chemistry/metabolism Magnesium/chemistry/metabolism Metals/*chemistry/metabolism Models
@article{,
title = {A crystallographic study of the binding of 13 metal ions to two related RNA duplexes},
author = {E Ennifar and P Walter and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12736317},
isbn = {12736317},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {10},
pages = {2671-2682},
abstract = {Metal ions, and magnesium in particular, are known to be involved in RNA folding by stabilizing secondary and tertiary structures, and, as cofactors, in RNA enzymatic activity. We have conducted a systematic crystallographic analysis of cation binding to the duplex form of the HIV-1 RNA dimerization initiation site for the subtype-A and -B natural sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+, Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)6]3+ and [Ru (NH3)6]3+ were found to bind to the DIS duplex structure. Although the two sequences are very similar, strong differences were found in their cation binding properties. Divalent cations bind almost exclusively, as Mg2+, at 'Hoogsteen' sites of guanine residues, with a cation-dependent affinity for each site. Notably, a given cation can have very different affinities for a priori equivalent sites within the same molecule. Surprisingly, none of the two hexammines used were able to efficiently replace hexahydrated magnesium. Instead, [Co (NH3)4]3+ was seen bound by inner-sphere coordination to the RNA. This raises some questions about the practical use of [Co (NH3)6]3+ as a [Mg (H2O)6]2+ mimetic. Also very unexpected was the binding of the small Au3+ cation exactly between the Watson-Crick sites of a G-C base pair after an obligatory deprotonation of N1 of the guanine base. This extensive study of metal ion binding using X-ray crystallography significantly enriches our knowledge on the binding of middleweight or heavy metal ions to RNA, particularly compared with magnesium.},
note = {1362-4962
Journal Article},
keywords = {Base Sequence Binding Sites/genetics Binding, Competitive Cations, Divalent/chemistry/metabolism Cobalt/chemistry/metabolism Comparative Study Crystallization Crystallography, ENNIFAR, Molecular Nucleic Acid Heteroduplexes/*chemistry/genetics/metabolism Oligoribonucleotides/chemistry/genetics/metabolism Platinum Compounds/chemistry/metabolism RNA/*chemistry/genetics/metabolism Ruthenium Compounds/chemistry/metabolism Support, Non-U.S. Gov't, Unité ARN, X-Ray Gold Compounds/chemistry/metabolism Magnesium/chemistry/metabolism Metals/*chemistry/metabolism Models},
pubstate = {published},
tppubtype = {article}
}
Metal ions, and magnesium in particular, are known to be involved in RNA folding by stabilizing secondary and tertiary structures, and, as cofactors, in RNA enzymatic activity. We have conducted a systematic crystallographic analysis of cation binding to the duplex form of the HIV-1 RNA dimerization initiation site for the subtype-A and -B natural sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+, Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)6]3+ and [Ru (NH3)6]3+ were found to bind to the DIS duplex structure. Although the two sequences are very similar, strong differences were found in their cation binding properties. Divalent cations bind almost exclusively, as Mg2+, at 'Hoogsteen' sites of guanine residues, with a cation-dependent affinity for each site. Notably, a given cation can have very different affinities for a priori equivalent sites within the same molecule. Surprisingly, none of the two hexammines used were able to efficiently replace hexahydrated magnesium. Instead, [Co (NH3)4]3+ was seen bound by inner-sphere coordination to the RNA. This raises some questions about the practical use of [Co (NH3)6]3+ as a [Mg (H2O)6]2+ mimetic. Also very unexpected was the binding of the small Au3+ cation exactly between the Watson-Crick sites of a G-C base pair after an obligatory deprotonation of N1 of the guanine base. This extensive study of metal ion binding using X-ray crystallography significantly enriches our knowledge on the binding of middleweight or heavy metal ions to RNA, particularly compared with magnesium.
Du W, Marsac C, Kruschina M, Ortigao F, Florentz C
Functionalized self-assembled monolayer on gold for detection of human mitochondrial tRNA gene mutations Article de journal
Dans: Anal Biochem, vol. 322, no. 1, p. 14-25, 2003, ISBN: 14705775, (0003-2697 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Alleles *Gold Human MELAS Syndrome/genetics MERRF Syndrome/genetics Nucleic Acid Hybridization/genetics Oligonucleotide Array Sequence Analysis Point Mutation/*genetics Polymerase Chain Reaction Polymorphism, FLORENTZ, Non-U.S. Gov't, Single Nucleotide/*genetics RNA/*genetics RNA, Transfer/*genetics Support, Unité ARN
@article{,
title = {Functionalized self-assembled monolayer on gold for detection of human mitochondrial tRNA gene mutations},
author = {W Du and C Marsac and M Kruschina and F Ortigao and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14705775},
isbn = {14705775},
year = {2003},
date = {2003-01-01},
journal = {Anal Biochem},
volume = {322},
number = {1},
pages = {14-25},
abstract = {We developed a rapid and simple method to identify single-nucleotide polymorphisms (SNPs) in the human mitochondrial tRNA genes. This method is based on a universal, functionalized, self-assembled monolayer, XNA on Gold chip platform. A set of probes sharing a given allele-specific sequence with a single base substitution near the middle of the sequence was immobilized on chips and the chips were then hybridized with fluorescence-labeled reference targets produced by asymmetric polymerase chain reaction from patient DNA. The ratio of the hybridization signals from the reference and test targets with each probe was then calculated. A ratio of above 3 indicates the presence of a wild-type sequence and a ratio of below 0.3 indicates a mutant sequence. We tested the sensitivity of the chip for known mutations in tRNA(Leu(UUR)) and tRNA(Lys) genes and found that it can also be used to discriminate multiple mutations and heteroplasmy, two typical features of human mitochondrial DNA. The XNA on Gold biochip method is a simple and rapid microarray method that can be used to test rapidly and reliably any SNP in the mitochondrial genome or elsewhere. It will be particularly useful for detecting SNPs associated with human diseases.},
note = {0003-2697
Journal Article},
keywords = {Alleles *Gold Human MELAS Syndrome/genetics MERRF Syndrome/genetics Nucleic Acid Hybridization/genetics Oligonucleotide Array Sequence Analysis Point Mutation/*genetics Polymerase Chain Reaction Polymorphism, FLORENTZ, Non-U.S. Gov't, Single Nucleotide/*genetics RNA/*genetics RNA, Transfer/*genetics Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
We developed a rapid and simple method to identify single-nucleotide polymorphisms (SNPs) in the human mitochondrial tRNA genes. This method is based on a universal, functionalized, self-assembled monolayer, XNA on Gold chip platform. A set of probes sharing a given allele-specific sequence with a single base substitution near the middle of the sequence was immobilized on chips and the chips were then hybridized with fluorescence-labeled reference targets produced by asymmetric polymerase chain reaction from patient DNA. The ratio of the hybridization signals from the reference and test targets with each probe was then calculated. A ratio of above 3 indicates the presence of a wild-type sequence and a ratio of below 0.3 indicates a mutant sequence. We tested the sensitivity of the chip for known mutations in tRNA(Leu(UUR)) and tRNA(Lys) genes and found that it can also be used to discriminate multiple mutations and heteroplasmy, two typical features of human mitochondrial DNA. The XNA on Gold biochip method is a simple and rapid microarray method that can be used to test rapidly and reliably any SNP in the mitochondrial genome or elsewhere. It will be particularly useful for detecting SNPs associated with human diseases.
Bogengruber E, Briza P, Doppler E, Wimmer H, Koller L, Fasiolo F, Senger B, Hegemann J H, Breitenbach M
Functional analysis in yeast of the Brix protein superfamily involved in the biogenesis of ribosomes Article de journal
Dans: FEMS Yeast Res, vol. 3, no. 1, p. 35-43, 2003, ISBN: 12702244, (1567-1356 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Biogenesis Cell Nucleolus/*metabolism Genes, Non-U.S. Gov't, Suppressor Peptide Initiation Factors/metabolism RNA-Binding Proteins/metabolism/*physiology Ribosomal Proteins/*biosynthesis/genetics Ribosomes/*physiology Saccharomyces cerevisiae/metabolism/*physiology Saccharomyces cerevisiae Proteins/metabolism/*physiology Support, Unité ARN
@article{,
title = {Functional analysis in yeast of the Brix protein superfamily involved in the biogenesis of ribosomes},
author = {E Bogengruber and P Briza and E Doppler and H Wimmer and L Koller and F Fasiolo and B Senger and J H Hegemann and M Breitenbach},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12702244},
isbn = {12702244},
year = {2003},
date = {2003-01-01},
journal = {FEMS Yeast Res},
volume = {3},
number = {1},
pages = {35-43},
abstract = {An extensive homology search based on the sequence of the yeast protein Brx1p (biogenesis of ribosomes in Xenopus, YOL077c) revealed that it is a member of a superfamily of proteins sharing remarkable sequence similarities. Previous work on Brx1p showed that this protein is involved in the process of ribosome biogenesis [Kaser et al., Biol. Chem. 382 (2001) 1637-1647]. Brx1p is the founding member of one of the five existing eukaryotic subfamilies which are all present in yeast. Four of them are represented by one essential gene each and one family is represented by two closely related genes which can functionally replace each other but are essential together for survival. We created conditional alleles of four of the five genes which allowed us to study the effect of depletion of the respective proteins on the ribosome profiles of the strains. In this study we show that not only Brx1p but also three additional superfamily members, namely YHR088w (Rpf1p), YKR081c (Rpf2p) and the homologous proteins Ssf1p (YHR066w)/Ssf2p (YDR312w) are all involved in the multistep process of the assembly of the large ribosomal subunit. This agrees well with the fact that these three proteins, like Brx1p, are located in the nucleolus. Moreover, all four proteins closely interact functionally, because all four mutants are suppressed by the same multicopy suppressor gene.},
note = {1567-1356
Journal Article},
keywords = {Biogenesis Cell Nucleolus/*metabolism Genes, Non-U.S. Gov't, Suppressor Peptide Initiation Factors/metabolism RNA-Binding Proteins/metabolism/*physiology Ribosomal Proteins/*biosynthesis/genetics Ribosomes/*physiology Saccharomyces cerevisiae/metabolism/*physiology Saccharomyces cerevisiae Proteins/metabolism/*physiology Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
An extensive homology search based on the sequence of the yeast protein Brx1p (biogenesis of ribosomes in Xenopus, YOL077c) revealed that it is a member of a superfamily of proteins sharing remarkable sequence similarities. Previous work on Brx1p showed that this protein is involved in the process of ribosome biogenesis [Kaser et al., Biol. Chem. 382 (2001) 1637-1647]. Brx1p is the founding member of one of the five existing eukaryotic subfamilies which are all present in yeast. Four of them are represented by one essential gene each and one family is represented by two closely related genes which can functionally replace each other but are essential together for survival. We created conditional alleles of four of the five genes which allowed us to study the effect of depletion of the respective proteins on the ribosome profiles of the strains. In this study we show that not only Brx1p but also three additional superfamily members, namely YHR088w (Rpf1p), YKR081c (Rpf2p) and the homologous proteins Ssf1p (YHR066w)/Ssf2p (YDR312w) are all involved in the multistep process of the assembly of the large ribosomal subunit. This agrees well with the fact that these three proteins, like Brx1p, are located in the nucleolus. Moreover, all four proteins closely interact functionally, because all four mutants are suppressed by the same multicopy suppressor gene.
2002
Gottar Marie, Gobert Vanessa, Michel Tatiana, Belvin Marcia, Duyk Geoffrey, Hoffmann Jules A, Ferrandon Dominique, Royet Julien
The Drosophila immune response against Gram-negative bacteria is mediated by a peptidoglycan recognition protein Article de journal
Dans: Nature, vol. 416, p. 640–644, 2002, ISBN: 0028-0836.
Résumé | Liens | BibTeX | Étiquettes: Animal, Anti-Infective Agents/metabolism, Carrier Proteins/biosynthesis/genetics/*immunology, Drosophila melanogaster/genetics/*immunology/*microbiology, Drosophila Proteins/genetics/metabolism, Epistasis, Female, ferrandon, Genes, Genetic, Genetic Predisposition to Disease, Gram-Negative Bacteria/*immunology/physiology, hoffmann, Human, Insect/genetics, M3i, Messenger/genetics/metabolism, Mutation, Non-U.S. Gov't, P.H.S., Phenotype, RNA, Signal Transduction, Support, Survival Rate, Transgenes/genetics, U.S. Gov't
@article{gottar_drosophila_2002b,
title = {The Drosophila immune response against Gram-negative bacteria is mediated by a peptidoglycan recognition protein},
author = {Marie Gottar and Vanessa Gobert and Tatiana Michel and Marcia Belvin and Geoffrey Duyk and Jules A Hoffmann and Dominique Ferrandon and Julien Royet},
doi = {10.1038/nature734},
isbn = {0028-0836},
year = {2002},
date = {2002-03-01},
journal = {Nature},
volume = {416},
pages = {640--644},
abstract = {The antimicrobial defence of Drosophila relies largely on the challenge-induced synthesis of an array of potent antimicrobial peptides by the fat body. The defence against Gram-positive bacteria and natural fungal infections is mediated by the Toll signalling pathway, whereas defence against Gram-negative bacteria is dependent on the Immune deficiency (IMD) pathway. Loss-of-function mutations in either pathway reduce the resistance to corresponding infections. The link between microbial infections and activation of these two pathways has remained elusive. The Toll pathway is activated by Gram-positive bacteria through a circulating Peptidoglycan recognition protein (PGRP-SA). PGRPs appear to be highly conserved from insects to mammals, and the Drosophila genome contains 13 members. Here we report a mutation in a gene coding for a putative transmembrane protein, PGRP-LC, which reduces survival to Gram-negative sepsis but has no effect on the response to Gram-positive bacteria or natural fungal infections. By genetic epistasis, we demonstrate that PGRP-LC acts upstream of the imd gene. The data on PGRP-SA with respect to the response to Gram-positive infections, together with the present report, indicate that the PGRP family has a principal role in sensing microbial infections in Drosophila.},
keywords = {Animal, Anti-Infective Agents/metabolism, Carrier Proteins/biosynthesis/genetics/*immunology, Drosophila melanogaster/genetics/*immunology/*microbiology, Drosophila Proteins/genetics/metabolism, Epistasis, Female, ferrandon, Genes, Genetic, Genetic Predisposition to Disease, Gram-Negative Bacteria/*immunology/physiology, hoffmann, Human, Insect/genetics, M3i, Messenger/genetics/metabolism, Mutation, Non-U.S. Gov't, P.H.S., Phenotype, RNA, Signal Transduction, Support, Survival Rate, Transgenes/genetics, U.S. Gov't},
pubstate = {published},
tppubtype = {article}
}
The antimicrobial defence of Drosophila relies largely on the challenge-induced synthesis of an array of potent antimicrobial peptides by the fat body. The defence against Gram-positive bacteria and natural fungal infections is mediated by the Toll signalling pathway, whereas defence against Gram-negative bacteria is dependent on the Immune deficiency (IMD) pathway. Loss-of-function mutations in either pathway reduce the resistance to corresponding infections. The link between microbial infections and activation of these two pathways has remained elusive. The Toll pathway is activated by Gram-positive bacteria through a circulating Peptidoglycan recognition protein (PGRP-SA). PGRPs appear to be highly conserved from insects to mammals, and the Drosophila genome contains 13 members. Here we report a mutation in a gene coding for a putative transmembrane protein, PGRP-LC, which reduces survival to Gram-negative sepsis but has no effect on the response to Gram-positive bacteria or natural fungal infections. By genetic epistasis, we demonstrate that PGRP-LC acts upstream of the imd gene. The data on PGRP-SA with respect to the response to Gram-positive infections, together with the present report, indicate that the PGRP family has a principal role in sensing microbial infections in Drosophila.
Xu M G, Chen J F, Martin F, Zhao M W, Eriani G, Wang E D
Leucyl-tRNA synthetase consisting of two subunits from hyperthermophilic bacteria Aquifex aeolicus Article de journal
Dans: J Biol Chem, vol. 277, no. 44, p. 41590-41596, 2002, ISBN: 12196521, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacteria/*enzymology Binding Sites Circular Dichroism Cloning, ERIANI, Leu Support, Molecular Enzyme Stability Escherichia coli/enzymology Kinetics Leucine-tRNA Ligase/*chemistry/genetics/isolation & purification Protein Subunits RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Leucyl-tRNA synthetase consisting of two subunits from hyperthermophilic bacteria Aquifex aeolicus},
author = {M G Xu and J F Chen and F Martin and M W Zhao and G Eriani and E D Wang},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12196521},
isbn = {12196521},
year = {2002},
date = {2002-01-01},
journal = {J Biol Chem},
volume = {277},
number = {44},
pages = {41590-41596},
abstract = {In a hyperthermophilic bacterium, Aquifex aeolicus, leucyl-tRNA synthetase (LeuRS) consists of two non-identical polypeptide subunits (alpha and beta), different from the canonical LeuRS, which has a single polypeptide chain. By PCR, using genome DNA of A. aeolicus as a template, genes encoding the alpha and beta subunits were amplified and cloned in Escherichia coli. The alpha subunit could not be expressed stably in vivo, whereas the beta subunit was overproduced and purified by a simple procedure. The beta subunit was inactive in catalysis but was able to bind tRNA(Leu). Interestingly, the heterodimer alphabeta-LeuRS could be overproduced in E. coli cells containing both genes and was purified to 95% homogeneity as a hybrid dimer. The kinetics of A. aeolicus LeuRS in pre-steady and steady states and cross-recognition of LeuRS and tRNA(Leu) from A. aeolicus and E. coli were studied. Magnesium concentration, pH value, and temperature aminoacylation optima were determined to be 12 mm, 7.8, and 70 degrees C, respectively. Under optimal conditions, A. aeolicus alphabeta-LeuRS is stable up to 65 degrees C.},
note = {0021-9258
Journal Article},
keywords = {Bacteria/*enzymology Binding Sites Circular Dichroism Cloning, ERIANI, Leu Support, Molecular Enzyme Stability Escherichia coli/enzymology Kinetics Leucine-tRNA Ligase/*chemistry/genetics/isolation & purification Protein Subunits RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In a hyperthermophilic bacterium, Aquifex aeolicus, leucyl-tRNA synthetase (LeuRS) consists of two non-identical polypeptide subunits (alpha and beta), different from the canonical LeuRS, which has a single polypeptide chain. By PCR, using genome DNA of A. aeolicus as a template, genes encoding the alpha and beta subunits were amplified and cloned in Escherichia coli. The alpha subunit could not be expressed stably in vivo, whereas the beta subunit was overproduced and purified by a simple procedure. The beta subunit was inactive in catalysis but was able to bind tRNA(Leu). Interestingly, the heterodimer alphabeta-LeuRS could be overproduced in E. coli cells containing both genes and was purified to 95% homogeneity as a hybrid dimer. The kinetics of A. aeolicus LeuRS in pre-steady and steady states and cross-recognition of LeuRS and tRNA(Leu) from A. aeolicus and E. coli were studied. Magnesium concentration, pH value, and temperature aminoacylation optima were determined to be 12 mm, 7.8, and 70 degrees C, respectively. Under optimal conditions, A. aeolicus alphabeta-LeuRS is stable up to 65 degrees C.
Waldsich C, Masquida B, Westhof E, Schroeder R
Monitoring intermediate folding states of the td group I intron in vivo Article de journal
Dans: EMBO J, vol. 21, no. 19, p. 5281-5291, 2002, ISBN: 12356744, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial/chemistry/genetics Escherichia coli/genetics Introns/*physiology Models, Base Sequence DNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Support, Non-U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Monitoring intermediate folding states of the td group I intron in vivo},
author = {C Waldsich and B Masquida and E Westhof and R Schroeder},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12356744},
isbn = {12356744},
year = {2002},
date = {2002-01-01},
journal = {EMBO J},
volume = {21},
number = {19},
pages = {5281-5291},
abstract = {Group I introns consist of two major structural domains, the P4-P6 and P3-P9 domains, which assemble through interactions with peripheral extensions to fold into an active ribozyme. To assess group I intron folding in vivo, we probed the structure of td wild-type and mutant introns using dimethyl sulfate. The results suggest that the majority of the intron population is in the native state in accordance with the current structural model, which was refined to include two novel tertiary contacts. The importance of the loop E motif in the P7.1-P7.2 extension in assisting ribozyme folding was deduced from modeling and mutational analyses. Destabilization of stem P6 results in a deficiency in tertiary structure formation in both major domains, while weakening of stem P7 only interferes with folding of the P3-P9 domain. The different impact of mutations on the tertiary structure suggests that they interfere with folding at different stages. These results provide a first insight into the structure of folding intermediates and suggest a putative order of events in a hierarchical folding pathway in vivo.},
note = {0261-4189
Journal Article},
keywords = {Bacterial/chemistry/genetics Escherichia coli/genetics Introns/*physiology Models, Base Sequence DNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Support, Non-U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Group I introns consist of two major structural domains, the P4-P6 and P3-P9 domains, which assemble through interactions with peripheral extensions to fold into an active ribozyme. To assess group I intron folding in vivo, we probed the structure of td wild-type and mutant introns using dimethyl sulfate. The results suggest that the majority of the intron population is in the native state in accordance with the current structural model, which was refined to include two novel tertiary contacts. The importance of the loop E motif in the P7.1-P7.2 extension in assisting ribozyme folding was deduced from modeling and mutational analyses. Destabilization of stem P6 results in a deficiency in tertiary structure formation in both major domains, while weakening of stem P7 only interferes with folding of the P3-P9 domain. The different impact of mutations on the tertiary structure suggests that they interfere with folding at different stages. These results provide a first insight into the structure of folding intermediates and suggest a putative order of events in a hierarchical folding pathway in vivo.
Wagner E G, Altuvia S, Romby P
Antisense RNAs in bacteria and their genetic elements. Chapitre d'ouvrage
Dans: Dunlap, J C; Wu, C. -ting (Ed.): Advances in Genetics: Homology Effects., vol. 46, p. 361-398, Academic Press, 2002, ISBN: 11931231, (0065-2660 Review Review, Academic).
Résumé | Liens | BibTeX | Étiquettes: 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}
}
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.
van Buuren B N, Hermann T, Wijmenga S S, Westhof E
Brownian-dynamics simulations of metal-ion binding to four-way junctions Article de journal
Dans: Nucleic Acids Res, vol. 30, no. 2, p. 507-514, 2002, ISBN: 11788713, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Pair Mismatch Base Sequence Binding Sites Cations/*metabolism *Computer Simulation DNA/*chemistry/genetics/*metabolism Diffusion Electrostatics Metals/*metabolism Models, Biomolecular *Nucleic Acid Conformation Nucleic Acid Hybridization RNA/chemistry/genetics/metabolism Recombination, Genetic/*genetics Support, Molecular Nuclear Magnetic Resonance, Non-U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Brownian-dynamics simulations of metal-ion binding to four-way junctions},
author = {B N van Buuren and T Hermann and S S Wijmenga and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11788713},
isbn = {11788713},
year = {2002},
date = {2002-01-01},
journal = {Nucleic Acids Res},
volume = {30},
number = {2},
pages = {507-514},
abstract = {Four-way junctions (4Hs) are important intermediates in DNA rearrangements such as genetic recombination. Under the influence of multivalent cations these molecules undergo a conformational change, from an extended planar form to a quasi-continuous stacked X-structure. Recently, a number of X-ray structures and a nuclear magnetic resonance (NMR) structure of 4Hs have been reported and in three of these the position of multivalent cations is revealed. These structures belong to two main families, characterized by the angle between the two co-axial stacked helices, which is either around +40 to +55 degrees or around -70 to -80 degrees. To investigate the role of metal-ion binding on the conformation of folded 4Hs we performed Brownian-dynamics simulations on the set of available structures. The simulations confirm the proposed metal-ion binding sites in the NMR structure and in one of the X-ray structures. Furthermore, the calculations suggest positions for metal-ion binding in the other X-ray structures. The results show a striking dependence of the ion density on the helical environment (B-helix or A-helix) and the structural family.},
note = {1362-4962
Journal Article},
keywords = {Base Pair Mismatch Base Sequence Binding Sites Cations/*metabolism *Computer Simulation DNA/*chemistry/genetics/*metabolism Diffusion Electrostatics Metals/*metabolism Models, Biomolecular *Nucleic Acid Conformation Nucleic Acid Hybridization RNA/chemistry/genetics/metabolism Recombination, Genetic/*genetics Support, Molecular Nuclear Magnetic Resonance, Non-U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Four-way junctions (4Hs) are important intermediates in DNA rearrangements such as genetic recombination. Under the influence of multivalent cations these molecules undergo a conformational change, from an extended planar form to a quasi-continuous stacked X-structure. Recently, a number of X-ray structures and a nuclear magnetic resonance (NMR) structure of 4Hs have been reported and in three of these the position of multivalent cations is revealed. These structures belong to two main families, characterized by the angle between the two co-axial stacked helices, which is either around +40 to +55 degrees or around -70 to -80 degrees. To investigate the role of metal-ion binding on the conformation of folded 4Hs we performed Brownian-dynamics simulations on the set of available structures. The simulations confirm the proposed metal-ion binding sites in the NMR structure and in one of the X-ray structures. Furthermore, the calculations suggest positions for metal-ion binding in the other X-ray structures. The results show a striking dependence of the ion density on the helical environment (B-helix or A-helix) and the structural family.
Rabilloud T, Strub J M, Carte N, Luche S, Dorsselaer A Van, Lunardi J, Giege R, Florentz C
Comparative proteomics as a new tool for exploring human mitochondrial tRNA disorders Article de journal
Dans: Biochemistry, vol. 41, no. 1, p. 144-150, 2002, ISBN: 11772011, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Cell Line Cell Nucleus/physiology Comparative Study DNA, FLORENTZ,