Publications
2000
Wilhelm M., Boutabout M., Wilhelm F. X.
Expression of an active form of recombinant Ty1 reverse transcriptase in Escherichia coli: a fusion protein containing the C-terminal region of the Ty1 integrase linked to the reverse transcriptase-RNase H domain exhibits polymerase and RNase H activities Article de journal
Dans: Biochem J, vol. 348, no. Pt 2, p. 337-42, 2000, (0264-6021 Journal Article).
Résumé | BibTeX | Étiquettes: &, Acid, affinity, Alignment, Amino, Calf, cerevisiae/*enzymology/*genetics, Chromatography, Cloning, Codon, coli, Comparative, Data, DNA, DNA/metabolism, Escherichia, Frames, Fusion, Genetic, Gov't, H, Heteroduplexes/metabolism, HIV-1, Homology, Integrases/chemistry/metabolism, Kinetics, Molecular, Non-U.S., Nucleic, Open, Polymerase/chemistry/isolation, Proteins/chemistry/isolation, purification/*metabolism, purification/metabolism, Reading, Recombinant, Retroelements/*genetics, Reverse, Ribonuclease, RNA-Directed, RNA/metabolism, Saccharomyces, Sequence, Study, Support, Templates, Terminator, Thymus/isolation, Transcriptase/chemistry
@article{,
title = {Expression of an active form of recombinant Ty1 reverse transcriptase in Escherichia coli: a fusion protein containing the C-terminal region of the Ty1 integrase linked to the reverse transcriptase-RNase H domain exhibits polymerase and RNase H activities},
author = { M. Wilhelm and M. Boutabout and F. X. Wilhelm},
year = {2000},
date = {2000-01-01},
journal = {Biochem J},
volume = {348},
number = {Pt 2},
pages = {337-42},
abstract = {Replication of the Saccharomyces cerevisiae Ty1 retrotransposon requires a reverse transcriptase capable of synthesizing Ty1 DNA. The first description of an active form of a recombinant Ty1 enzyme with polymerase and RNase H activities is reported here. The Ty1 enzyme was expressed as a hexahistidine-tagged fusion protein in Escherichia coli to facilitate purification of the recombinant protein by metal-chelate chromatography. Catalytic activity of the recombinant protein was detected only when amino acid residues encoded by the integrase gene were added to the N-terminus of the reverse transcriptase-RNase H domain. This suggests that the integrase domain could play a role in proper folding of reverse transcriptase. Several biochemical properties of the Ty1 enzyme were analysed, including the effect of MgCl(2), NaCl, temperature and of the chain terminator dideoxy GTP on its polymerase activity. RNase H activity was examined by monitoring the cleavage of a RNA-DNA template-primer. Our results suggest that the distance between the RNase H and polymerase active sites corresponds to the length of a 14-nucleotide RNA-DNA heteroduplex. The recombinant protein produced in E. coli should be useful for further biochemical and structural analyses and for a better understanding of the role of integrase in the activation of reverse transcriptase.},
note = {0264-6021
Journal Article},
keywords = {&, Acid, affinity, Alignment, Amino, Calf, cerevisiae/*enzymology/*genetics, Chromatography, Cloning, Codon, coli, Comparative, Data, DNA, DNA/metabolism, Escherichia, Frames, Fusion, Genetic, Gov't, H, Heteroduplexes/metabolism, HIV-1, Homology, Integrases/chemistry/metabolism, Kinetics, Molecular, Non-U.S., Nucleic, Open, Polymerase/chemistry/isolation, Proteins/chemistry/isolation, purification/*metabolism, purification/metabolism, Reading, Recombinant, Retroelements/*genetics, Reverse, Ribonuclease, RNA-Directed, RNA/metabolism, Saccharomyces, Sequence, Study, Support, Templates, Terminator, Thymus/isolation, Transcriptase/chemistry},
pubstate = {published},
tppubtype = {article}
}
Imler Jean-Luc, Tauszig Servane, Jouanguy Emmanuelle, Forestier C, Hoffmann Jules A
LPS-induced immune response in Drosophila Article de journal
Dans: Journal of Endotoxin Research, vol. 6, no. 6, p. 459–462, 2000, ISSN: 0968-0519.
Résumé | BibTeX | Étiquettes: Animals, Biological, Cell Line, Cell Surface, Defensins, Genes, Genetic, hoffmann, imler, Insect, Insect Proteins, Lipopolysaccharides, M3i, Membrane Glycoproteins, Models, Mutation, Promoter Regions, Receptors, Signal Transduction, Toll-Like Receptors
@article{imler_lps-induced_2000,
title = {LPS-induced immune response in Drosophila},
author = {Jean-Luc Imler and Servane Tauszig and Emmanuelle Jouanguy and C Forestier and Jules A Hoffmann},
issn = {0968-0519},
year = {2000},
date = {2000-01-01},
journal = {Journal of Endotoxin Research},
volume = {6},
number = {6},
pages = {459--462},
abstract = {The study of the regulation of the inducible synthesis of antimicrobial peptides in Drosophila melanogaster has established this insect as a powerful model in which to study innate immunity. In particular, the molecular characterization of the regulatory pathway controlling the antifungal peptide drosomycin has revealed the importance of Toll receptors in innate immunity. We report here that injection of LPS into flies induces an immune response, suggesting that LPS receptors are used in Drosophila to detect Gram-negative bacteria infection. We have identified in the recently sequenced genome of Drosophila eight genes coding for Toll-like receptors in addition to Toll, which may function as LPS receptors. However, overexpression of a selection of these genes in tissue-culture cells does not result in up-regulation of the antibacterial peptide genes. These results are discussed in light of the recent data from genetic screens aimed at identifying the genes controlling the antibacterial response in Drosophila.},
keywords = {Animals, Biological, Cell Line, Cell Surface, Defensins, Genes, Genetic, hoffmann, imler, Insect, Insect Proteins, Lipopolysaccharides, M3i, Membrane Glycoproteins, Models, Mutation, Promoter Regions, Receptors, Signal Transduction, Toll-Like Receptors},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M, Boutabout M, Wilhelm F X
Dans: Biochem J, vol. 348, no. Pt 2, p. 337-342, 2000, ISBN: 10816427, (0264-6021 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Affinity Cloning, Amino Acid Support, Amino Acid Sequence Chromatography, Calf Thymus/isolation & purification/*metabolism Saccharomyces cerevisiae/*enzymology/*genetics Sequence Alignment Sequence Homology, Genetic, Molecular Codon, Non-U.S. Gov't Templates, Unité ARN
@article{,
title = {Expression of an active form of recombinant Ty1 reverse transcriptase in Escherichia coli: a fusion protein containing the C-terminal region of the Ty1 integrase linked to the reverse transcriptase-RNase H domain exhibits polymerase and RNase H activities},
author = {M Wilhelm and M Boutabout and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10816427},
isbn = {10816427},
year = {2000},
date = {2000-01-01},
journal = {Biochem J},
volume = {348},
number = {Pt 2},
pages = {337-342},
abstract = {Replication of the Saccharomyces cerevisiae Ty1 retrotransposon requires a reverse transcriptase capable of synthesizing Ty1 DNA. The first description of an active form of a recombinant Ty1 enzyme with polymerase and RNase H activities is reported here. The Ty1 enzyme was expressed as a hexahistidine-tagged fusion protein in Escherichia coli to facilitate purification of the recombinant protein by metal-chelate chromatography. Catalytic activity of the recombinant protein was detected only when amino acid residues encoded by the integrase gene were added to the N-terminus of the reverse transcriptase-RNase H domain. This suggests that the integrase domain could play a role in proper folding of reverse transcriptase. Several biochemical properties of the Ty1 enzyme were analysed, including the effect of MgCl(2), NaCl, temperature and of the chain terminator dideoxy GTP on its polymerase activity. RNase H activity was examined by monitoring the cleavage of a RNA-DNA template-primer. Our results suggest that the distance between the RNase H and polymerase active sites corresponds to the length of a 14-nucleotide RNA-DNA heteroduplex. The recombinant protein produced in E. coli should be useful for further biochemical and structural analyses and for a better understanding of the role of integrase in the activation of reverse transcriptase.},
note = {0264-6021
Journal Article},
keywords = {Affinity Cloning, Amino Acid Support, Amino Acid Sequence Chromatography, Calf Thymus/isolation & purification/*metabolism Saccharomyces cerevisiae/*enzymology/*genetics Sequence Alignment Sequence Homology, Genetic, Molecular Codon, Non-U.S. Gov't Templates, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lanchy J M, Isel C, Keith G, Grice S F Le, Ehresmann C, Ehresmann B, Marquet R
Dynamics of the HIV-1 reverse transcription complex during initiation of DNA synthesis Article de journal
Dans: J Biol Chem, vol. 275, no. 16, p. 12306-12312, 2000, ISBN: 10766870, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Anticodon Base Sequence *DNA Replication *Hiv-1 Human Molecular Sequence Data Mutagenesis Nucleic Acid Conformation RNA, Genetic, Lys/genetics/metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/genetics/metabolism RNA-Directed DNA Polymerase/*metabolism Support
@article{,
title = {Dynamics of the HIV-1 reverse transcription complex during initiation of DNA synthesis},
author = {J M Lanchy and C Isel and G Keith and S F Le Grice and C Ehresmann and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10766870},
isbn = {10766870},
year = {2000},
date = {2000-01-01},
journal = {J Biol Chem},
volume = {275},
number = {16},
pages = {12306-12312},
abstract = {Initiation of human immunodeficiency virus-1 (HIV-1) reverse transcription requires formation of a complex containing the viral RNA (vRNA), tRNA(3)(Lys) and reverse transcriptase (RT). The vRNA and the primer tRNA(3)(Lys) form several intermolecular interactions in addition to annealing of the primer 3' end to the primer binding site (PBS). These interactions are crucial for the efficiency and the specificity of the initiation of reverse transcription. However, as they are located upstream of the PBS, they must unwind as DNA synthesis proceeds. Here, the dynamics of the complex during initiation of reverse transcription was followed by enzymatic probing. Our data revealed reciprocal effects of the tertiary structure of the vRNA.tRNA(3)(Lys) complex and reverse transcriptase (RT) at a distance from the polymerization site. The structure of the initiation complex allowed RT to interact with the template strand up to 20 nucleotides upstream from the polymerization site. Conversely, nucleotide addition by RT modified the tertiary structure of the complex at 10-14 nucleotides from the catalytic site. The viral sequences became exposed at the surface of the complex as they dissociated from the tRNA following primer extension. However, the counterpart tRNA sequences became buried inside the complex. Surprisingly, they became exposed when mutations prevented the intermolecular interactions in the initial complex, indicating that the fate of the tRNA depended on the tertiary structure of the initial complex.},
note = {0021-9258
Journal Article},
keywords = {*Anticodon Base Sequence *DNA Replication *Hiv-1 Human Molecular Sequence Data Mutagenesis Nucleic Acid Conformation RNA, Genetic, Lys/genetics/metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/genetics/metabolism RNA-Directed DNA Polymerase/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Klinck R, Westhof E, Walker S, Afshar M, Collier A, Aboul-Ela F
A potential RNA drug target in the hepatitis C virus internal ribosomal entry site Article de journal
Dans: RNA, vol. 6, no. 10, p. 1423-1431, 2000, ISBN: 11073218, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Pairing Base Sequence Computational Biology *Drug Design Endoribonucleases/metabolism Genetic Engineering Hepacivirus/*genetics Models, Biomolecular *Nucleic Acid Conformation RNA, Genetic, Messenger/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Mutation Nuclear Magnetic Resonance, Nucleic Acid/*genetics Reproducibility of Results Ribosomes/*metabolism Ricin/metabolism Structure-Activity Relationship Substrate Specificity Translation, Unité ARN, Viral/*chemistry/genetics/*metabolism Regulatory Sequences
@article{,
title = {A potential RNA drug target in the hepatitis C virus internal ribosomal entry site},
author = {R Klinck and E Westhof and S Walker and M Afshar and A Collier and F Aboul-Ela},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11073218},
isbn = {11073218},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {10},
pages = {1423-1431},
abstract = {Subdomain IlId from the hepatitis C virus (HCV) internal ribosome entry site (IRES) has been shown to be essential for cap-independent translation. We have conducted a structural study of a 27-nt fragment, identical in sequence to IlId, to explore the structural features of this subdomain. The proposed secondary structure of IlId is comprised of two 3 bp helical regions separated by an internal loop and closed at one end by a 6-nt terminal loop. NMR and molecular modeling were used interactively to formulate a validated model of the three-dimensional structure of IlId. We found that this fragment contains several noncanonical structural motifs and non-Watson-Crick base pairs, some of which are common to other RNAs. In particular, a motif characteristic of the rRNA alpha-sarcin/ricin loop was located in the internal loop. The terminal loop, 5'-UUGGGU, was found to fold to form a trinucleotide loop closed by a trans-wobble U.G base pair. The sixth nucleotide was bulged out to allow stacking of this U.G pair on the adjacent helical region. In vivo mutational analysis in the context of the full IRES confirmed the importance of each structural motif within IIId for IRES function. These findings may provide clues as to host cellular proteins that play a role in IRES-directed translation and, in particular, the mechanism through which host ribosomes are sequestered for viral function.},
note = {1355-8382
Journal Article},
keywords = {Base Pairing Base Sequence Computational Biology *Drug Design Endoribonucleases/metabolism Genetic Engineering Hepacivirus/*genetics Models, Biomolecular *Nucleic Acid Conformation RNA, Genetic, Messenger/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Mutation Nuclear Magnetic Resonance, Nucleic Acid/*genetics Reproducibility of Results Ribosomes/*metabolism Ricin/metabolism Structure-Activity Relationship Substrate Specificity Translation, Unité ARN, Viral/*chemistry/genetics/*metabolism Regulatory Sequences},
pubstate = {published},
tppubtype = {article}
}
Costa M, Michel F, Westhof E
A three-dimensional perspective on exon binding by a group II self-splicing intron Article de journal
Dans: EMBO J, vol. 19, no. 18, p. 5007-5018, 2000, ISBN: 10990464, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Catalysis *Exons Hydroxyl Radical *Introns Kinetics *Models, Catalytic/metabolism Support, Genetic, Genetic Molecular Sequence Data Nucleic Acid Conformation *RNA Splicing RNA, Non-U.S. Gov't Support, P.H.S. Temperature Transcription, U.S. Gov't, Unité ARN
@article{,
title = {A three-dimensional perspective on exon binding by a group II self-splicing intron},
author = {M Costa and F Michel and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10990464},
isbn = {10990464},
year = {2000},
date = {2000-01-01},
journal = {EMBO J},
volume = {19},
number = {18},
pages = {5007-5018},
abstract = {We have used chemical footprinting, kinetic dissection of reactions and comparative sequence analysis to show that in self-splicing introns belonging to subgroup IIB, the sites that bind the 5' and 3' exons are connected to one another by tertiary interactions. This unanticipated arrangement, which contrasts with the direct covalent linkage that prevails in the other major subdivision of group II (subgroup IIA), results in a unique three-dimensional architecture for the complex between the exons, their binding sites and intron domain V. A key feature of the modeled complex is the presence of several close contacts between domain V and one of the intron-exon pairings. These contacts, whose existence is supported by hydroxyl radical footprinting, provide a structural framework for the known role of domain V in catalysis and its recently demonstrated involvement in binding of the 5' exon.},
note = {0261-4189
Journal Article},
keywords = {Base Sequence Catalysis *Exons Hydroxyl Radical *Introns Kinetics *Models, Catalytic/metabolism Support, Genetic, Genetic Molecular Sequence Data Nucleic Acid Conformation *RNA Splicing RNA, Non-U.S. Gov't Support, P.H.S. Temperature Transcription, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Brunel C, Romby P
Probing RNA structure and RNA-ligand complexes with chemical probes Article de journal
Dans: Methods Enzymol, vol. 318, p. 3-21, 2000, ISBN: 10889976, (0076-6879 Journal Article Review Review, Tutorial).
Liens | BibTeX | Étiquettes: Crystallography, Genetic, ROMBY, Unité ARN, X-Ray *Ligands Nucleic Acid Conformation Nucleotides/chemistry/metabolism Proteins/chemistry RNA/*chemistry/drug effects/*metabolism Transcription
@article{,
title = {Probing RNA structure and RNA-ligand complexes with chemical probes},
author = {C Brunel and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10889976},
isbn = {10889976},
year = {2000},
date = {2000-01-01},
journal = {Methods Enzymol},
volume = {318},
pages = {3-21},
note = {0076-6879
Journal Article
Review
Review, Tutorial},
keywords = {Crystallography, Genetic, ROMBY, Unité ARN, X-Ray *Ligands Nucleic Acid Conformation Nucleotides/chemistry/metabolism Proteins/chemistry RNA/*chemistry/drug effects/*metabolism Transcription},
pubstate = {published},
tppubtype = {article}
}
Brule F, Bec G, Keith G, Grice S F Le, Roques B P, Ehresmann B, Ehresmann C, Marquet R
In vitro evidence for the interaction of tRNA(3)(Lys) with U3 during the first strand transfer of HIV-1 reverse transcription Article de journal
Dans: Nucleic Acids Res, vol. 28, no. 2, p. 634-640, 2000, ISBN: 10606665, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence HIV-1 Reverse Transcriptase/*metabolism Nucleic Acid Conformation Polymerase Chain Reaction RNA, Genetic, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/chemistry/*metabolism Support
@article{,
title = {In vitro evidence for the interaction of tRNA(3)(Lys) with U3 during the first strand transfer of HIV-1 reverse transcription},
author = {F Brule and G Bec and G Keith and S F Le Grice and B P Roques and B Ehresmann and C Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10606665},
isbn = {10606665},
year = {2000},
date = {2000-01-01},
journal = {Nucleic Acids Res},
volume = {28},
number = {2},
pages = {634-640},
abstract = {Over the course of its evolution, HIV-1 has taken maximum advantage of its tRNA(3)(Lys)primer by utilizing it in several steps of reverse transcription. Here, we have identified a conserved nonanucleotide sequence in the U3 region of HIV-1 RNA that is complementary to the anticodon stem of tRNA(3)(Lys). In order to test its possible role in the first strand transfer reaction, we applied an assay using a donor RNA corresponding to the 5'-part and an acceptor RNA spanning the 3'-part of HIV-1 RNA. In addition, we constructed two acceptor RNAs in which the nonanucleotide sequence complementary to tRNA(3)(Lys)was either substituted (S) or deleted (Delta). We used either natural tRNA(3)(Lys)or an 18 nt DNA as primer and measured the efficiency of (-) strand strong stop DNA transfer in the presence of wild-type, S or Delta acceptor RNA. Mutations in U3 did not decrease the transfer efficiency when reverse transcription was primed with the 18mer DNA. However, they significantly reduced the strand transfer efficiency in the tRNA(3)(Lys)-primed reactions. This reduction was also observed in the presence of nucleocapsid protein. These results suggest that tRNA(3)(Lys)increases (-) strand strong stop transfer by interacting with the U3 region of the genomic RNA. Sequence comparisons suggest that such long range interactions also exist in other lentiviruses.},
note = {1362-4962
Journal Article},
keywords = {Base Sequence HIV-1 Reverse Transcriptase/*metabolism Nucleic Acid Conformation Polymerase Chain Reaction RNA, Genetic, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/chemistry/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
1999
Auxilien S., Keith G., Grice S. F. Le, Darlix J. L.
Role of post-transcriptional modifications of primer tRNALys,3 in the fidelity and efficacy of plus strand DNA transfer during HIV-1 reverse transcription Article de journal
Dans: J Biol Chem, vol. 274, no. 7, p. 4412-20, 1999, (0021-9258 Journal Article).
Résumé | BibTeX | Étiquettes: *RNA, *Transcription, Acid, Base, Calf, Conformation, Data, DNA, Genetic, Gov't, H, HIV-1, HIV-1/*physiology, Lys/*metabolism, Molecular, Non-U.S., Nucleic, post-transcriptional, Processing, Reverse, Ribonuclease, RNA, Sequence, Support, Templates, Thymus/metabolism, Transcriptase/metabolism, Transfer, Viral/*metabolism, Viral/metabolism
@article{,
title = {Role of post-transcriptional modifications of primer tRNALys,3 in the fidelity and efficacy of plus strand DNA transfer during HIV-1 reverse transcription},
author = { S. Auxilien and G. Keith and S. F. Le Grice and J. L. Darlix},
year = {1999},
date = {1999-01-01},
journal = {J Biol Chem},
volume = {274},
number = {7},
pages = {4412-20},
abstract = {During HIV reverse transcription, (+) strand DNA synthesis is primed by an RNase H-resistant sequence, the polypurine tract, and continues as far as a 18-nt double-stranded RNA region corresponding to the 3' end of tRNALys,3 hybridized to the viral primer binding site (PBS). Before (+) strand DNA transfer, reverse transcriptase (RT) needs to unwind the double-stranded tRNA-PBS RNA in order to reverse-transcribe the 3' end of primer tRNALys,3. Since the detailed mechanism of (+) strand DNA transfer remains incompletely understood, we developed an in vitro system to closely examine this mechanism, composed of HIV 5' RNA, natural modified tRNALys,3, synthetic unmodified tRNALys,3 or oligonucleotides (RNA or DNA) complementary to the PBS, as well as the viral proteins RT and nucleocapsid protein (NCp7). Prior to (+) strand DNA transfer, RT stalls at the double-stranded tRNA-PBS RNA complex and is able to reverse-transcribe modified nucleosides of natural tRNALys,3. Modified nucleoside m1A-58 of natural tRNALys,3 is only partially effective as a stop signal, as RT can transcribe as far as the hyper-modified adenosine (ms2t6A-37) in the anticodon loop. m1A-58 is almost always transcribed into A, whereas other modified nucleosides are transcribed correctly, except for m7G-46, which is sometimes transcribed into T. In contrast, synthetic tRNALys,3, an RNA PBS primer, and a DNA PBS primer are completely reverse-transcribed. In the presence of an acceptor template, (+) strand DNA transfer is efficient only with templates containing natural tRNALys,3 or the RNA PBS primer. Sequence analysis of transfer products revealed frequent errors at the transfer site with synthetic tRNALys,3, not observed with natural tRNALys,3. Thus, modified nucleoside m1A-58, present in all retroviral tRNA primers, appears to be important for both efficacy and fidelity of (+) strand DNA transfer. We show that other factors such as the nature of the (-) PBS of the acceptor template and the RNase H activity of RT also influence the efficacy of (+) strand DNA transfer.},
note = {0021-9258
Journal Article},
keywords = {*RNA, *Transcription, Acid, Base, Calf, Conformation, Data, DNA, Genetic, Gov't, H, HIV-1, HIV-1/*physiology, Lys/*metabolism, Molecular, Non-U.S., Nucleic, post-transcriptional, Processing, Reverse, Ribonuclease, RNA, Sequence, Support, Templates, Thymus/metabolism, Transcriptase/metabolism, Transfer, Viral/*metabolism, Viral/metabolism},
pubstate = {published},
tppubtype = {article}
}
Perreau V. M., Keith G., Holmes W. M., Przykorska A., Santos M. A., Tuite M. F.
The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure Article de journal
Dans: J Mol Biol, vol. 293, no. 5, p. 1039-53, 1999, (0022-2836 Journal Article).
Résumé | BibTeX | Étiquettes: *Nucleic, Acid, albicans/*genetics, Anticodon/*chemistry/*genetics/metabolism, Base, Candida, cerevisiae/genetics, Code/genetics, Conformation, Evolution, Fungal/chemistry/genetics/metabolism, Genetic, Gov't, Imidazoles/metabolism, Lead/metabolism, Methylation, Methyltransferases/metabolism, Molecular, Mutation/genetics, Non-P.H.S., Non-U.S., Nucleosides/genetics/metabolism, P.H.S., Ribonucleases/metabolism, RNA, Saccharomyces, Sequence, Ser/*chemistry/*genetics/metabolism, Solutions, Support, Transfer, tRNA, U.S.
@article{,
title = {The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure},
author = { V. M. Perreau and G. Keith and W. M. Holmes and A. Przykorska and M. A. Santos and M. F. Tuite},
year = {1999},
date = {1999-01-01},
journal = {J Mol Biol},
volume = {293},
number = {5},
pages = {1039-53},
abstract = {In many Candida species, the leucine CUG codon is decoded by a tRNA with two unusual properties: it is a ser-tRNA and, uniquely, has guanosine at position 33 (G33). Using a combination of enzymatic (V1 RNase, RnI nuclease) and chemical (Pb(2+), imidazole) probing of the native Candida albicans ser-tRNACAG, we demonstrate that the overall tertiary structure of this tRNA resembles that of a ser-tRNA rather than a leu-tRNA, except within the anticodon arm where there is considerable disruption of the anticodon stem. Using non-modified in vitro transcripts of the C. albicans ser-tRNACAG carrying G, C, U or A at position 33, we demonstrate that it is specifically a G residue at this position that induces the atypical anticodon stem structure. Further quantitative evidence for an unusual structure in the anticodon arm of the G33-tRNA is provided by the observed change in kinetics of methylation of the G at position 37, by purified Escherichia coli m(1)G37 methyltransferase. We conclude that the anticodon arm distortion, induced by a guanosine base at position 33 in the anticodon loop of this novel tRNA, results in reduced decoding ability which has facilitated the evolution of this tRNA without extinction of the species encoding it.},
note = {0022-2836
Journal Article},
keywords = {*Nucleic, Acid, albicans/*genetics, Anticodon/*chemistry/*genetics/metabolism, Base, Candida, cerevisiae/genetics, Code/genetics, Conformation, Evolution, Fungal/chemistry/genetics/metabolism, Genetic, Gov't, Imidazoles/metabolism, Lead/metabolism, Methylation, Methyltransferases/metabolism, Molecular, Mutation/genetics, Non-P.H.S., Non-U.S., Nucleosides/genetics/metabolism, P.H.S., Ribonucleases/metabolism, RNA, Saccharomyces, Sequence, Ser/*chemistry/*genetics/metabolism, Solutions, Support, Transfer, tRNA, U.S.},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M., Boutabout M., Heyman T., Wilhelm F. X.
Reverse transcription of the yeast Ty1 retrotransposon: the mode of first strand transfer is either intermolecular or intramolecular Article de journal
Dans: J Mol Biol, vol. 288, no. 4, p. 505-10, 1999, (0022-2836 Journal Article).
Résumé | BibTeX | Étiquettes: *Retroelements, *Transcription, Acid, Base, cerevisiae/*genetics, DNA, Genetic, Gov't, Non-U.S., Nucleic, Repetitive, Saccharomyces, Sequence, Sequences, Single-Stranded/genetics, Support
@article{,
title = {Reverse transcription of the yeast Ty1 retrotransposon: the mode of first strand transfer is either intermolecular or intramolecular},
author = { M. Wilhelm and M. Boutabout and T. Heyman and F. X. Wilhelm},
year = {1999},
date = {1999-01-01},
journal = {J Mol Biol},
volume = {288},
number = {4},
pages = {505-10},
abstract = {Replication of the yeast Ty1 retrotransposon occurs by a mechanism similar to that of retroviruses. According to the current model of retroviral reverse transcription, two strand transfers (the so-called minus-strand and plus-strand strong-stop DNA transfers) are required to produce full-length preintegrative DNA. Because two genomic RNA molecules are packaged inside the viral particles, the strand transfers can be either intra- or intermolecular. To study the mode of transfer of minus-strand strong-stop DNA during reverse transcription of the yeast Ty1 retrotransposon, we have analyzed the cDNA products that accumulate in the cytoplasmic virus-like particles of yeast cells harboring two marked Ty1 elements. Our results indicate that Ty1 minus-strand transfer occurs in a random manner with approximately similar frequencies of intra- and intermolecular transfer. It has been observed recently that intra- and intermolecular minus-strand transfer occur at similar frequencies during replication of a complex retrovirus such as HIV-1. These results together with the observation that genetic recombination occurs with a high frequency during minus-strand synthesis suggest that both packaged RNA molecules are needed for the synthesis of one minus-strand DNA.},
note = {0022-2836
Journal Article},
keywords = {*Retroelements, *Transcription, Acid, Base, cerevisiae/*genetics, DNA, Genetic, Gov't, Non-U.S., Nucleic, Repetitive, Saccharomyces, Sequence, Sequences, Single-Stranded/genetics, Support},
pubstate = {published},
tppubtype = {article}
}
Lowenberger C A, Kamal S, Chiles J, Paskewitz S, Bulet Philippe, Hoffmann Jules A, Christensen B M
Mosquito-Plasmodium interactions in response to immune activation of the vector Article de journal
Dans: Exp. Parasitol., vol. 91, no. 1, p. 59–69, 1999, ISSN: 0014-4894.
Résumé | Liens | BibTeX | Étiquettes: Aedes, Animals, Anopheles, Culicidae, Defensins, Digestive System, Escherichia coli, Female, Genetic, Hemolymph, hoffmann, Insect Vectors, M3i, messenger, Micrococcus luteus, Plasmodium, Plasmodium berghei, Plasmodium gallinaceum, Proteins, Reverse Transcriptase Polymerase Chain Reaction, RNA, Transcription
@article{lowenberger_mosquito-plasmodium_1999,
title = {Mosquito-Plasmodium interactions in response to immune activation of the vector},
author = {C A Lowenberger and S Kamal and J Chiles and S Paskewitz and Philippe Bulet and Jules A Hoffmann and B M Christensen},
doi = {10.1006/expr.1999.4350},
issn = {0014-4894},
year = {1999},
date = {1999-01-01},
journal = {Exp. Parasitol.},
volume = {91},
number = {1},
pages = {59--69},
abstract = {During the development of Plasmodium sp. within the mosquito midgut, the parasite undergoes a series of developmental changes. The elongated ookinete migrates through the layers of the midgut where it forms the oocyst under the basal lamina. We demonstrate here that if Aedes aegypti or Anopheles gambiae, normally susceptible to Plasmodium gallinaceum and P. berghei, respectively, are immune activated by the injection of bacteria into the hemocoel, and subsequently are fed on an infectious bloodmeal, there is a significant reduction in the prevalence and mean intensity of infection of oocysts on the midgut. Only those mosquitoes immune activated prior to, or immediately after, parasite ingestion exhibit this reduction in parasite development. Mosquitoes immune activated 2-5 days after bloodfeeding show no differences in parasite burdens compared with naive controls. Northern analyses reveal that transcriptional activity for mosquito defensins is not detected in the whole bodies of Ae. aegypti from 4 h to 10 days after ingesting P. gallinaceum, suggesting that parasite ingestion, passage from the food bolus through the midgut, oocyst formation, and subsequent release of sporozoites into the hemolymph do not induce the production of defensin. However, reverse transcriptase-PCR of RNA isolated solely from the midguts of Ae. aegypti indicates that transcription of mosquito defensins occurs in the midguts of naive mosquitoes and those ingesting an infectious or noninfectious bloodmeal. Bacteria-challenged Ae. aegypti showed high levels of mature defensin in the hemolymph that correlate with a lower prevalence and mean intensity of infection with oocysts. Because few oocysts were found on the midgut of immune-activated mosquitoes, the data suggest that some factor, induced by bacterial challenge, kills the parasite at a preoocyst stage.},
keywords = {Aedes, Animals, Anopheles, Culicidae, Defensins, Digestive System, Escherichia coli, Female, Genetic, Hemolymph, hoffmann, Insect Vectors, M3i, messenger, Micrococcus luteus, Plasmodium, Plasmodium berghei, Plasmodium gallinaceum, Proteins, Reverse Transcriptase Polymerase Chain Reaction, RNA, Transcription},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M, Boutabout M, Heyman T, Wilhelm F X
Reverse transcription of the yeast Ty1 retrotransposon: the mode of first strand transfer is either intermolecular or intramolecular Article de journal
Dans: J Mol Biol, vol. 288, no. 4, p. 505-510, 1999, ISBN: 10329158, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Genetic, Non-U.S. Gov't *Transcription, Nucleic Acid *Retroelements Saccharomyces cerevisiae/*genetics Support, Single-Stranded/genetics Repetitive Sequences, Unité ARN
@article{,
title = {Reverse transcription of the yeast Ty1 retrotransposon: the mode of first strand transfer is either intermolecular or intramolecular},
author = {M Wilhelm and M Boutabout and T Heyman and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10329158},
isbn = {10329158},
year = {1999},
date = {1999-01-01},
journal = {J Mol Biol},
volume = {288},
number = {4},
pages = {505-510},
abstract = {Replication of the yeast Ty1 retrotransposon occurs by a mechanism similar to that of retroviruses. According to the current model of retroviral reverse transcription, two strand transfers (the so-called minus-strand and plus-strand strong-stop DNA transfers) are required to produce full-length preintegrative DNA. Because two genomic RNA molecules are packaged inside the viral particles, the strand transfers can be either intra- or intermolecular. To study the mode of transfer of minus-strand strong-stop DNA during reverse transcription of the yeast Ty1 retrotransposon, we have analyzed the cDNA products that accumulate in the cytoplasmic virus-like particles of yeast cells harboring two marked Ty1 elements. Our results indicate that Ty1 minus-strand transfer occurs in a random manner with approximately similar frequencies of intra- and intermolecular transfer. It has been observed recently that intra- and intermolecular minus-strand transfer occur at similar frequencies during replication of a complex retrovirus such as HIV-1. These results together with the observation that genetic recombination occurs with a high frequency during minus-strand synthesis suggest that both packaged RNA molecules are needed for the synthesis of one minus-strand DNA.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence DNA, Genetic, Non-U.S. Gov't *Transcription, Nucleic Acid *Retroelements Saccharomyces cerevisiae/*genetics Support, Single-Stranded/genetics Repetitive Sequences, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1998
Bergdoll M., Eltis L. D., Cameron A. D., Dumas P., Bolin J. T.
All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly Article de journal
Dans: Protein Sci, vol. 7, no. 8, p. 1661-70, 1998, (0961-8368 Journal Article).
Résumé | BibTeX | Étiquettes: *Acetyltransferases, *Evolution, Acid, Amino, Bacterial, Burkholderia/*chemistry, Crystallography, Data, Genetic, Gov't, Homology, Human, Lactoylglutathione, Lyase/*chemistry, Models, Molecular, Non-U.S., Oxygenases/chemistry, P.H.S., Phylogeny, Protein, Proteins/*chemistry, Secondary, Sequence, structure, Support, U.S., X-Ray
@article{,
title = {All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly},
author = { M. Bergdoll and L. D. Eltis and A. D. Cameron and P. Dumas and J. T. Bolin},
year = {1998},
date = {1998-01-01},
journal = {Protein Sci},
volume = {7},
number = {8},
pages = {1661-70},
abstract = {The crystal structures of three proteins of diverse function and low sequence similarity were analyzed to evaluate structural and evolutionary relationships. The proteins include a bacterial bleomycin resistance protein, a bacterial extradiol dioxygenase, and human glyoxalase I. Structural comparisons, as well as phylogenetic analyses, strongly indicate that the modern family of proteins represented by these structures arose through a rich evolutionary history that includes multiple gene duplication and fusion events. These events appear to be historically shared in some cases, but parallel and historically independent in others. A significant early event is proposed to be the establishment of metal-binding in an oligomeric ancestor prior to the first gene fusion. Variations in the spatial arrangements of homologous modules are observed that are consistent with the structural principles of three-dimensional domain swapping, but in the unusual context of the formation of larger monomers from smaller dimers or tetramers. The comparisons support a general mechanism for metalloprotein evolution that exploits the symmetry of a homooligomeric protein to originate a metal binding site and relies upon the relaxation of symmetry, as enabled by gene duplication, to establish and refine specific functions.},
note = {0961-8368
Journal Article},
keywords = {*Acetyltransferases, *Evolution, Acid, Amino, Bacterial, Burkholderia/*chemistry, Crystallography, Data, Genetic, Gov't, Homology, Human, Lactoylglutathione, Lyase/*chemistry, Models, Molecular, Non-U.S., Oxygenases/chemistry, P.H.S., Phylogeny, Protein, Proteins/*chemistry, Secondary, Sequence, structure, Support, U.S., X-Ray},
pubstate = {published},
tppubtype = {article}
}
Friant S., Heyman T., Bystrom A. S., Wilhelm M., Wilhelm F. X.
Interactions between Ty1 retrotransposon RNA and the T and D regions of the tRNA(iMet) primer are required for initiation of reverse transcription in vivo Article de journal
Dans: Mol Cell Biol, vol. 18, no. 2, p. 799-806, 1998, (0270-7306 Journal Article).
Résumé | BibTeX | Étiquettes: *Retroelements, *Transcription, Acid, Base, Binding, cerevisiae, Conformation, Data, DNA, Fungal/*metabolism, Fungal/biosynthesis, Genetic, Gov't, Met/*metabolism, Molecular, Mutagenesis, Non-U.S., Nucleic, Primers, Replication, RNA, Saccharomyces, Sequence, Sites, Support, Transfer
@article{,
title = {Interactions between Ty1 retrotransposon RNA and the T and D regions of the tRNA(iMet) primer are required for initiation of reverse transcription in vivo},
author = { S. Friant and T. Heyman and A. S. Bystrom and M. Wilhelm and F. X. Wilhelm},
year = {1998},
date = {1998-01-01},
journal = {Mol Cell Biol},
volume = {18},
number = {2},
pages = {799-806},
abstract = {Reverse transcription of the Saccharomyces cerevisiae Ty1 retrotransposon is primed by tRNA(iMet) base paired to the primer binding site (PBS) near the 5' end of Ty1 genomic RNA. The 10-nucleotide PBS is complementary to the last 10 nucleotides of the acceptor stem of tRNA(iMet). A structural probing study of the interactions between the Ty1 RNA template and the tRNA(iMet) primer showed that besides interactions between the PBS and the 3' end of tRNA(iMet), three short regions of Ty1 RNA, named boxes 0, 1, and 2.1, interact with the T and D stems and loops of tRNA(iMet). To determine if these sequences are important for the reverse transcription pathway of the Ty1 retrotransposon, mutant Ty1 elements and tRNA(iMet) were tested for the ability to support transposition. We show that the Ty1 boxes and the complementary sequences in the T and D stems and loops of tRNA(iMet) contain bases that are critical for Ty1 retrotransposition. Disruption of 1 or 2 bp between tRNA(iMet) and box 0, 1, or 2.1 dramatically decreases the level of transposition. Compensatory mutations which restore base pairing between the primer and the template restore transposition. Analysis of the reverse transcription intermediates generated inside Ty1 virus-like particles indicates that initiation of minus-strand strong-stop DNA synthesis is affected by mutations disrupting complementarity between Ty1 RNA and primer tRNA(iMet).},
note = {0270-7306
Journal Article},
keywords = {*Retroelements, *Transcription, Acid, Base, Binding, cerevisiae, Conformation, Data, DNA, Fungal/*metabolism, Fungal/biosynthesis, Genetic, Gov't, Met/*metabolism, Molecular, Mutagenesis, Non-U.S., Nucleic, Primers, Replication, RNA, Saccharomyces, Sequence, Sites, Support, Transfer},
pubstate = {published},
tppubtype = {article}
}
Levashina Elena A, Ohresser S, Lemaitre Bruno, Imler Jean-Luc
Two distinct pathways can control expression of the gene encoding the Drosophila antimicrobial peptide metchnikowin Article de journal
Dans: Journal of Molecular Biology, vol. 278, no. 3, p. 515–527, 1998, ISSN: 0022-2836.
Résumé | Liens | BibTeX | Étiquettes: Animals, Anti-Infective Agents, Antimicrobial Cationic Peptides, Base Sequence, Cloning, Gene Expression Regulation, Genes, Genetic, Genetically Modified, Glycopeptides, imler, Insect, Insect Proteins, Larva, M3i, Molecular, Mutation, Peptides, Promoter Regions, Recombinant Fusion Proteins, Reporter, Restriction Mapping, Transcription
@article{levashina_two_1998,
title = {Two distinct pathways can control expression of the gene encoding the Drosophila antimicrobial peptide metchnikowin},
author = {Elena A Levashina and S Ohresser and Bruno Lemaitre and Jean-Luc Imler},
doi = {10.1006/jmbi.1998.1705},
issn = {0022-2836},
year = {1998},
date = {1998-01-01},
journal = {Journal of Molecular Biology},
volume = {278},
number = {3},
pages = {515--527},
abstract = {Metchnikowin is a recently discovered proline-rich peptide from Drosophila with antibacterial and antifungal properties. Like most other antimicrobial peptides from insects, its expression is immune-inducible. Here we present evidence that induction of metchnikowin gene expression can be mediated either by the TOLL pathway or by the imd gene product. We show that the gene remains inducible in Toll-deficient mutants, in which the antifungal response is blocked, as well as in imd mutants, which fail to mount an antibacterial response. However, in Toll-deficient;imd double mutants, metchnikowin gene expression can no longer be detected after immune challenge. Our results suggest that expression of this peptide with dual activity can be triggered by signals generated by either bacterial or fungal infection. Cloning of the metchnikowin gene revealed the presence in the 5' flanking region of several putative cis-regulatory motifs characterized in the promoters of insect immune genes: namely, Rel sites, GATA motifs, interferon consensus response elements and NF-IL6 response elements. Establishment of transgenic fly lines in which the GFP reporter gene was placed under the control of 1.5 kb of metchnikowin gene upstream sequences indicates that this fragment is able to confer full immune inducibility and tissue specificity of expression on the transgene.},
keywords = {Animals, Anti-Infective Agents, Antimicrobial Cationic Peptides, Base Sequence, Cloning, Gene Expression Regulation, Genes, Genetic, Genetically Modified, Glycopeptides, imler, Insect, Insect Proteins, Larva, M3i, Molecular, Mutation, Peptides, Promoter Regions, Recombinant Fusion Proteins, Reporter, Restriction Mapping, Transcription},
pubstate = {published},
tppubtype = {article}
}
1997
Meister Marie, Lemaitre Bruno, Hoffmann Jules A
Antimicrobial peptide defense in Drosophila Article de journal
Dans: Bioessays, vol. 19, no. 11, p. 1019–1026, 1997, ISSN: 0265-9247.
Résumé | Liens | BibTeX | Étiquettes: Animals, Anti-Infective Agents, Gene Expression Regulation, Genetic, hoffmann, Insect Proteins, M3i, Models, Peptides, Promoter Regions, Signal Transduction
@article{meister_antimicrobial_1997,
title = {Antimicrobial peptide defense in Drosophila},
author = {Marie Meister and Bruno Lemaitre and Jules A Hoffmann},
doi = {10.1002/bies.950191112},
issn = {0265-9247},
year = {1997},
date = {1997-11-01},
journal = {Bioessays},
volume = {19},
number = {11},
pages = {1019--1026},
abstract = {Drosophila responds to a septic injury by the rapid synthesis of antimicrobial peptides. These molecules are predominantly produced by the fat body, a functional equivalent of mammalian liver, and are secreted into the hemolymph where their concentrations can reach up to 100 microM. Six distinct antibacterial peptides (plus isoforms) and one antifungal peptide have been characterized in Drosophila and their genes cloned. The induction of the gene encoding the antifungal peptide relies on the spätzle/Toll/cactus gene cassette, which is involved in the control of dorsoventral patterning in the embryo, and shows interesting structural and functional similarities with cytokine-induced activation of NF-kappa B in mammalian cells. An additional pathway, dependent on the as yet unidentified imd (for immune-deficiency) gene, is required for the full induction of the antibacterial peptide genes. Mutants deficient for the Toll and imd pathways exhibit a severely reduced survival to fungal and bacterial infections, respectively. Recent data on the molecular mechanisms underlying recognition of non-self are also discussed in this review.},
keywords = {Animals, Anti-Infective Agents, Gene Expression Regulation, Genetic, hoffmann, Insect Proteins, M3i, Models, Peptides, Promoter Regions, Signal Transduction},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M., Heyman T., Friant S., Wilhelm F. X.
Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts Article de journal
Dans: Nucleic Acids Res, vol. 25, no. 11, p. 2161-6, 1997, (0305-1048 Journal Article).
Résumé | BibTeX | Étiquettes: *Nucleic, *Transcription, Acid, Calf, Chain, Conformation, DNA, Fungal/*chemistry/metabolism, Genetic, Gov't, H, Hybridization, Non-U.S., Nucleic, Plasmids/chemistry/genetics/metabolism, Polymerase, Reaction, Replication, Retroelements/*genetics, Ribonuclease, RNA, Support, Thymus/metabolism, Transfer/chemistry
@article{,
title = {Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts},
author = { M. Wilhelm and T. Heyman and S. Friant and F. X. Wilhelm},
year = {1997},
date = {1997-01-01},
journal = {Nucleic Acids Res},
volume = {25},
number = {11},
pages = {2161-6},
abstract = {A specific terminal structure of preintegrative DNA is required for transposition of retroviruses and LTR-retrotransposons. We have used an anchored PCR technique to map the 3'ends of DNA intermediates synthesized inside yeast Ty1 and Ty3 retrotransposon virus-like particles. We find that, unlike retroviruses, Ty1 replicated DNA does not have two extra base pairs at its 3'ends. In contrast some Ty3 preintegrative DNA molecules have two extra nucleotides at the 3'end of upstream and downstream long terminal repeats. Moreover we find that some molecules of replicated Ty3 DNA have more than two extra nucleotides at the 3'end of the upstream LTR. This observation could be accounted for by imprecise RNAse H cutting of the PPT sequence. The site of Ty1 and Ty3 plus-strand strong-stop DNA termination was also examined. Our results confirm that the prominent Ty1 and Ty3 plus-strand strong-stop molecules harbor 12 tRNA templated bases but also show that some Ty1 and Ty3 plus-strand strong-stop DNA molecules harbor less tRNA templated bases. We propose that these less than full length plus-strand molecules could be active intermediates in Ty retrotransposon replication.},
note = {0305-1048
Journal Article},
keywords = {*Nucleic, *Transcription, Acid, Calf, Chain, Conformation, DNA, Fungal/*chemistry/metabolism, Genetic, Gov't, H, Hybridization, Non-U.S., Nucleic, Plasmids/chemistry/genetics/metabolism, Polymerase, Reaction, Replication, Retroelements/*genetics, Ribonuclease, RNA, Support, Thymus/metabolism, Transfer/chemistry},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M, Heyman T, Friant S, Wilhelm F X
Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts Article de journal
Dans: Nucleic Acids Res, vol. 25, no. 11, p. 2161-2166, 1997, ISBN: 9153316, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Calf Thymus/metabolism Support, DNA Replication DNA, Fungal/*chemistry/metabolism *Nucleic Acid Conformation Nucleic Acid Hybridization Plasmids/chemistry/genetics/metabolism Polymerase Chain Reaction RNA, Genetic, Non-U.S. Gov't *Transcription, Transfer/chemistry Retroelements/*genetics Ribonuclease H, Unité ARN
@article{,
title = {Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts},
author = {M Wilhelm and T Heyman and S Friant and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9153316},
isbn = {9153316},
year = {1997},
date = {1997-01-01},
journal = {Nucleic Acids Res},
volume = {25},
number = {11},
pages = {2161-2166},
abstract = {A specific terminal structure of preintegrative DNA is required for transposition of retroviruses and LTR-retrotransposons. We have used an anchored PCR technique to map the 3'ends of DNA intermediates synthesized inside yeast Ty1 and Ty3 retrotransposon virus-like particles. We find that, unlike retroviruses, Ty1 replicated DNA does not have two extra base pairs at its 3'ends. In contrast some Ty3 preintegrative DNA molecules have two extra nucleotides at the 3'end of upstream and downstream long terminal repeats. Moreover we find that some molecules of replicated Ty3 DNA have more than two extra nucleotides at the 3'end of the upstream LTR. This observation could be accounted for by imprecise RNAse H cutting of the PPT sequence. The site of Ty1 and Ty3 plus-strand strong-stop DNA termination was also examined. Our results confirm that the prominent Ty1 and Ty3 plus-strand strong-stop molecules harbor 12 tRNA templated bases but also show that some Ty1 and Ty3 plus-strand strong-stop DNA molecules harbor less tRNA templated bases. We propose that these less than full length plus-strand molecules could be active intermediates in Ty retrotransposon replication.},
note = {0305-1048
Journal Article},
keywords = {Calf Thymus/metabolism Support, DNA Replication DNA, Fungal/*chemistry/metabolism *Nucleic Acid Conformation Nucleic Acid Hybridization Plasmids/chemistry/genetics/metabolism Polymerase Chain Reaction RNA, Genetic, Non-U.S. Gov't *Transcription, Transfer/chemistry Retroelements/*genetics Ribonuclease H, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ferrandon D, Koch I, Westhof E, Nusslein-Volhard C
RNA-RNA interaction is required for the formation of specific bicoid mRNA 3' UTR-STAUFEN ribonucleoprotein particles Article de journal
Dans: EMBO J, vol. 16, no. 7, p. 1751-1758, 1997, ISBN: 9130719, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence DNA Primers Dimerization Drosophila/embryology/genetics/*physiology *Drosophila Proteins Embryo, Genetic, Messenger/*biosynthesis/*chemistry/metabolism RNA-Binding Proteins/*biosynthesis/*metabolism Ribonucleoproteins/*metabolism Trans-Activators/*biosynthesis Translation, Nonmammalian/*physiology Homeodomain Proteins/*biosynthesis Insect Proteins/biosynthesis Models, Structural Molecular Sequence Data *Nucleic Acid Conformation RNA, Unité ARN
@article{,
title = {RNA-RNA interaction is required for the formation of specific bicoid mRNA 3' UTR-STAUFEN ribonucleoprotein particles},
author = {D Ferrandon and I Koch and E Westhof and C Nusslein-Volhard},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9130719},
isbn = {9130719},
year = {1997},
date = {1997-01-01},
journal = {EMBO J},
volume = {16},
number = {7},
pages = {1751-1758},
abstract = {The formation of the anterior pattern of the Drosophila embryo is dependent on the localization of the mRNA of the morphogen Bicoid (bcd) to the anterior pole of the egg cell. Staufen protein (STAU) is required in a late step of the localization to anchor the bcd mRNA in the anterior cytoplasm. We have shown previously that endogenous STAU associates specifically with injected bcd mRNA 3'-untranslated region (UTR), resulting in the formation of characteristic RNA-protein particles that are transported along microtubules of the mitotic spindles in a directed manner. The regions recognized by STAU in this in vivo assay are predicted to form three stem-loop structures involving large double-stranded stretches. Here, we show that the STAU interaction requires a double-stranded conformation of the stems within the RNA localization signal. In addition, base pairing between two single-stranded loops plays a major role in particle formation. This loop-loop interaction is intermolecular, not intramolecular; thus dimers or multimers of the RNA localization signal must be associated with STAU in these particles. The bcd mRNA 3' UTR can also dimerize in vitro in the absence of STAU. Thus, in addition to RNA-protein interactions, RNA-RNA interaction might be involved in the formation of ribonucleoprotein particles for transport and localization.},
note = {0261-4189
Journal Article},
keywords = {Animals Base Sequence DNA Primers Dimerization Drosophila/embryology/genetics/*physiology *Drosophila Proteins Embryo, Genetic, Messenger/*biosynthesis/*chemistry/metabolism RNA-Binding Proteins/*biosynthesis/*metabolism Ribonucleoproteins/*metabolism Trans-Activators/*biosynthesis Translation, Nonmammalian/*physiology Homeodomain Proteins/*biosynthesis Insect Proteins/biosynthesis Models, Structural Molecular Sequence Data *Nucleic Acid Conformation RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Eckardt S, Romby P, Sczakiel G
Implications of RNA structure on the annealing of a potent antisense RNA directed against the human immunodeficiency virus type 1 Article de journal
Dans: Biochemistry, vol. 36, no. 42, p. 12711-12721, 1997, ISBN: 9335527, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anti-HIV Agents/*chemistry/pharmacology Base Sequence Cells, Antisense/*chemistry/*pharmacology RNA, Calf Thymus Ribonuclease T1 Software Support, Cultured Electrophoresis, Genetic, Insertional Mutagenesis, Non-U.S. Gov't Thermodynamics Transcription, Polyacrylamide Gel HIV-1/*drug effects/genetics Human Kinetics Molecular Sequence Data Mutagenesis, ROMBY, Site-Directed *Nucleic Acid Conformation Oligodeoxyribonucleotides Oligoribonucleotides/*chemistry/pharmacology RNA, Unité ARN, Viral/*chemistry/drug effects Ribonuclease H
@article{,
title = {Implications of RNA structure on the annealing of a potent antisense RNA directed against the human immunodeficiency virus type 1},
author = {S Eckardt and P Romby and G Sczakiel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9335527},
isbn = {9335527},
year = {1997},
date = {1997-01-01},
journal = {Biochemistry},
volume = {36},
number = {42},
pages = {12711-12721},
abstract = {Antisense RNA-mediated regulation in bacterial systems is related to the kinetics of RNA-RNA annealing in vitro. Here, we investigated the secondary structure of alphaY69, an effective HIV-directed antisense RNA in human cells. Purified RNA preparations contain a single conformer. The global structure was identified by a cleavage experiment under native conditions using a short complementary oligonucleotide and RNase H. Structural analyses indicate a three-domain structure of alphaY69 consisting of two stem-loop elements connected by a seven-nucleotide single-stranded hinge region. Kinetic data suggest that the formation of base pairs between a CGC triplet of alphaY69 and its target RNA is essential for fast annealing. The complementary sequence stretch of the target folds into a high-energy secondary structure. The relationship between modifications in structural elements of alphaY69 and the annealing kinetics suggested that rate-limiting steps of the annealing involve a single site of alphaY69 and do not involve its 5' or 3'-end. Further, the data indicate that both initial base-specific interactions and duplex formation are dependent on the CGC triplet of the central region of alphaY69. This mechanism represents a specific and efficient way of RNA-RNA annealing that is initiated by the interaction of unstructured RNA regions.},
note = {0006-2960
Journal Article},
keywords = {Anti-HIV Agents/*chemistry/pharmacology Base Sequence Cells, Antisense/*chemistry/*pharmacology RNA, Calf Thymus Ribonuclease T1 Software Support, Cultured Electrophoresis, Genetic, Insertional Mutagenesis, Non-U.S. Gov't Thermodynamics Transcription, Polyacrylamide Gel HIV-1/*drug effects/genetics Human Kinetics Molecular Sequence Data Mutagenesis, ROMBY, Site-Directed *Nucleic Acid Conformation Oligodeoxyribonucleotides Oligoribonucleotides/*chemistry/pharmacology RNA, Unité ARN, Viral/*chemistry/drug effects Ribonuclease H},
pubstate = {published},
tppubtype = {article}
}
Aphasizhev R, Théobald-Dietrich A, Kostyuk D, Kochetkov S N, Kisselev L, Giege R, Fasiolo F
Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides Article de journal
Dans: RNA, vol. 3, no. 8, p. 893-904, 1997, ISBN: 9257648, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/metabolism RNA, Base Sequence DNA-Directed RNA Polymerases/genetics/metabolism Deoxyribonucleotides/chemistry/*metabolism Models, Genetic, Met/chemistry/genetics/metabolism Structure-Activity Relationship Support, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Transfer/*chemistry/genetics/*metabolism RNA, Unité ARN
@article{,
title = {Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides},
author = {R Aphasizhev and A Théobald-Dietrich and D Kostyuk and S N Kochetkov and L Kisselev and R Giege and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9257648},
isbn = {9257648},
year = {1997},
date = {1997-01-01},
journal = {RNA},
volume = {3},
number = {8},
pages = {893-904},
abstract = {The contribution of the ribose 2'-hydroxyls to RNA structure and function has been analyzed, but still remains controversial. In this work, we report the use of a mutant T7 RNA polymerase as a tool in RNA studies, applied to the aspartate and methionine tRNA aminoacylation systems from yeast. Our approach consists of determining the effect of substituting natural ribonucleotides by deoxyribonucleotides in RNA and, thereby, defining the subset of important 2'-hydroxyl groups. We show that deoxyribose-containing RNA can be folded in a global conformation similar to that of natural RNA. Melting curves of tRNAs, obtained by temperature-gradient gel electrophoresis, indicate that in deoxyribo-containing molecules, the thermal stability of the tertiary network drops down, whereas the stability of the secondary structure remains unaltered. Nuclease footprinting reveals a significant increase in the accessibility of both single- and double-stranded regions. As to the functionality of the deoxyribose-containing tRNAs, their in vitro aminoacylation efficiency indicates striking differential effects depending upon the nature of the substituted ribonucleotides. Strongest decrease in charging occurs for yeast initiator tRNA(Met) transcripts containing dG or dC residues and for yeast tRNA(Asp) transcripts with dU or dG. In the aspartate system, the decreased aminoacylation capacities can be correlated with the substitution of the ribose moieties of U11 and G27, disrupting two hydrogen bond contacts with the synthetase. Altogether, this suggests that specific 2'-hydroxyl groups in tRNAs can act as determinants specifying aminoacylation identity.},
note = {1355-8382
Journal Article},
keywords = {Asp/chemistry/genetics/metabolism RNA, Base Sequence DNA-Directed RNA Polymerases/genetics/metabolism Deoxyribonucleotides/chemistry/*metabolism Models, Genetic, Met/chemistry/genetics/metabolism Structure-Activity Relationship Support, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Transfer/*chemistry/genetics/*metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1996
Lowenberger C A, Ferdig M T, Bulet Philippe, Khalili S, Hoffmann Jules A, Christensen B M
Aedes aegypti: induced antibacterial proteins reduce the establishment and development of Brugia malayi Article de journal
Dans: Exp. Parasitol., vol. 83, no. 2, p. 191–201, 1996, ISSN: 0014-4894.
Résumé | Liens | BibTeX | Étiquettes: Aedes, Analysis of Variance, Animals, Anti-Bacterial Agents, Base Sequence, Blood Proteins, Blotting, Brugia malayi, Culicidae, Defensins, DNA, Escherichia coli, Fat Body, Genetic, Gerbillinae, hoffmann, M3i, Micrococcus luteus, Microfilaria, Northern, RNA, Transcription
@article{lowenberger_aedes_1996,
title = {Aedes aegypti: induced antibacterial proteins reduce the establishment and development of Brugia malayi},
author = {C A Lowenberger and M T Ferdig and Philippe Bulet and S Khalili and Jules A Hoffmann and B M Christensen},
doi = {10.1006/expr.1996.0066},
issn = {0014-4894},
year = {1996},
date = {1996-07-01},
journal = {Exp. Parasitol.},
volume = {83},
number = {2},
pages = {191--201},
abstract = {The effect of host immune activation on the development of Brugia malayi in one susceptible and four refractory strains of Aedes aegypti and in Armigeres subalbatus was assessed. A. aegypti that were immune activated by the injection of saline or bacteria 24 hr before feeding on a B. malayi-infected gerbil had significantly reduced prevalences and mean intensities of infection from those of naive controls when exposed to bloodmeals with low (105 mf/20 microliters) and medium (160 mf/20 microliters) microfilaremias. At a higher microfilaremia (237 mf/20 microliters) there were no significant differences in mean intensities, suggesting that the number of parasites ingested may affect the host's ability to mount an effective defense response. Because the major immune proteins in A. aegypti are defensins, we did Northern analyses of fat body RNA 8 hr after immune activation or bloodfeeding. All mosquitoes demonstrated rapid transcriptional activity for defensins following immune activation by intrathoracic inoculation with either saline or bacteria. However, no strain of A. aegypti, susceptible or refractory to B. malayi, nor Ar. subalbatus produced defensin transcripts after bloodfeeding on an uninfected or a B. malayi-infected gerbil. These data suggest that inducible immune proteins of mosquitoes can reduce the prevalence and mean intensity of infections with ingested parasites, but these proteins are not expressed routinely after parasite ingestion and midgut penetration and probably do not contribute to existing refractory mechanisms. Immune proteins such as defensins, however, represent potential candidates to genetically engineer mosquitoes for resistance to filarial worms.},
keywords = {Aedes, Analysis of Variance, Animals, Anti-Bacterial Agents, Base Sequence, Blood Proteins, Blotting, Brugia malayi, Culicidae, Defensins, DNA, Escherichia coli, Fat Body, Genetic, Gerbillinae, hoffmann, M3i, Micrococcus luteus, Microfilaria, Northern, RNA, Transcription},
pubstate = {published},
tppubtype = {article}
}
Gross I, Georgel Philippe, Kappler Christine, Reichhart Jean-Marc, Hoffmann Jules A
Drosophila immunity: a comparative analysis of the Rel proteins dorsal and Dif in the induction of the genes encoding diptericin and cecropin Article de journal
Dans: Nucleic Acids Res., vol. 24, no. 7, p. 1238–1245, 1996, ISSN: 0305-1048.
Résumé | BibTeX | Étiquettes: Animals, Antimicrobial Cationic Peptides, Base Sequence, DNA Primers, DNA-Binding Proteins, Gene Expression Regulation, Genetic, hoffmann, Insect Hormones, Insect Proteins, M3i, NF-kappa B, Nuclear Proteins, Peptides, Phosphoproteins, reichhart, Transcription, Transcription Factors, Transcriptional Activation
@article{gross_drosophila_1996,
title = {Drosophila immunity: a comparative analysis of the Rel proteins dorsal and Dif in the induction of the genes encoding diptericin and cecropin},
author = {I Gross and Philippe Georgel and Christine Kappler and Jean-Marc Reichhart and Jules A Hoffmann},
issn = {0305-1048},
year = {1996},
date = {1996-04-01},
journal = {Nucleic Acids Res.},
volume = {24},
number = {7},
pages = {1238--1245},
abstract = {In Drosophila, bacterial challenge induces the rapid transcription of several genes encoding potent antibacterial peptides. The upstream sequences of the diptericin and cecropin Al genes, which have been investigated in detail, contain two, respectively one sequence element homologous to the binding site of the mammalian nuclear factor kappaB. These elements have been shown to be mandatory for immune-induced transcription of both genes. Functional studies have shown that these kappaB-related elements can be the target for the Drosophila Rel proteins dorsal and Dif. Here we present a comparative analysis of the transactivating capacities of these proteins on reporter genes fused to either the diptericin or the cecropin kappaB-related motifs. We conclude from our results: (i) the kappaB motifs of the diptericin and cecropin genes are not functionally equivalent; (ii) the dorsal and Dif proteins have distinct DNA-binding characteristics; (iii) dorsal and Dif can heterodimerize in vitro; (iv) mutants containing no copies of dorsal and a single copy of Dif retain their full capacity to express the diptericin and cecropin genes in response to challenge.},
keywords = {Animals, Antimicrobial Cationic Peptides, Base Sequence, DNA Primers, DNA-Binding Proteins, Gene Expression Regulation, Genetic, hoffmann, Insect Hormones, Insect Proteins, M3i, NF-kappa B, Nuclear Proteins, Peptides, Phosphoproteins, reichhart, Transcription, Transcription Factors, Transcriptional Activation},
pubstate = {published},
tppubtype = {article}
}
Romby P, Caillet J, Ebel C, Sacerdot C, Graffe M, Eyermann F, Brunel C, Moine H, Ehresmann C, Ehresmann B, Springer M
The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions Article de journal
Dans: EMBO J, vol. 15, no. 21, p. 5976-5987, 1996, ISBN: 8918475, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon Base Sequence Binding Sites Binding, Bacterial Gene Expression Regulation, Bacterial/chemistry/genetics/metabolism RNA, Biological Molecular Sequence Data Mutagenesis, Competitive Escherichia coli/*enzymology/*genetics/metabolism Gene Expression Regulation, Enzymologic Models, Genetic, Messenger/genetics/metabolism Repressor Proteins/genetics Support, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics Translation, ROMBY, Site-Directed Nucleic Acid Conformation Operator Regions (Genetics) RNA, Unité ARN
@article{,
title = {The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions},
author = {P Romby and J Caillet and C Ebel and C Sacerdot and M Graffe and F Eyermann and C Brunel and H Moine and C Ehresmann and B Ehresmann and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8918475},
isbn = {8918475},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {21},
pages = {5976-5987},
abstract = {Threonyl-tRNA synthetase from Escherichia coli represses the translation of its own mRNA by binding to the operator region located upstream from the ribosome binding site. The operator contains two stemloop structures which interact specifically with the homodimeric enzyme. Here, we provide in vitro and in vivo evidence that these two stem-loop structures are recognized by the enzyme in an analogous way and mimic the anticodon arm of E.coli tRNA(Thr). Determination of the stoichiometry of the different RNA-threonyl-tRNA synthetase complexes reveals that two tRNA(Thr) molecules bind to the enzyme whereas only one thrS operator interacts with the homodimeric enzyme. A model is presented in which the two anticodon-like domains of the operator bind symmetrically to the two tRNA(Thr) anticodon recognition sites (one per subunit) of the dimeric threonyl-tRNA synthetase. Although symmetrical operator-repressor interactions in transcriptional control are widespread, this report stresses the importance of such interactions in translational regulation of gene expression.},
note = {0261-4189
Journal Article},
keywords = {Anticodon Base Sequence Binding Sites Binding, Bacterial Gene Expression Regulation, Bacterial/chemistry/genetics/metabolism RNA, Biological Molecular Sequence Data Mutagenesis, Competitive Escherichia coli/*enzymology/*genetics/metabolism Gene Expression Regulation, Enzymologic Models, Genetic, Messenger/genetics/metabolism Repressor Proteins/genetics Support, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics Translation, ROMBY, Site-Directed Nucleic Acid Conformation Operator Regions (Genetics) RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Skripkin E, Ehresmann B, Ehresmann C, Marquet R
A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 11, p. 5572-5577, 1996, ISBN: 8643617, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Composition Base Sequence HIV-1/*genetics Heat Human Kinetics Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Nucleic Acid Denaturation Plasmids RNA, Genetic, MARQUET, Non-U.S. Gov't Thermodynamics Transcription, PAILLART, Unité ARN, Viral/biosynthesis/*chemistry/*metabolism Support
@article{,
title = {A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA},
author = {J C Paillart and E Skripkin and B Ehresmann and C Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8643617},
isbn = {8643617},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {11},
pages = {5572-5577},
abstract = {RNA-RNA interactions govern a number of biological processes. Several RNAs, including natural sense and antisense RNAs, interact by means of a two-step mechanism: recognition is mediated by a loop-loop complex, which is then stabilized by formation of an extended intermolecular duplex. It was proposed that the same mechanism holds for dimerization of the genomic RNA of human immunodeficiency virus type 1 (HIV-1), an event thought to control crucial steps of HIV-1 replication. However, whereas interaction between the partially self-complementary loop of the dimerization initiation site (DIS) of each monomer is well established, formation of the extended duplex remained speculative. Here we first show that in vitro dimerization of HIV-1 RNA is a specific process, not resulting from simple annealing of denatured molecules. Next we used mutants of the DIS to test the formation of the extended duplex. Four pairs of transcomplementary mutants were designed in such a way that all pairs can form the loop-loop "kissing" complex, but only two of them can potentially form the extended duplex. All pairs of mutants form heterodimers whose thermal stability, dissociation constant, and dynamics were analyzed. Taken together, our results indicate that, in contrast with the interactions between natural sense and antisense RNAs, no extended duplex is formed during dimerization of HIV-1 RNA. We also showed that 55-mer sense RNAs containing the DIS are able to interfere with the preformed HIV-1 RNA dimer.},
note = {0027-8424
Journal Article},
keywords = {Base Composition Base Sequence HIV-1/*genetics Heat Human Kinetics Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Nucleic Acid Denaturation Plasmids RNA, Genetic, MARQUET, Non-U.S. Gov't Thermodynamics Transcription, PAILLART, Unité ARN, Viral/biosynthesis/*chemistry/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Martin F, Reinbolt J, Dirheimer G, Gangloff J, Eriani G
Selection of tRNA(Asp) amber suppressor mutants having alanine, arginine, glutamine, and lysine identity Article de journal
Dans: RNA, vol. 2, no. 9, p. 919-927, 1996, ISBN: 8809018, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Alanine/genetics Arginine/genetics Base Sequence Escherichia coli/genetics Genes, Asp/*genetics *Selection (Genetics) Support, ERIANI, Genetic, Genetic Molecular Sequence Data *Mutation RNA, Non-U.S. Gov't *Suppression, Suppressor Glutamine/genetics Lysine/genetics Models, Transfer, Unité ARN
@article{,
title = {Selection of tRNA(Asp) amber suppressor mutants having alanine, arginine, glutamine, and lysine identity},
author = {F Martin and J Reinbolt and G Dirheimer and J Gangloff and G Eriani},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8809018},
isbn = {8809018},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {9},
pages = {919-927},
abstract = {Elements that confer identity to a tRNA in the cellular environment, where all aminoacyl-tRNA synthetases are competing for substrates, may be delineated by in vivo experiments using suppressor tRNAs. Here we describe the selection of active Escherichia coli tRNAAsp amber mutants and analyze their identity. Starting from a library containing randomly mutated tRNA(CUA)Asp genes, we isolated four amber suppressors presenting either lysine, alanine, or glutamine activity. Two of them, presenting mainly alanine or lysine activity, were further submitted to a second round of mutagenesis selection in order to improve their efficiency of suppression. Eleven suppressors were isolated, each containing two or three mutations. Ten presented identities of the two parental mutants, whereas one had switched from lysine to arginine identity. Analysis of the different mutants revealed (or confirmed for some nucleotides) their role as positive and/or negative determinants in AlaRS, LysRS, and ArgRS recognition. More generally, it appears that tRNAAsp presents identity characteristics closely related to those of tRNALys, as well as a structural basis for acquiring alanine or arginine identity upon moderate mutational changes; these consist of addition or suppression of the corresponding positive or negative determinants, as well as tertiary interactions. Failure to isolate aspartic acid-inserting suppressors is probably due to elimination of the important G34 identity element and its replacement by an antideterminant when changing the anticodon of the tRNAAsp to the CUA triplet.},
note = {1355-8382
Journal Article},
keywords = {Alanine/genetics Arginine/genetics Base Sequence Escherichia coli/genetics Genes, Asp/*genetics *Selection (Genetics) Support, ERIANI, Genetic, Genetic Molecular Sequence Data *Mutation RNA, Non-U.S. Gov't *Suppression, Suppressor Glutamine/genetics Lysine/genetics Models, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Romby P, Caillet J, Ebel C, Sacerdot C, Graffe M, Eyermann F, Brunel C, Moine H, Ehresmann C, Ehresmann B, Springer M
The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions Article de journal
Dans: EMBO J, vol. 15, no. 21, p. 5976-5987, 1996, ISBN: 8918475, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon Base Sequence Binding Sites Binding, Bacterial Gene Expression Regulation, Bacterial/chemistry/genetics/metabolism RNA, Biological Molecular Sequence Data Mutagenesis, Competitive Escherichia coli/*enzymology/*genetics/metabolism Gene Expression Regulation, Enzymologic Models, Genetic, Messenger/genetics/metabolism Repressor Proteins/genetics Support, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics Translation, ROMBY, Site-Directed Nucleic Acid Conformation Operator Regions (Genetics) RNA, Unité ARN
@article{,
title = {The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions},
author = {P Romby and J Caillet and C Ebel and C Sacerdot and M Graffe and F Eyermann and C Brunel and H Moine and C Ehresmann and B Ehresmann and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8918475},
isbn = {8918475},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {21},
pages = {5976-5987},
abstract = {Threonyl-tRNA synthetase from Escherichia coli represses the translation of its own mRNA by binding to the operator region located upstream from the ribosome binding site. The operator contains two stemloop structures which interact specifically with the homodimeric enzyme. Here, we provide in vitro and in vivo evidence that these two stem-loop structures are recognized by the enzyme in an analogous way and mimic the anticodon arm of E.coli tRNA(Thr). Determination of the stoichiometry of the different RNA-threonyl-tRNA synthetase complexes reveals that two tRNA(Thr) molecules bind to the enzyme whereas only one thrS operator interacts with the homodimeric enzyme. A model is presented in which the two anticodon-like domains of the operator bind symmetrically to the two tRNA(Thr) anticodon recognition sites (one per subunit) of the dimeric threonyl-tRNA synthetase. Although symmetrical operator-repressor interactions in transcriptional control are widespread, this report stresses the importance of such interactions in translational regulation of gene expression.},
note = {0261-4189
Journal Article},
keywords = {Anticodon Base Sequence Binding Sites Binding, Bacterial Gene Expression Regulation, Bacterial/chemistry/genetics/metabolism RNA, Biological Molecular Sequence Data Mutagenesis, Competitive Escherichia coli/*enzymology/*genetics/metabolism Gene Expression Regulation, Enzymologic Models, Genetic, Messenger/genetics/metabolism Repressor Proteins/genetics Support, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics Translation, ROMBY, Site-Directed Nucleic Acid Conformation Operator Regions (Genetics) RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Skripkin E, Ehresmann B, Ehresmann C, Marquet R
A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 11, p. 5572-5577, 1996, ISBN: 8643617, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Composition Base Sequence HIV-1/*genetics Heat Human Kinetics Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Nucleic Acid Denaturation Plasmids RNA, Genetic, MARQUET, Non-U.S. Gov't Thermodynamics Transcription, PAILLART, Unité ARN, Viral/biosynthesis/*chemistry/*metabolism Support
@article{,
title = {A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA},
author = {J C Paillart and E Skripkin and B Ehresmann and C Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8643617},
isbn = {8643617},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {11},
pages = {5572-5577},
abstract = {RNA-RNA interactions govern a number of biological processes. Several RNAs, including natural sense and antisense RNAs, interact by means of a two-step mechanism: recognition is mediated by a loop-loop complex, which is then stabilized by formation of an extended intermolecular duplex. It was proposed that the same mechanism holds for dimerization of the genomic RNA of human immunodeficiency virus type 1 (HIV-1), an event thought to control crucial steps of HIV-1 replication. However, whereas interaction between the partially self-complementary loop of the dimerization initiation site (DIS) of each monomer is well established, formation of the extended duplex remained speculative. Here we first show that in vitro dimerization of HIV-1 RNA is a specific process, not resulting from simple annealing of denatured molecules. Next we used mutants of the DIS to test the formation of the extended duplex. Four pairs of transcomplementary mutants were designed in such a way that all pairs can form the loop-loop "kissing" complex, but only two of them can potentially form the extended duplex. All pairs of mutants form heterodimers whose thermal stability, dissociation constant, and dynamics were analyzed. Taken together, our results indicate that, in contrast with the interactions between natural sense and antisense RNAs, no extended duplex is formed during dimerization of HIV-1 RNA. We also showed that 55-mer sense RNAs containing the DIS are able to interfere with the preformed HIV-1 RNA dimer.},
note = {0027-8424
Journal Article},
keywords = {Base Composition Base Sequence HIV-1/*genetics Heat Human Kinetics Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Nucleic Acid Denaturation Plasmids RNA, Genetic, MARQUET, Non-U.S. Gov't Thermodynamics Transcription, PAILLART, Unité ARN, Viral/biosynthesis/*chemistry/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Martin F, Reinbolt J, Dirheimer G, Gangloff J, Eriani G
Selection of tRNA(Asp) amber suppressor mutants having alanine, arginine, glutamine, and lysine identity Article de journal
Dans: RNA, vol. 2, no. 9, p. 919-927, 1996, ISBN: 8809018, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Alanine/genetics Arginine/genetics Base Sequence Escherichia coli/genetics Genes, Asp/*genetics *Selection (Genetics) Support, ERIANI, Genetic, Genetic Molecular Sequence Data *Mutation RNA, Non-U.S. Gov't *Suppression, Suppressor Glutamine/genetics Lysine/genetics Models, Transfer, Unité ARN
@article{,
title = {Selection of tRNA(Asp) amber suppressor mutants having alanine, arginine, glutamine, and lysine identity},
author = {F Martin and J Reinbolt and G Dirheimer and J Gangloff and G Eriani},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8809018},
isbn = {8809018},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {9},
pages = {919-927},
abstract = {Elements that confer identity to a tRNA in the cellular environment, where all aminoacyl-tRNA synthetases are competing for substrates, may be delineated by in vivo experiments using suppressor tRNAs. Here we describe the selection of active Escherichia coli tRNAAsp amber mutants and analyze their identity. Starting from a library containing randomly mutated tRNA(CUA)Asp genes, we isolated four amber suppressors presenting either lysine, alanine, or glutamine activity. Two of them, presenting mainly alanine or lysine activity, were further submitted to a second round of mutagenesis selection in order to improve their efficiency of suppression. Eleven suppressors were isolated, each containing two or three mutations. Ten presented identities of the two parental mutants, whereas one had switched from lysine to arginine identity. Analysis of the different mutants revealed (or confirmed for some nucleotides) their role as positive and/or negative determinants in AlaRS, LysRS, and ArgRS recognition. More generally, it appears that tRNAAsp presents identity characteristics closely related to those of tRNALys, as well as a structural basis for acquiring alanine or arginine identity upon moderate mutational changes; these consist of addition or suppression of the corresponding positive or negative determinants, as well as tertiary interactions. Failure to isolate aspartic acid-inserting suppressors is probably due to elimination of the important G34 identity element and its replacement by an antideterminant when changing the anticodon of the tRNAAsp to the CUA triplet.},
note = {1355-8382
Journal Article},
keywords = {Alanine/genetics Arginine/genetics Base Sequence Escherichia coli/genetics Genes, Asp/*genetics *Selection (Genetics) Support, ERIANI, Genetic, Genetic Molecular Sequence Data *Mutation RNA, Non-U.S. Gov't *Suppression, Suppressor Glutamine/genetics Lysine/genetics Models, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lanchy J M, Isel C, Ehresmann C, Marquet R, Ehresmann B
Structural and functional evidence that initiation and elongation of HIV-1 reverse transcription are distinct processes Article de journal
Dans: Biochimie, vol. 78, no. 11-12, p. 1087-1096, 1996, ISBN: 9150889, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/*biosynthesis/*chemistry RNA, Base Sequence Comparative Study HIV-1/*genetics/*metabolism HIV-1 Reverse Transcriptase/*metabolism Human Molecular Sequence Data *Nucleic Acid Conformation RNA, Genetic, MARQUET, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/biosynthesis/chemistry Retroviridae/metabolism Support
@article{,
title = {Structural and functional evidence that initiation and elongation of HIV-1 reverse transcription are distinct processes},
author = {J M Lanchy and C Isel and C Ehresmann and R Marquet and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9150889},
isbn = {9150889},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {11-12},
pages = {1087-1096},
abstract = {Retroviral reverse transcription starts with the extension of a cellular tRNA primer bound near the 5' end of the viral genomic RNA at a site called the primer binding site (PBS). Formation of the HIV-1 initiation complex between tRNA3(Lys), viral RNA and reverse transcriptase probably occurs during encapsidation of these components. tRNA3(Lys) is thought to be selectively packaged by interaction with the reverse transcriptase domain of the Pr160Gag-Pol precursor protein, then annealed to the PBS of viral RNA with the help of the nucleocapsid protein. tRNA3(Lys) and HIV-1 viral RNA form a highly-structured complex, with extended interactions between the two molecules. Two different modes of reverse transcription have been distinguished: initiation, a tRNA3(Lys)-specific and distributive mode of polymerization corresponding to the addition of the first five nucleotides, followed by elongation, a non-specific and processive mode of DNA synthesis. These two modes are reminiscent of the initiation and elongation processes previously observed with DNA-dependent RNA polymerases.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Amino Acyl/*biosynthesis/*chemistry RNA, Base Sequence Comparative Study HIV-1/*genetics/*metabolism HIV-1 Reverse Transcriptase/*metabolism Human Molecular Sequence Data *Nucleic Acid Conformation RNA, Genetic, MARQUET, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/biosynthesis/chemistry Retroviridae/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Lanchy J M, Ehresmann C, Grice S F Le, Ehresmann B, Marquet R
Binding and kinetic properties of HIV-1 reverse transcriptase markedly differ during initiation and elongation of reverse transcription Article de journal
Dans: EMBO J, vol. 15, no. 24, p. 7178-7187, 1996, ISBN: 9003793, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: DNA Primers HIV-1/*enzymology HIV-1 Reverse Transcriptase/*metabolism Kinetics Protein Binding Support, Genetic, Genetic *Transcription, MARQUET, Non-U.S. Gov't Support, P.H.S. Templates, U.S. Gov't, Unité ARN
@article{,
title = {Binding and kinetic properties of HIV-1 reverse transcriptase markedly differ during initiation and elongation of reverse transcription},
author = {J M Lanchy and C Ehresmann and S F Le Grice and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9003793},
isbn = {9003793},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {24},
pages = {7178-7187},
abstract = {We recently showed that primer tRNA3Lys, human immunodeficiency virus type 1 (HIV-1) RNA and HIV-1 reverse transcriptase (RT) form a specific complex of initiation of reverse transcription that can be functionally distinguished from the elongation complex, which can be obtained by substituting an 18mer oligodeoxyribonucleotide (ODN) for the natural primer (Isel et al., 1996). Here, we compared the binding properties and the single and multiple turnover kinetics of HIV-1 RT in the initiation and elongation complexes. Even though the equilibrium dissociation constants of HIV-1 RT are not very different for the two complexes, RT dissociates approximately 200-fold faster from the initiation complex. Furthermore, nucleotide incorporation by the pre-formed primer-template-RT complexes is reduced by a approximately 50-fold factor during initiation of reverse transcription, compared with elongation. As a consequence, processivity of HIV-1 RT in the initiation complex is close to unity, while it increases by four orders of magnitude during elongation, as expected for a replication enzyme. This processivity change is reminiscent of the transition from initiation to elongation of transcription. Furthermore, our results indicate that the post-transcriptional modifications of tRNA3Lys play a role similar to that of the sigma factor in transcription by the Escherichia coli RNA polymerase: they favour the formation of the specific initiation complex but do not affect the polymerization rate of the bound enzyme.},
note = {0261-4189
Journal Article},
keywords = {DNA Primers HIV-1/*enzymology HIV-1 Reverse Transcriptase/*metabolism Kinetics Protein Binding Support, Genetic, Genetic *Transcription, MARQUET, Non-U.S. Gov't Support, P.H.S. Templates, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Hubert N, Walczak R, Carbon P, Krol A
A protein binds the selenocysteine insertion element in the 3'-UTR of mammalian selenoprotein mRNAs Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 3, p. 464-469, 1996, ISBN: 8602359, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence DNA Transposable Elements/*genetics Molecular Sequence Data Protein Binding Proteins/*genetics/metabolism RNA, Genetic, Messenger/genetics/*metabolism Rats Selenocysteine/genetics/*metabolism Support, Non-U.S. Gov't Translation, Unité ARN
@article{,
title = {A protein binds the selenocysteine insertion element in the 3'-UTR of mammalian selenoprotein mRNAs},
author = {N Hubert and R Walczak and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8602359},
isbn = {8602359},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {3},
pages = {464-469},
abstract = {Several gene products are involved in co-translational insertion of selenocysteine by the tRNA(Sec). In addition, a stem-loop structure in the mRNAs coding for selenoproteins is essential to mediate the selection of the proper selenocysteine UGA codon. Interestingly, in eukaryotic selenoprotein mRNAs, this stem-loop structure, the selenocysteine insertion sequence (SECIS) element, resides in the 3'-untranslated region, far downstream of the UGA codon. In view of unravelling the underlying complex mechanism, we have attempted to detect RNA-binding proteins with specificity for the SECIS element. Using mobility shift assays, we could show that a protein, present in different types of mammalian cell extracts, possesses the capacity of binding the SECIS element of the selenoprotein glutathione peroxidase (GPx) mRNA. We have termed this protein SBP, for Secis Binding Protein. Competition experiments attested that the binding is highly specific and UV cross-linking indicated that the protein has an apparent molecular weight in the range of 60-65 kDa. Finally, some data suggest that the SECIS elements in the mRNAs of GPx and another selenoprotein, type I iodothyronine 5' deiodinase, recognize the same SBP protein. This constitutes the first report of the existence of a 3' UTR binding protein possibly involved in the eukaryotic selenocysteine insertion mechanism.},
note = {0305-1048
Journal Article},
keywords = {Animals Base Sequence DNA Transposable Elements/*genetics Molecular Sequence Data Protein Binding Proteins/*genetics/metabolism RNA, Genetic, Messenger/genetics/*metabolism Rats Selenocysteine/genetics/*metabolism Support, Non-U.S. Gov't Translation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Benard L, Philippe C, Ehresmann B, Ehresmann C, Portier C
Pseudoknot and translational control in the expression of the S15 ribosomal protein Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 568-576, 1996, ISBN: 8955900, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Molecular Sequence Data Nucleic Acid Conformation Ribosomal Proteins/*biosynthesis/chemistry/genetics/metabolism Structure-Activity Relationship Support, Genetic, Non-U.S. Gov't *Translation, Unité ARN
@article{,
title = {Pseudoknot and translational control in the expression of the S15 ribosomal protein},
author = {L Benard and C Philippe and B Ehresmann and C Ehresmann and C Portier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955900},
isbn = {8955900},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {568-576},
abstract = {Translational autocontrol of the expression of the ribosomal protein S15 proceeds through the transitory formation of a pseudoknot. A synopsis of the known data is used to propose a molecular model of the mechanism involved and for the role of the pseudoknot. This latter structure is able to recruit 30S ribosomal subunits to initiate translation, but also to bind S15 and to stop translation by trapping the ribosome on its loading site. Information on the S15 protein recognition of the messenger RNA site was deduced from mutational analyses and chemical probing. A comparison of this messenger site with the S15 ribosomal binding site was conducted by analysing hydroxyl radical footprintings of these two sites. The existence of two subsites in 16S RNA suggests that the ribosomal protein S15 might present either two different binding sites or at least one common subsite. Clues for the presence of a common site between the messenger and 16S RNA are given which cannot rule out that recognition specificity is linked to a few other determinants. Whether these determinants are different or not remains an open question.},
note = {0300-9084
Journal Article},
keywords = {Base Sequence Molecular Sequence Data Nucleic Acid Conformation Ribosomal Proteins/*biosynthesis/chemistry/genetics/metabolism Structure-Activity Relationship Support, Genetic, Non-U.S. Gov't *Translation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Becker H D, Giege R, Kern D
Identity of prokaryotic and eukaryotic tRNA(Asp) for aminoacylation by aspartyl-tRNA synthetase from Thermus thermophilus Article de journal
Dans: Biochemistry, vol. 35, no. 23, p. 7447-7458, 1996, ISBN: 8652522, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Substrate Specificity Support, Amino Acid Sequence Anticodon Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Comparative Study Escherichia coli Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Asp/biosynthesis/*metabolism RNA, Genetic, Non-U.S. Gov't Thermus thermophilus/*enzymology Transcription, Phe/biosynthesis/metabolism Recombinant Proteins/chemistry/metabolism Saccharomyces cerevisiae Sequence Homology, Transfer, Unité ARN
@article{,
title = {Identity of prokaryotic and eukaryotic tRNA(Asp) for aminoacylation by aspartyl-tRNA synthetase from Thermus thermophilus},
author = {H D Becker and R Giege and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8652522},
isbn = {8652522},
year = {1996},
date = {1996-01-01},
journal = {Biochemistry},
volume = {35},
number = {23},
pages = {7447-7458},
abstract = {The aspartate identity of tRNA for AspRS from Thermus thermophilus has been investigated by kinetic analysis of the aspartylation reaction of different tRNA molecules and their variants as well as of tRNAPhe variants with transplanted aspartate identity elements. It is shown that G10, G34, U35, C36, C38, and G73 determine recognition and aspartylation of yeast and T.thermophilus tRNA(Asp) by the thermophilic AspRS. This set of nucleotides specifies also tRNA aspartylation in the homologous yeast and Escherichia coli systems. Structural considerations indicate that the major aspartate identity elements interact with amino acids conserved in all AspRSs. It follows that the structural features of tRNA and synthetase specifying aspartylation are mainly conserved in various structural contexts and in organisms adapted to different life conditions. Mutations of tRNA identity elements provoke drastic losses of charging in the heterologous system involving yeast tRNA(Asp) and T. thermophilus AspRS. In the homologous systems, the mutational effects are less pronounced. However, effects in E. coli and T. thermophilus exceed those in yeast which are particularly moderate, indicating variations in the individual contributions of identity elements for aspartylation in prokaryotes and eukaryotes. Analysis of multiple tRNA mutants reveals cooperativity between the cluster of determinants of the anticodon loop and the additional determinants G10 and G73 for efficient aspartylation in the thermophilic system, suggesting that conformational changes trigger formation of the functional tRNA/synthetase complex.},
note = {0006-2960
Journal Article},
keywords = {Amino Acid Substrate Specificity Support, Amino Acid Sequence Anticodon Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Comparative Study Escherichia coli Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Asp/biosynthesis/*metabolism RNA, Genetic, Non-U.S. Gov't Thermus thermophilus/*enzymology Transcription, Phe/biosynthesis/metabolism Recombinant Proteins/chemistry/metabolism Saccharomyces cerevisiae Sequence Homology, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Arts E J, Stetor S R, Li X, Rausch J W, Howard K J, Ehresmann B, North T W, Wohrl B M, Goody R S, Wainberg M A, Grice S F
Dans: Proc Natl Acad Sci U S A, vol. 93, no. 19, p. 10063-10068, 1996, ISBN: 8816751, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/chemistry/*metabolism RNA, Animals Base Sequence Cats DNA, Equine/genetics/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Non-U.S. Gov't Support, P.H.S. Templates, Transfer, U.S. Gov't, Unité ARN, Viral HIV-1/genetics/*metabolism Horses Human Infectious Anemia Virus, Viral/*biosynthesis Genome, Viral/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism SIV/genetics/*metabolism Support
@article{,
title = {Initiation of (-) strand DNA synthesis from tRNA(3Lys) on lentiviral RNAs: implications of specific HIV-1 RNA-tRNA(3Lys) interactions inhibiting primer utilization by retroviral reverse transcriptases},
author = {E J Arts and S R Stetor and X Li and J W Rausch and K J Howard and B Ehresmann and T W North and B M Wohrl and R S Goody and M A Wainberg and S F Grice},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8816751},
isbn = {8816751},
year = {1996},
date = {1996-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {93},
number = {19},
pages = {10063-10068},
abstract = {Initiation of minus (-) strand DNA synthesis was examined on templates containing R, U5, and primer-binding site regions of the human immunodeficiency virus type 1 (HIV-1), feline immunodeficiency virus (FIV), and equine infectious anemia virus (EIAV) genomic RNA. DNA synthesis was initiated from (i) an oligoribonucleotide complementary to the primer-binding sites, (ii) synthetic tRNA(3Lys), and (iii) natural tRNA(3Lys), by the reverse transcriptases of HIV-1, FIV, EIAV, simian immunodeficiency virus, HIV type 2 (HIV-2), Moloney murine leukemia virus, and avian myeloblastosis virus. All enzymes used an oligonucleotide on wild-type HIV-1 RNA, whereas only a limited number initiated (-) strand DNA synthesis from either tRNA(3Lys). In contrast, all enzymes supported efficient tRNA(3Lys)-primed (-) strand DNA synthesis on the genomes of FIV and EIAV. This may be in part attributable to the observation that the U5-inverted repeat stem-loop of the EIAV and FIV genomes lacks an A-rich loop shown with HIV-1 to interact with the U-rich tRNA anticodon loop. Deletion of this loop in HIV-1 RNA, or disrupting a critical loop-loop complex by tRNA(3Lys) extended by 9 nt, restored synthesis of HIV-1 (-) strand DNA from primer tRNA(3Lys) by all enzymes. Thus, divergent evolution of lentiviruses may have resulted in different mechanisms to use the same host tRNA for initiation of reverse transcription.},
note = {0027-8424
Journal Article},
keywords = {Amino Acyl/chemistry/*metabolism RNA, Animals Base Sequence Cats DNA, Equine/genetics/*metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Non-U.S. Gov't Support, P.H.S. Templates, Transfer, U.S. Gov't, Unité ARN, Viral HIV-1/genetics/*metabolism Horses Human Infectious Anemia Virus, Viral/*biosynthesis Genome, Viral/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism SIV/genetics/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
1995
Levashina Elena A, Ohresser S, Bulet Philippe, Reichhart Jean-Marc, Hetru Charles, Hoffmann Jules A
Metchnikowin, a novel immune-inducible proline-rich peptide from Drosophila with antibacterial and antifungal properties Article de journal
Dans: Eur. J. Biochem., vol. 233, no. 2, p. 694–700, 1995, ISSN: 0014-2956.
Résumé | BibTeX | Étiquettes: Animals, Anti-Bacterial Agents, Antifungal Agents, Antimicrobial Cationic Peptides, bacteria, Base Sequence, Cells, Chromosome Mapping, Cloning, Cultured, Genetic, hoffmann, M3i, Molecular, Peptides, Proline, reichhart, Transcription
@article{levashina_metchnikowin_1995,
title = {Metchnikowin, a novel immune-inducible proline-rich peptide from Drosophila with antibacterial and antifungal properties},
author = {Elena A Levashina and S Ohresser and Philippe Bulet and Jean-Marc Reichhart and Charles Hetru and Jules A Hoffmann},
issn = {0014-2956},
year = {1995},
date = {1995-10-01},
journal = {Eur. J. Biochem.},
volume = {233},
number = {2},
pages = {694--700},
abstract = {One of the characteristics of the host defense of higher insects is the rapid and transient synthesis of a variety of potent antimicrobial peptides. To date, several distinct inducible antimicrobial peptides or peptide families have been totally or partially characterized. We present here the isolation and characterization of a novel 26-residue proline-rich immune-inducible peptide from Drosophila, which exhibits both antibacterial (Gram-positive) and antifungal activities. Peptide sequencing and cDNA cloning indicate the presense of two isoforms in our Drosophila Oregon strain, which differ by one residue (His compared to Arg) as a consequence of a single nucleotide change. The gene, which maps in position 52A1-2 on the right arm of the second chromosome, is expressed in the fat body after immune challenge. The novel peptide, which we propose to name metchnikowin, is a member of a family of proline-rich peptides, and we discuss the possible evolutionary relationships within this family.},
keywords = {Animals, Anti-Bacterial Agents, Antifungal Agents, Antimicrobial Cationic Peptides, bacteria, Base Sequence, Cells, Chromosome Mapping, Cloning, Cultured, Genetic, hoffmann, M3i, Molecular, Peptides, Proline, reichhart, Transcription},
pubstate = {published},
tppubtype = {article}
}
Georgel Philippe, Kappler Christine, Langley E, Gross I, Nicolas E, Reichhart Jean-Marc, Hoffmann Jules A
Drosophila immunity. A sequence homologous to mammalian interferon consensus response element enhances the activity of the diptericin promoter Article de journal
Dans: Nucleic Acids Res., vol. 23, no. 7, p. 1140–1145, 1995, ISSN: 0305-1048.
Résumé | BibTeX | Étiquettes: Animals, Base Sequence, CCAAT-Enhancer-Binding Proteins, DNA, DNA-Binding Proteins, Genes, Genetic, hoffmann, Immunity, Insect, Insect Hormones, Insect Proteins, interferons, Lipopolysaccharides, M3i, NF-kappa B, Nuclear Proteins, Plasmids, Promoter Regions, reichhart, Up-Regulation
@article{georgel_drosophila_1995,
title = {Drosophila immunity. A sequence homologous to mammalian interferon consensus response element enhances the activity of the diptericin promoter},
author = {Philippe Georgel and Christine Kappler and E Langley and I Gross and E Nicolas and Jean-Marc Reichhart and Jules A Hoffmann},
issn = {0305-1048},
year = {1995},
date = {1995-04-01},
journal = {Nucleic Acids Res.},
volume = {23},
number = {7},
pages = {1140--1145},
abstract = {Bacterial challenge of larvae or adults of Drosophila induces the rapid transcription of several genes encoding antibacterial peptides with a large spectrum of activity. One of these peptides, the 82-residue anti-gram negative diptericin, is encoded by a single intronless gene and we are investigating the control of expression of this gene. Previous studies using both transgenic experiments and footprint analysis have highlighted the role in the induction of this gene of a 30 nucleotide region which contains three partially overlapping motifs with sequence homology to mammalian NF-kappa B and NF-IL6 response elements and to the GAAANN sequence present in the interferon consensus response elements of some mammalian interferon-induced genes. We now show that the latter sequence binds in immune responsive tissues (fat body, blood cells) of Drosophila a approximately 45 kDa polypeptide which cross-reacts with a polyserum directed against mammalian interferon Regulatory Factor-I. Using a transfection assay of Drosophila tumorous blood cells, we show that the GAAANN sequence positively regulates the activity of the diptericin promoter. We propose that this motif cooperatively interacts with the other response elements in the regulation of the diptericin gene expression.},
keywords = {Animals, Base Sequence, CCAAT-Enhancer-Binding Proteins, DNA, DNA-Binding Proteins, Genes, Genetic, hoffmann, Immunity, Insect, Insect Hormones, Insect Proteins, interferons, Lipopolysaccharides, M3i, NF-kappa B, Nuclear Proteins, Plasmids, Promoter Regions, reichhart, Up-Regulation},
pubstate = {published},
tppubtype = {article}
}
Heyman T., Agoutin B., Friant S., Wilhelm F. X., Wilhelm M. L.
Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition Article de journal
Dans: J Mol Biol, vol. 253, no. 2, p. 291-303, 1995, (0022-2836 Journal Article).
Résumé | BibTeX | Étiquettes: *DNA, *Genes, *Repetitive, *Retroelements, Acid, Base, C/analysis, cerevisiae/genetics/*virology, Chain, Cloning, Data, DNA, Fungal, Fungal/biosynthesis, Genes, Genetic, Genome, Gov't, Mapping, Molecular, Non-U.S., Nucleic, pol, Poly, Polymerase, Primers, Reaction, Replication, Restriction, Saccharomyces, Sequence, Sequences, Support, Transcription, Viral, Viral/*biosynthesis
@article{,
title = {Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition},
author = { T. Heyman and B. Agoutin and S. Friant and F. X. Wilhelm and M. L. Wilhelm},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {253},
number = {2},
pages = {291-303},
abstract = {Long terminal repeat elements and retroviruses require primers for initiation of minus and plus-strand DNA synthesis by reverse transcriptase. Here we demonstrate genetically that plus-strand DNA synthesis of the yeast Ty1 element is initiated at two sites located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the pol gene in the integrase coding sequence (PPT2). A consequence of the presence of two PPTs is that Ty1 plus-strand DNA exists as segments at some time during replication. Three fragments have been identified: the plus-strand strong-stop DNA initiated at PPT1, a downstream fragment initiated at PPT2 and an upstream fragment spanning the 5'-terminal part of Ty1 and a portion of the TyB gene. Characterization of the 3' ends of the plus-strand DNA fragments reveals (1) that the upstream fragment is elongated beyond PPT2 creating a plus-strand overlap and (2) that the majority of plus-strand strong-stop DNA fragments bear a copy of the minus-strand primer binding site in agreement with the accepted model of retroviral genomic RNA reverse transcription. The two polypurine tracts, PPT1 and PPT2, have an identical sequence GGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.},
note = {0022-2836
Journal Article},
keywords = {*DNA, *Genes, *Repetitive, *Retroelements, Acid, Base, C/analysis, cerevisiae/genetics/*virology, Chain, Cloning, Data, DNA, Fungal, Fungal/biosynthesis, Genes, Genetic, Genome, Gov't, Mapping, Molecular, Non-U.S., Nucleic, pol, Poly, Polymerase, Primers, Reaction, Replication, Restriction, Saccharomyces, Sequence, Sequences, Support, Transcription, Viral, Viral/*biosynthesis},
pubstate = {published},
tppubtype = {article}
}
Keith G., Dirheimer G.
Postlabeling: a sensitive method for studying DNA adducts and their role in carcinogenesis Article de journal
Dans: Curr Opin Biotechnol, vol. 6, no. 1, p. 3-11, 1995, (0958-1669 Journal Article Review Review, Academic).
Résumé | BibTeX | Étiquettes: *Cell, *Genome, Adducts/*analysis, and, Animals, Base, Cell, Conditions/genetics/pathology, Data, Dilution, Division, DNA, Genetic, Gov't, Human, Models, Molecular, Mutagenesis, Neoplasms/*genetics/pathology, Neoplastic, Non-U.S., Phosphorus, Precancerous, Radioisotope, Radioisotopes, Sensitivity, Sequence, Specificity, Support, Technique, Transformation, Xenobiotics
@article{,
title = {Postlabeling: a sensitive method for studying DNA adducts and their role in carcinogenesis},
author = { G. Keith and G. Dirheimer},
year = {1995},
date = {1995-01-01},
journal = {Curr Opin Biotechnol},
volume = {6},
number = {1},
pages = {3-11},
abstract = {The covalent binding of xenobiotics to DNA is an important trigger of the multistage process that leads to carcinogenesis. 32P-postlabeling represents a highly sensitive method for biomonitoring exposure to genotoxic agents and for cancer risk assessment; it is capable of detecting less than one DNA adduct per human genome. Recent improvements to the technique have shown that the resistance of adducted DNA to enzyme digestion may lead to an overestimation of the number of different adducts present in a sample.},
note = {0958-1669
Journal Article
Review
Review, Academic},
keywords = {*Cell, *Genome, Adducts/*analysis, and, Animals, Base, Cell, Conditions/genetics/pathology, Data, Dilution, Division, DNA, Genetic, Gov't, Human, Models, Molecular, Mutagenesis, Neoplasms/*genetics/pathology, Neoplastic, Non-U.S., Phosphorus, Precancerous, Radioisotope, Radioisotopes, Sensitivity, Sequence, Specificity, Support, Technique, Transformation, Xenobiotics},
pubstate = {published},
tppubtype = {article}
}
Lemaitre Bruno, Meister Marie, Govind S, Georgel Philippe, Steward R, Reichhart Jean-Marc, Hoffmann Jules A
Functional analysis and regulation of nuclear import of dorsal during the immune response in Drosophila Article de journal
Dans: EMBO J., vol. 14, no. 3, p. 536–545, 1995, ISSN: 0261-4189.
Résumé | BibTeX | Étiquettes: Animals, Anti-Bacterial Agents, Anti-Infective Agents, Antimicrobial Cationic Peptides, Biological Transport, Cell Nucleus, Cell Surface, DNA-Binding Proteins, Fat Body, Gene Expression Regulation, Genetic, hoffmann, Immunity, Immunohistochemistry, Insect Hormones, Insect Proteins, M3i, Melanins, Membrane Glycoproteins, Mutation, Neoplasms, Nuclear Proteins, Phosphoproteins, Receptors, reichhart, Signal Transduction, Toll-Like Receptors, Transcription, Transcription Factors
@article{lemaitre_functional_1995,
title = {Functional analysis and regulation of nuclear import of dorsal during the immune response in Drosophila},
author = {Bruno Lemaitre and Marie Meister and S Govind and Philippe Georgel and R Steward and Jean-Marc Reichhart and Jules A Hoffmann},
issn = {0261-4189},
year = {1995},
date = {1995-01-01},
journal = {EMBO J.},
volume = {14},
number = {3},
pages = {536--545},
abstract = {In addition to its function in embryonic development, the NF-kappa B/rel-related gene dorsal (dl) of Drosophila is expressed in larval and adult fat body where its RNA expression is enhanced upon injury. Injury also leads to a rapid nuclear translocation of dl from the cytoplasm in fat body cells. Here we present data which strongly suggest that the nuclear localization of dl during the immune response is controlled by the Toll signaling pathway, comprising gene products that participate in the intracellular part of the embryonic dorsoventral pathway. We also report that in mutants such as Toll or cactus, which exhibit melanotic tumor phenotypes, dl is constitutively nuclear. Together, these results point to a potential link between the Toll signaling pathway and melanotic tumor induction. Although dl has been shown previously to bind to kappa B-related motifs within the promoter of the antibacterial peptide coding gene diptericin, we find that injury-induced expression of diptericin can occur in the absence of dl. Furthermore, the melanotic tumor phenotype of Toll and cactus is not dl dependent. These data underline the complexity of the Drosophila immune response. Finally, we observed that like other rel proteins, dl can control the level of its own transcription.},
keywords = {Animals, Anti-Bacterial Agents, Anti-Infective Agents, Antimicrobial Cationic Peptides, Biological Transport, Cell Nucleus, Cell Surface, DNA-Binding Proteins, Fat Body, Gene Expression Regulation, Genetic, hoffmann, Immunity, Immunohistochemistry, Insect Hormones, Insect Proteins, M3i, Melanins, Membrane Glycoproteins, Mutation, Neoplasms, Nuclear Proteins, Phosphoproteins, Receptors, reichhart, Signal Transduction, Toll-Like Receptors, Transcription, Transcription Factors},
pubstate = {published},
tppubtype = {article}
}
Zenkova M, Ehresmann C, Caillet J, Springer M, Karpova G, Ehresmann B, Romby P
Dans: Eur J Biochem, vol. 231, no. 3, p. 726-735, 1995, ISBN: 7544283, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Alkylation Base Sequence Cross-Linking Reagents Escherichia coli/enzymology/*genetics Molecular Sequence Data Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/*chemistry/genetics RNA-Binding Proteins/*chemistry/genetics Support, Genetic, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics *Translation, ROMBY, Unité ARN
@article{,
title = {A novel approach to introduce site-directed specific cross-links within RNA-protein complexes. Application to the Escherichia coli threonyl-tRNA synthetase/translational operator complex},
author = {M Zenkova and C Ehresmann and J Caillet and M Springer and G Karpova and B Ehresmann and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7544283},
isbn = {7544283},
year = {1995},
date = {1995-01-01},
journal = {Eur J Biochem},
volume = {231},
number = {3},
pages = {726-735},
abstract = {We describe a methodology which allows the introduction of a photoactivatable azido group at specific internal positions of any RNA in order to identify the neighboring elements of an interacting protein. The first step involves site-directed modification of the target RNA with an antisense oligodeoxyribonucleotide bearing, at its 3' or 5' phosphate, a 4-[-N-(2-chloroethyl)-N-methylamino]benzylmethylamino group. Position N7 of a guanine residue located in the close vicinity of the hybrid is the main target for alkylation. The antisense oligodeoxyribonucleotide is then removed by acidic pH treatment and a photoreactive reagent (2,4-dinitro-5-fluorophenylazide) is condensed to the modified nucleotide. This method was used to induce specific cross-links between Escherichia coli threonyl-tRNA synthetase and the leader region of threonyl-tRNA synthetase mRNA, which is involved in translational feedback regulation. Control experiments revealed that the modification affects neither the structure of the mRNA nor the interaction with the enzyme. More than 50% of the modified mRNA complexed with threonyl-tRNA synthetase can be cross-linked to the enzyme, depending on the nucleotide modified.},
note = {0014-2956
Journal Article},
keywords = {Alkylation Base Sequence Cross-Linking Reagents Escherichia coli/enzymology/*genetics Molecular Sequence Data Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/*chemistry/genetics RNA-Binding Proteins/*chemistry/genetics Support, Genetic, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics *Translation, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Sturchler-Pierrat C, Hubert N, Totsuka T, Mizutani T, Carbon P, Krol A
Selenocysteylation in eukaryotes necessitates the uniquely long aminoacyl acceptor stem of selenocysteine tRNA(Sec) Article de journal
Dans: J Biol Chem, vol. 270, no. 31, p. 18570-18574, 1995, ISBN: 7629188, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Animals Base Composition Base Sequence Cattle Eukaryotic Cells Kinetics Molecular Sequence Data Mutagenesis, Amino Acid-Specific RNA, Amino Acyl/*biosynthesis/*genetics/metabolism Selenocysteine/*biosynthesis Sequence Deletion Serine-tRNA Ligase/*metabolism Structure-Activity Relationship Support, Genetic, Non-U.S. Gov't Transcription, Site-Directed Phylogeny *RNA, Transfer, Unité ARN
@article{,
title = {Selenocysteylation in eukaryotes necessitates the uniquely long aminoacyl acceptor stem of selenocysteine tRNA(Sec)},
author = {C Sturchler-Pierrat and N Hubert and T Totsuka and T Mizutani and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7629188},
isbn = {7629188},
year = {1995},
date = {1995-01-01},
journal = {J Biol Chem},
volume = {270},
number = {31},
pages = {18570-18574},
abstract = {Selenocysteine synthesis is achieved on a specific tRNA, tRNA(Sec), which is first charged with serine to yield seryl-tRNA(Sec). Eukaryotic tRNA(Sec) exhibits an aminoacyl acceptor stem with a unique length of 9 base pairs. Within this stem, two base pairs, G5a.U67b and U6.U67, drew our attention, whose non-Watson-Crick status is maintained in the course of evolution either through U6.U67 base conservation or base covariation at G5a.U67b. Single or double point mutations were performed, which modified the identity of either or both of the base pairs. Serylation by seryl-tRNA synthetase was unaffected by substitutions at either G5a.U67b or U6.U67. Instead, and quite surprisingly, changing G5a.U67b and U6.U67 to G5a-C67b/U6.G67 or G5a-C67b/C6-G67 gave rise to a tRNA(Sec) mutant exhibiting a gain of function in serylation. This finding sheds light on the negative influence born by a few base pairs in the acceptor stem of tRNA(Sec) on its serylation abilities. The tRNA(Sec) capacities to support selenocysteylation were next examined with regard to a possible role played by the two non-Watson-Crick base pairs and the unique length of the acceptor stem. It first emerges from our study that tRNA(Sec) transcribed in vitro is able to support selenocysteylation. Second, none of the point mutations engineered at G5a.U67b and/or U6.U67 significantly modified the selenocysteylation level. In contrast, reduction of the acceptor stem length to 8 base pairs led tRNA(Sec) to lose its ability to efficiently support selenocysteylation. Thus, our study provides strong evidence that the length of the acceptor stem is of prime importance for the serine to selenocysteine conversion step.},
note = {0021-9258
Journal Article},
keywords = {Acylation Animals Base Composition Base Sequence Cattle Eukaryotic Cells Kinetics Molecular Sequence Data Mutagenesis, Amino Acid-Specific RNA, Amino Acyl/*biosynthesis/*genetics/metabolism Selenocysteine/*biosynthesis Sequence Deletion Serine-tRNA Ligase/*metabolism Structure-Activity Relationship Support, Genetic, Non-U.S. Gov't Transcription, Site-Directed Phylogeny *RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Philippe C, Benard L, Portier C, Westhof E, Ehresmann B, Ehresmann C
Molecular dissection of the pseudoknot governing the translational regulation of Escherichia coli ribosomal protein S15 Article de journal
Dans: Nucleic Acids Res, vol. 23, no. 1, p. 18-28, 1995, ISBN: 7532857, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial/genetics/metabolism RNA, Base Sequence Binding Sites/genetics Escherichia coli/*genetics/metabolism Models, Genetic, Messenger/genetics/metabolism Ribosomal Proteins/*chemistry/*genetics/metabolism Support, Molecular Molecular Sequence Data Mutation Protein Conformation RNA, Non-U.S. Gov't Thermodynamics *Translation, Unité ARN
@article{,
title = {Molecular dissection of the pseudoknot governing the translational regulation of Escherichia coli ribosomal protein S15},
author = {C Philippe and L Benard and C Portier and E Westhof and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7532857},
isbn = {7532857},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Res},
volume = {23},
number = {1},
pages = {18-28},
abstract = {The ribosomal protein S15 controls its own translation by binding to a mRNA region overlapping the ribosome binding site. That region of the mRNA can fold in two mutually exclusive conformations that are in dynamic equilibrium: a structure with two hairpins and a pseudoknot. A mutational analysis provided evidence for the existence and requirement of the pseudoknot for translational control in vivo and S15 recognition in vitro. In this study, we used chemical probing to analyze the structural consequences of mutations and their effect on the stem-loop/pseudoknot equilibrium. Interactions between S15 and the pseudoknot structure were further investigated by footprinting experiments. These data, combined with computer modelling and the previously published data on S15 binding and in vivo control, provide important clues on pseudoknot formation and S15 recognition. An unexpected result is that the relevant control element, here the pseudoknot form, can exist in a variety of topologically equivalent structures recognizable and shapable by S15. S15 sits on the deep groove of the co-axial stack and makes contacts with both stems, shielding the bridging adenine. The only specific sequence determinants are found in the helix common to the pseudoknot and the hairpin structures.},
note = {0305-1048
Journal Article},
keywords = {Bacterial/genetics/metabolism RNA, Base Sequence Binding Sites/genetics Escherichia coli/*genetics/metabolism Models, Genetic, Messenger/genetics/metabolism Ribosomal Proteins/*chemistry/*genetics/metabolism Support, Molecular Molecular Sequence Data Mutation Protein Conformation RNA, Non-U.S. Gov't Thermodynamics *Translation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Kreutzer R, Kern D, Giege R, Rudinger J
Footprinting of tRNA(Phe) transcripts from Thermus thermophilus HB8 with the homologous phenylalanyl-tRNA synthetase reveals a novel mode of interaction Article de journal
Dans: Nucleic Acids Res, vol. 23, no. 22, p. 4598-4602, 1995, ISBN: 8524648, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Composition Base Sequence Cloning, Genetic, Molecular Comparative Study Escherichia coli Kinetics Models, Phe/biosynthesis/chemistry/*metabolism Thermus thermophilus/*enzymology/*genetics *Transcription, Structural Molecular Sequence Data Nucleic Acid Conformation Phenylalanine-tRNA Ligase/*metabolism Protein Binding RNA, Transfer, Unité ARN
@article{,
title = {Footprinting of tRNA(Phe) transcripts from Thermus thermophilus HB8 with the homologous phenylalanyl-tRNA synthetase reveals a novel mode of interaction},
author = {R Kreutzer and D Kern and R Giege and J Rudinger},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8524648},
isbn = {8524648},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Res},
volume = {23},
number = {22},
pages = {4598-4602},
abstract = {The phosphates of the tRNA(Phe) transcript from Thermus thermophilus interacting with the cognate synthetase were determined by footprinting. Backbone bond protection against cleavage by iodine of the phosphorothioate-containing transcripts was found in the anticodon stem-loop, the D stem-loop and the acceptor stem and weak protection was also seen in the variable loop. Most of the protected phosphates correspond to regions around known identity elements of tRNA(Phe). Enhancement of cleavage at certain positions indicates bending of tRNAPhe upon binding to the enzyme. When applied to the three-dimensional model of tRNA(Phe) from yeast the majority of the protections occur on the D loop side of the molecule, revealing that phenylalanyl-tRNA synthetase has a rather complex and novel pattern of interaction with tRNAPhe, differing from that of other known class II aminoacyl-tRNA synthetases.},
note = {0305-1048
Journal Article},
keywords = {Base Composition Base Sequence Cloning, Genetic, Molecular Comparative Study Escherichia coli Kinetics Models, Phe/biosynthesis/chemistry/*metabolism Thermus thermophilus/*enzymology/*genetics *Transcription, Structural Molecular Sequence Data Nucleic Acid Conformation Phenylalanine-tRNA Ligase/*metabolism Protein Binding RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Isel C, Ehresmann C, Keith G, Ehresmann B, Marquet R
Initiation of reverse transcription of HIV-1: secondary structure of the HIV-1 RNA/tRNA(3Lys) (template/primer) Article de journal
Dans: J Mol Biol, vol. 247, no. 2, p. 236-250, 1995, ISBN: 7707372, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites Conserved Sequence HIV-1/*genetics Models, Genetic, Lys/*genetics/metabolism RNA, MARQUET, Molecular Molecular Probes Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/*genetics/metabolism Structure-Activity Relationship Support
@article{,
title = {Initiation of reverse transcription of HIV-1: secondary structure of the HIV-1 RNA/tRNA(3Lys) (template/primer)},
author = {C Isel and C Ehresmann and G Keith and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7707372},
isbn = {7707372},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {247},
number = {2},
pages = {236-250},
abstract = {Reverse transcription of human immunodeficiency virus type-1 (HIV-1) genomic RNA is primed by tRNA(3Lys), whose 3' end 18 nucleotides are complementary to the viral primer binding site (PBS). We used chemical and enzymatic probes to test the conformation of the viral RNA and tRNA(3Lys), in their free form and in the HIV-1 RNA/tRNA(3Lys) binary complex. Extensive reactivity changes were observed in both molecules upon formation of the binary complex. In the viral RNA, reactivity changes occurred up to 69 nucleotides upstream and 72 nucleotides downstream of the PBS. A secondary structure model of the HIV-1 RNA/tRNA(3Lys) complex accounting for all probing data has been constructed. It reveals an unexpectedly complex and compact pseudoknot-like structure in which most of the anticodon loop, the 3' strand of the anticodon stem and the 5' part of the variable loop of tRNA(3Lys) interact with viral sequences 12 to 39 nucleotides upstream of the PBS. The core of the binary complex is a complex junction formed by two single-stranded sequences of tRNA(3Lys), an intramolecular viral helix, an intramolecular tRNA helix, and two intermolecular helices formed by the template/primer interaction. This junction probably highly constrains the tertiary structure of the HIV-1 RNA/tRNA(3Lys) complex. Compared to the structure of the free molecules, only the D arm of tRNA(3Lys) and a small viral stem-loop downstream of the PBS are unaffected in the binary complex. Sequence comparison reveals that the main characteristics of the binary complex model are conserved among all HIV-1 isolates.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Binding Sites Conserved Sequence HIV-1/*genetics Models, Genetic, Lys/*genetics/metabolism RNA, MARQUET, Molecular Molecular Probes Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral/*genetics/metabolism Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
Heyman T, Agoutin B, Friant S, Wilhelm F X, Wilhelm M L
Dans: J Mol Biol, vol. 253, no. 2, p. 291-303, 1995, ISBN: 7563090, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Cloning, Fungal *Genes, Fungal/biosynthesis DNA, Genetic, Molecular DNA Primers *DNA Replication DNA, Non-U.S. Gov't Transcription, Nucleic Acid Restriction Mapping *Retroelements Saccharomyces cerevisiae/genetics/*virology Support, pol Genome, Unité ARN, Viral Molecular Sequence Data Poly C/analysis Polymerase Chain Reaction *Repetitive Sequences, Viral/*biosynthesis Genes
@article{,
title = {Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition},
author = {T Heyman and B Agoutin and S Friant and F X Wilhelm and M L Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7563090},
isbn = {7563090},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {253},
number = {2},
pages = {291-303},
abstract = {Long terminal repeat elements and retroviruses require primers for initiation of minus and plus-strand DNA synthesis by reverse transcriptase. Here we demonstrate genetically that plus-strand DNA synthesis of the yeast Ty1 element is initiated at two sites located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the pol gene in the integrase coding sequence (PPT2). A consequence of the presence of two PPTs is that Ty1 plus-strand DNA exists as segments at some time during replication. Three fragments have been identified: the plus-strand strong-stop DNA initiated at PPT1, a downstream fragment initiated at PPT2 and an upstream fragment spanning the 5'-terminal part of Ty1 and a portion of the TyB gene. Characterization of the 3' ends of the plus-strand DNA fragments reveals (1) that the upstream fragment is elongated beyond PPT2 creating a plus-strand overlap and (2) that the majority of plus-strand strong-stop DNA fragments bear a copy of the minus-strand primer binding site in agreement with the accepted model of retroviral genomic RNA reverse transcription. The two polypurine tracts, PPT1 and PPT2, have an identical sequence GGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Cloning, Fungal *Genes, Fungal/biosynthesis DNA, Genetic, Molecular DNA Primers *DNA Replication DNA, Non-U.S. Gov't Transcription, Nucleic Acid Restriction Mapping *Retroelements Saccharomyces cerevisiae/genetics/*virology Support, pol Genome, Unité ARN, Viral Molecular Sequence Data Poly C/analysis Polymerase Chain Reaction *Repetitive Sequences, Viral/*biosynthesis Genes},
pubstate = {published},
tppubtype = {article}
}
Ehresmann C, Philippe C, Westhof E, Benard L, Portier C, Ehresmann B
A pseudoknot is required for efficient translational initiation and regulation of the Escherichia coli rpsO gene coding for ribosomal protein S15 Article de journal
Dans: Biochem Cell Biol, vol. 73, no. 11-12, p. 1131-1140, 1995, ISBN: 8722030, (0829-8211 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Bacterial Genetic Code Molecular Sequence Data Nucleic Acid Conformation *Peptide Chain Initiation Ribosomal Proteins/*genetics *Translation, Bacterial/*physiology *Genes, Base Sequence Escherichia coli/*genetics Gene Expression Regulation, Genetic, Unité ARN
@article{,
title = {A pseudoknot is required for efficient translational initiation and regulation of the Escherichia coli rpsO gene coding for ribosomal protein S15},
author = {C Ehresmann and C Philippe and E Westhof and L Benard and C Portier and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8722030},
isbn = {8722030},
year = {1995},
date = {1995-01-01},
journal = {Biochem Cell Biol},
volume = {73},
number = {11-12},
pages = {1131-1140},
abstract = {Escherichia coli ribosomal protein S15 down regulates its own synthesis by binding to its mRNA in a region overlapping the ribosome binding site, called the translational operator. This binding stabilizes a pseudoknot structure that exists in equilibrium with two stem-loop structures. When synthesized in excess over 16S rRNA, S15 binds to its translational operator and traps the ribosome on its loading site in a transient state, preventing the formation of the active ternary (30S-mRNA-rRNA(f)Met) complex. This inhibition can be suppressed by 16S rRNA, which displaces S15 from the mRNA. An extensive mutational analysis showed that the pseudoknot is the structural element required for S15 recognition and in vivo translational control. Specific sequence determinants are located in limited regions of the structure formed by the pseudoknot. An unexpected result is that the pseudoknot can exist in a variety of topologically equivalent structures recognizable and shapable by S15. Based on footprinting experiments and computer graphic modelling, S15 shields the two stems of the pseudoknot, sitting in the major groove of the coaxial stack.},
note = {0829-8211
Journal Article
Review
Review, Tutorial},
keywords = {Bacterial Genetic Code Molecular Sequence Data Nucleic Acid Conformation *Peptide Chain Initiation Ribosomal Proteins/*genetics *Translation, Bacterial/*physiology *Genes, Base Sequence Escherichia coli/*genetics Gene Expression Regulation, Genetic, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1994
Meister Marie, Braun A, Kappler Christine, Reichhart Jean-Marc, Hoffmann Jules A
Insect immunity. A transgenic analysis in Drosophila defines several functional domains in the diptericin promoter Article de journal
Dans: EMBO J., vol. 13, no. 24, p. 5958–5966, 1994, ISSN: 0261-4189.
Résumé | BibTeX | Étiquettes: Animals, Anti-Infective Agents, Base Sequence, beta-Galactosidase, DNA Mutational Analysis, Female, Gene Expression Regulation, Genetic, Genetically Modified, Germ Cells, hoffmann, Insect Hormones, Insect Proteins, M3i, Male, Models, Nucleic Acid, Promoter Regions, Recombinant Fusion Proteins, reichhart, Repetitive Sequences, Transformation
@article{meister_insect_1994,
title = {Insect immunity. A transgenic analysis in Drosophila defines several functional domains in the diptericin promoter},
author = {Marie Meister and A Braun and Christine Kappler and Jean-Marc Reichhart and Jules A Hoffmann},
issn = {0261-4189},
year = {1994},
date = {1994-12-01},
journal = {EMBO J.},
volume = {13},
number = {24},
pages = {5958--5966},
abstract = {Diptericins are antibacterial polypeptides which are strongly induced in the fat body and blood cells of dipteran insects in response to septic injury. The promoter of the single-copy, intronless diptericin gene of Drosophila contains several nucleotide sequences homologous to mammalian cis-regulatory motifs involved in the control of acute phase response genes. Extending our previous studies on the expression of the diptericin gene, we now report a quantitative analysis of the contribution of various putative regulatory elements to the bacterial inducibility of this gene, based on the generation of 60 transgenic fly lines carrying different elements fused to a reporter gene. Our data definitively identify two Kappa B-related motifs in the proximal promoter as the sites conferring inducibility and tissue-specific expression to the diptericin gene. These motifs alone, however, mediate only minimal levels of expression. Additional proximal regulatory elements are necessary to attain some 20% of the full response and we suspect a role for sequences homologous to mammalian IL6 response elements and interferon-gamma responsive sites in this up-regulation. The transgenic experiments also reveal the existence of a distal regulatory element located upstream of -0.6 kb which increases the level of expression by a factor of five.},
keywords = {Animals, Anti-Infective Agents, Base Sequence, beta-Galactosidase, DNA Mutational Analysis, Female, Gene Expression Regulation, Genetic, Genetically Modified, Germ Cells, hoffmann, Insect Hormones, Insect Proteins, M3i, Male, Models, Nucleic Acid, Promoter Regions, Recombinant Fusion Proteins, reichhart, Repetitive Sequences, Transformation},
pubstate = {published},
tppubtype = {article}
}
Auble D T, Hansen K E, Mueller C G, Lane W S, Thorner J, Hahn S
Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism Article de journal
Dans: Genes & Development, vol. 8, no. 16, p. 1920–1934, 1994, ISSN: 0890-9369.
Résumé | Liens | BibTeX | Étiquettes: Adenosine Triphosphatases, Adenosine Triphosphate, Amino Acid Sequence, Base Sequence, Biological, DNA, DNA Helicases, DNA Probes, DNA-Binding Proteins, Fungal, Fungal Proteins, Genes, Genetic, Models, Molecular Sequence Data, Mutagenesis, Repressor Proteins, RNA Polymerase II, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Site-Directed, TATA Box, TATA-Binding Protein Associated Factors, TATA-Box Binding Protein, Team-Mueller, Transcription, Transcription Factors
@article{auble_mot1_1994,
title = {Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism},
author = {D T Auble and K E Hansen and C G Mueller and W S Lane and J Thorner and S Hahn},
doi = {10.1101/gad.8.16.1920},
issn = {0890-9369},
year = {1994},
date = {1994-08-01},
journal = {Genes & Development},
volume = {8},
number = {16},
pages = {1920--1934},
abstract = {Basal transcription of many genes in yeast is repressed by Mot1, an essential protein which is a member of the Snf2/Swi2 family of conserved nuclear factors. ADI is an ATP-dependent inhibitor of TATA-binding protein (TBP) binding to DNA that inhibits transcription in vitro. Here we demonstrate that ADI is encoded by the MOT1 gene. Mutation of MOT1 abolishes ADI activity and derepresses basal transcription in vitro and in vivo. Recombinant Mot1 removes TBP from DNA and Mot1 contains an ATPase activity which is essential for its function. Genetic interactions between Mot1 and TBP indicate that their functions are interlinked in vivo. These results provide a general model for understanding the mechanism of action of a large family of nuclear factors involved in processes such as transcription and DNA repair.},
keywords = {Adenosine Triphosphatases, Adenosine Triphosphate, Amino Acid Sequence, Base Sequence, Biological, DNA, DNA Helicases, DNA Probes, DNA-Binding Proteins, Fungal, Fungal Proteins, Genes, Genetic, Models, Molecular Sequence Data, Mutagenesis, Repressor Proteins, RNA Polymerase II, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Site-Directed, TATA Box, TATA-Binding Protein Associated Factors, TATA-Box Binding Protein, Team-Mueller, Transcription, Transcription Factors},
pubstate = {published},
tppubtype = {article}
}