Bernacchi S, Ennifar E, Toth K, Walter P, Langowski J, Dumas P
Mechanism of hairpin-duplex conversion for the HIV-1 dimerization initiation site Article de journal
Dans: J Biol Chem, vol. 280, no. 48, p. 40112-40121, 2005, ISBN: 16169845, (0021-9258 (Print) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites Crystallography, Drug Electrophoresis Genome, ENNIFAR, Fluorescence Spectrophotometry Temperature Thermodynamics Time Factors Ultraviolet Rays Virus Replication, MARQUET, Non-U.S. Gov't Spectrometry, PAILLART, Unité ARN, Viral HIV-1/*chemistry Kinetics Molecular Sequence Data *Nucleic Acid Conformation Protein Binding RNA/chemistry RNA, Viral/*chemistry Research Support, X-Ray Dimerization Dose-Response Relationship
@article{,
title = {Mechanism of hairpin-duplex conversion for the HIV-1 dimerization initiation site},
author = {S Bernacchi and E Ennifar and K Toth and P Walter and J Langowski and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16169845},
isbn = {16169845},
year = {2005},
date = {2005-01-01},
journal = {J Biol Chem},
volume = {280},
number = {48},
pages = {40112-40121},
abstract = {We have used the dimerization initiation site of HIV-1 genomic RNA as a model to investigate hairpin-duplex interconversion with a combination of fluorescence, UV melting, gel electrophoresis, and x-ray crystallographic techniques. Fluorescence studies with molecular beacons and crystallization experiments with 23-nucleotide dimerization initiation site fragments showed that the ratio of hairpin to duplex formed after annealing in water essentially depends on RNA concentration and not on cooling kinetics. With natural sequences allowing to form the most stable duplex, and thus also the loop-loop complex (or "kissing complex"), concentrations as low as 3 mum in strands are necessary to obtain a majority of the hairpin form. With a mutated sequence preventing kissing complex formation, a majority of hairpins was even obtained at 80 mum in strands. However, this did not prevent an efficient conversion from hairpin to duplex in the presence of salts. Kinetic considerations are in favor of duplex formation from intermediates involving hairpins engaged in cruciform dimers rather than from free strands. The very first step of formation of such a cruciform intermediate could be trapped in a crystal structure. This mechanism might be significant for the dynamics of small RNAs beyond the strict field of HIV-1.},
note = {0021-9258 (Print)
Journal Article},
keywords = {Base Sequence Binding Sites Crystallography, Drug Electrophoresis Genome, ENNIFAR, Fluorescence Spectrophotometry Temperature Thermodynamics Time Factors Ultraviolet Rays Virus Replication, MARQUET, Non-U.S. Gov't Spectrometry, PAILLART, Unité ARN, Viral HIV-1/*chemistry Kinetics Molecular Sequence Data *Nucleic Acid Conformation Protein Binding RNA/chemistry RNA, Viral/*chemistry Research Support, X-Ray Dimerization Dose-Response Relationship},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Shehu-Xhilaga M, Marquet R, Mak J
Dimerization of retroviral RNA genomes: an inseparable pair Article de journal
Dans: Nat Rev Microbiol, vol. 2, no. 6, p. 461-472, 2004, ISBN: 15152202, (1740-1526 Journal Article Review Review, Tutorial).
Liens | BibTeX | Étiquettes: Base Sequence Dimerization *Genome, MARQUET, Molecular Molecular Sequence Data Nucleic Acid Conformation Virus Replication/*genetics, PAILLART, Unité ARN, Viral HIV-1/*genetics/growth & development Human Models
@article{,
title = {Dimerization of retroviral RNA genomes: an inseparable pair},
author = {J C Paillart and M Shehu-Xhilaga and R Marquet and J Mak},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15152202},
isbn = {15152202},
year = {2004},
date = {2004-01-01},
journal = {Nat Rev Microbiol},
volume = {2},
number = {6},
pages = {461-472},
note = {1740-1526
Journal Article
Review
Review, Tutorial},
keywords = {Base Sequence Dimerization *Genome, MARQUET, Molecular Molecular Sequence Data Nucleic Acid Conformation Virus Replication/*genetics, PAILLART, Unité ARN, Viral HIV-1/*genetics/growth & development Human Models},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Dettenhofer M, Yu X F, Ehresmann C, Ehresmann B, Marquet R
First snapshots of the HIV-1 RNA structure in infected cells and in virions Article de journal
Dans: J Biol Chem, vol. 279, no. 46, p. 48397-48403, 2004, ISBN: 15355993, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@article{,
title = {First snapshots of the HIV-1 RNA structure in infected cells and in virions},
author = {J C Paillart and M Dettenhofer and X F Yu 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=15355993},
isbn = {15355993},
year = {2004},
date = {2004-01-01},
journal = {J Biol Chem},
volume = {279},
number = {46},
pages = {48397-48403},
abstract = {With the increasing interest of RNAs in regulating a range of cell biological processes, very little is known about the structure of RNAs in tissue culture cells. We focused on the 5'-untranslated region of the human immunodeficiency virus type 1 RNA genome, a highly conserved RNA region, which contains structural domains that regulate key steps in the viral replication cycle. Up until now, structural information only came from in vitro studies. Here, we developed chemical modification assays to test nucleotide accessibility directly in infected cells and viral particles, thus circumventing possible biases and artifacts linked to in vitro assays. The secondary structure of the 5'-untranslated region in infected cells points to the existence of the various stem-loop motifs associated to distinct functions, proposed from in vitro probing, mutagenesis, and phylogeny. However, compared with in vitro data, subtle differences were observed in the dimerization initiation site hairpin, and none of the proposed long range interactions were observed between the functional domains. Moreover, no global RNA rearrangement was observed; structural differences between infected cells and viral particles were limited to the primer binding site, which became protected against chemical modification upon tRNA(3) (Lys) annealing in virions and to the main packaging signal. In addition, our data suggested that the genomic RNA could already dimerize in the cytoplasm of infected cells. Taken together, our results provided the first analysis of the dynamic of RNA structure of the human immunodeficiency virus type 1 RNA genome during virus assembly ex vivo.},
note = {0021-9258
Journal Article},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Goldschmidt V, Paillart J C, Rigourd M, Ehresmann B, Aubertin A M, Ehresmann C, Marquet R
Structural variability of the initiation complex of HIV-1 reverse transcription Article de journal
Dans: J Biol Chem, vol. 279, no. 34, p. 35923-35931, 2004, ISBN: 15194685, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@article{,
title = {Structural variability of the initiation complex of HIV-1 reverse transcription},
author = {V Goldschmidt and J C Paillart and M Rigourd and B Ehresmann and A M Aubertin and C Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15194685},
isbn = {15194685},
year = {2004},
date = {2004-01-01},
journal = {J Biol Chem},
volume = {279},
number = {34},
pages = {35923-35931},
abstract = {HIV-1 reverse transcription is initiated from a tRNA(3)(Lys) molecule annealed to the viral RNA at the primer binding site (PBS), but the structure of the initiation complex of reverse transcription remains controversial. Here, we performed in situ structural probing, as well as in vitro structural and functional studies, of the initiation complexes formed by highly divergent isolates (MAL and NL4.3/HXB2). Our results show that the structure of the initiation complex is not conserved. In MAL, and according to sequence analysis in 14% of HIV-1 isolates, formation of the initiation complex is accompanied by complex rearrangements of the viral RNA, and extensive interactions with tRNA(3)(Lys) are required for efficient initiation of reverse transcription. In NL4.3, HXB2, and most isolates, tRNA(3)(Lys) annealing minimally affects the viral RNA structure and no interaction outside the PBS is required for optimal initiation of reverse transcription. We suggest that in MAL, extensive interactions with tRNA(3)(Lys) are required to drive the structural rearrangements generating the structural elements ultimately recognized by reverse transcriptase. In NL4.3 and HXB2, these elements are already present in the viral RNA prior to tRNA(3)(Lys) annealing, thus explaining that extensive interactions with the primer are not required. Interestingly, such interactions are required in HXB2 mutants designed to use a non-cognate tRNA as primer (tRNA(His)). In the latter case, the extended interactions are required to counteract a negative contribution associate with the alternate primer.},
note = {0021-9258
Journal Article},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Goldschmidt V, Marquet R
Primer unblocking by HIV-1 reverse transcriptase and resistance to nucleoside RT inhibitors (NRTIs) Article de journal
Dans: Int J Biochem Cell Biol, vol. 36, no. 9, p. 1687-1705, 2004, ISBN: 15183338, (1357-2725 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: MARQUET, Unité ARN
@article{,
title = {Primer unblocking by HIV-1 reverse transcriptase and resistance to nucleoside RT inhibitors (NRTIs)},
author = {V Goldschmidt and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15183338},
isbn = {15183338},
year = {2004},
date = {2004-01-01},
journal = {Int J Biochem Cell Biol},
volume = {36},
number = {9},
pages = {1687-1705},
abstract = {During zidovudine and stavudine treatment, HIV-1 selects several mutations (thymidine-associated mutations, TAMs) in the reverse transcriptase gene that confer high- and moderate-levels of resistance, respectively, to these nucleoside reverse transcriptase inhibitors (NRTIs). The mechanism of the resistance provided by these mutations has long remained elusive. However, recent data showed that ATP-phosphorolysis, a reaction analogous to pyrophosphorolysis (the reverse of the nucleotide incorporation reaction) in which ATP is the pyrophosphate donor, is central to this mechanism by allowing repair of the chain-terminated primer. A detailed structural and mechanistic model accounting for the specificity of the ATP-phosphorolysis and its inhibition by the next complementary nucleotide is now available. In the context of multiresistant viruses, the TAMs are also associated with resistance to abacavir, and to a lesser extent to didanisone, zalcitabine and tenofovir. When associated with the TAMs, a dipeptide insertion in the fingers of reverse transcriptase increases the ATP-phosphorolysis of most chain terminators, stressing the increasing importance of this mechanism. However, some non-nucleoside reverse transcriptase inhibitors (NNRTIs) inhibit this process. In addition, point mutations conferring resistance to NNRTIs (Y181C and L100I) or NRTIs (K65R, L74V, and M184V) partially resensitize the resistant viruses to AZT by inhibiting ATP-phosphorolysis. These findings allow rationalizing the beneficial effects of some drug combinations and should contribute to improve drug cocktails. The development of NRTIs that would not allow the ATP-mediated excision to take place should prove beneficial for future treatments, even though high-level resistance to multiple NRTIs can ultimately develop in the absence of any significant primer unblocking.},
note = {1357-2725
Journal Article},
keywords = {MARQUET, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Goldschmidt V, Ehresmann C, Ehresmann B, Marquet R
Does the HIV-1 primer activation signal interact with tRNA3(Lys) during the initiation of reverse transcription? Article de journal
Dans: Nucleic Acids Res, vol. 31, no. 3, p. 850-859, 2003, ISBN: 12560480, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl/chemistry/*metabolism RNA, Base Sequence Binding Sites DNA Primers DNA, Genetic, MARQUET, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral HIV-1/*genetics HIV-1 Reverse Transcriptase/*metabolism Kinetics Molecular Sequence Data Mutation Nucleic Acid Conformation Oligoribonucleotides RNA, Viral/biosynthesis *Gene Expression Regulation, Viral/chemistry/genetics/metabolism Support
@article{,
title = {Does the HIV-1 primer activation signal interact with tRNA3(Lys) during the initiation of reverse transcription?},
author = {V Goldschmidt 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=12560480},
isbn = {12560480},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {3},
pages = {850-859},
abstract = {Reverse transcription of HIV-1 RNA is primed by a tRNA3(Lys) molecule bound at the primer binding site (PBS). Complex intermolecular interactions were proposed between tRNA3(Lys) and the RNA of the HIV-1 Mal isolate. Recently, an alternative interaction was proposed between the TPsiC stem of tRNA3(Lys) and a primer activation signal (PAS) of the Lai and Hxb2 RNAs, suggesting major structural variations in the reverse transcription complex of different HIV-1 strains. Here, we analyzed mutants of the Hxb2 RNA that prevent the interaction between the PAS and tRNA3(Lys) or/and a complementary sequence in the viral RNA. We compared the kinetics of reverse transcription of the wild type and mutant Hxb2 RNAs, using either tRNA3(Lys) or an 18mer oligoribonucleotide complementary to the PBS, which cannot interact with the PAS, as primers. We also used chemical probing to test the structure of the mutant and wild type RNAs, as well as the complex formed between the later RNA and tRNA3(Lys). These experiments, together with the analysis of long term replication data of mutant viruses obtained by C. Morrow and coworkers (Birmingham, USA) that use alternate tRNAs as primers, strongly suggest that the interaction between the Hxb2 PAS and tRNA3(Lys) does not exist. Instead, the effects of the vRNA mutations on reverse transcription seem to be linked to incorrect folding of the mutant RNAs.},
note = {1362-4962
Journal Article},
keywords = {Amino Acyl/chemistry/*metabolism RNA, Base Sequence Binding Sites DNA Primers DNA, Genetic, MARQUET, Non-U.S. Gov't *Transcription, Transfer, Unité ARN, Viral HIV-1/*genetics HIV-1 Reverse Transcriptase/*metabolism Kinetics Molecular Sequence Data Mutation Nucleic Acid Conformation Oligoribonucleotides RNA, Viral/biosynthesis *Gene Expression Regulation, Viral/chemistry/genetics/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Rigourd M, Goldschmidt V, Brule F, Morrow C D, Ehresmann B, Ehresmann C, Marquet R
Structure-function relationships of the initiation complex of HIV-1 reverse transcription: the case of mutant viruses using tRNA(His) as primer Article de journal
Dans: Nucleic Acids Res, vol. 31, no. 19, p. 5764-5775, 2003, ISBN: 14500840, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Comparative Study DNA, Genetic, Genetic *Transcription Initiation Site *Transcription, His/*metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Post-Transcriptional RNA, Transfer, Unité ARN, Viral HIV-1/*genetics/metabolism HIV-1 Reverse Transcriptase/metabolism Kinetics Macromolecular Systems Molecular Sequence Data Mutation RNA Probes RNA Processing, Viral/*biosynthesis/genetics Sequence Alignment Structure-Activity Relationship Support, Viral/biosynthesis *Gene Expression Regulation
@article{,
title = {Structure-function relationships of the initiation complex of HIV-1 reverse transcription: the case of mutant viruses using tRNA(His) as primer},
author = {M Rigourd and V Goldschmidt and F Brule and C D Morrow 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=14500840},
isbn = {14500840},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {19},
pages = {5764-5775},
abstract = {Reverse transcription of HIV-1 RNA is initiated from the 3' end of a tRNA3Lys molecule annealed to the primer binding site (PBS). An additional interaction between the anticodon loop of tRNA3Lys and a viral A-rich loop is required for efficient initiation of reverse transcription of the HIV-1 MAL isolate. In the HIV-1 HXB2 isolate, simultaneous mutations of the PBS and the A-rich loop (mutant His-AC), but not of the PBS alone (mutant His) allows the virus to stably utilize tRNA(His) as primer. However, mutant His-AC selects additional mutations during cell culture, generating successively His-AC-GAC and His-AC-AT-GAC. Here, we wanted to establish direct relationships between the evolution of these mutants in cell culture, their efficiency in initiating reverse transcription and the structure of the primer/template complexes in vitro. The initiation of reverse transcription of His and His-AC RNAs was dramatically reduced. However, His-AC-GAC RNA, which incorporated three adaptative point mutations, was reverse transcribed more efficiently than the wild type RNA. Incorporation of two additional mutations decreased the efficiency of the initiation of reverse transcription, which remained at the wild type level. Structural probing showed that even though both His-AC and His-AC-GAC RNAs can potentially interact with the anticodon loop of tRNA(His), only the latter template formed a stable interaction. Thus, our results showed that the selection of adaptative mutations by HIV-1 mutants utilizing tRNA(His) as primer was initially dictated by the efficiency of the initiation of reverse transcription, which relied on the existence of a stable interaction between the mutated A-rich loop and the anticodon loop of tRNA(His).},
note = {1362-4962
Journal Article},
keywords = {Base Sequence Comparative Study DNA, Genetic, Genetic *Transcription Initiation Site *Transcription, His/*metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Post-Transcriptional RNA, Transfer, Unité ARN, Viral HIV-1/*genetics/metabolism HIV-1 Reverse Transcriptase/metabolism Kinetics Macromolecular Systems Molecular Sequence Data Mutation RNA Probes RNA Processing, Viral/*biosynthesis/genetics Sequence Alignment Structure-Activity Relationship Support, Viral/biosynthesis *Gene Expression Regulation},
pubstate = {published},
tppubtype = {article}
}
Rigourd M, Bec G, Benas P, Grice S F Le, Ehresmann B, Ehresmann C, Marquet R
Effects of tRNA 3 Lys aminoacylation on the initiation of HIV-1 reverse transcription Article de journal
Dans: Biochimie, vol. 85, no. 5, p. 521-525, 2003, ISBN: 12763311, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acetyltransferases/metabolism *Acylation Animals Cattle HIV-1/*physiology HIV-1 Reverse Transcriptase/pharmacology RNA/genetics RNA, Genetic/drug effects/*physiology Virus Assembly, Lys/*chemistry/drug effects Support, MARQUET, Non-U.S. Gov't Transcription, Transfer, Unité ARN
@article{,
title = {Effects of tRNA 3 Lys aminoacylation on the initiation of HIV-1 reverse transcription},
author = {M Rigourd and G Bec and P Benas and S F Le Grice 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=12763311},
isbn = {12763311},
year = {2003},
date = {2003-01-01},
journal = {Biochimie},
volume = {85},
number = {5},
pages = {521-525},
abstract = {HIV-1 utilizes cellular tRNA(3)(Lys) to prime the initiation of reverse transcription. The selective incorporation of cytoplasmic tRNA(3)(Lys) into HIV-1 particles was recently shown to involve the lysyl-tRNA synthetase, and hence, the encapsidated tRNA(3)(Lys) is likely to be aminoacylated. Here, we tested the effect of aminoacylation on the initiation of reverse transcription. We show that HIV-1 reverse transcriptase is unable to extend lysyl-tRNA(3)(Lys). In addition, the viral polymerase does not significantly enhance the rate of tRNA deacylation, in contrast with previous studies on avian retroviruses. Thus, aminoacylation of the primer tRNA might prevent the initiation of HIV-1 reverse transcription from taking place before viral budding and maturation.},
note = {0300-9084
Journal Article},
keywords = {Acetyltransferases/metabolism *Acylation Animals Cattle HIV-1/*physiology HIV-1 Reverse Transcriptase/pharmacology RNA/genetics RNA, Genetic/drug effects/*physiology Virus Assembly, Lys/*chemistry/drug effects Support, MARQUET, Non-U.S. Gov't Transcription, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ennifar E, Paillart J C, Marquet R, Ehresmann B, Ehresmann C, Dumas P, Walter P
HIV-1 RNA dimerization initiation site is structurally similar to the ribosomal A site and binds aminoglycoside antibiotics Article de journal
Dans: J Biol Chem, vol. 278, no. 4, p. 2723-2730, 2003, ISBN: 12435744, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anti-Bacterial Agents/*pharmacology Binding Sites Dimerization HIV-1/*metabolism Models, ENNIFAR, MARQUET, Molecular Neomycin/pharmacology Nucleic Acid Conformation Paromomycin/pharmacology Protein Binding RNA/metabolism *RNA, Non-U.S. Gov't Temperature Ultraviolet Rays, PAILLART, Unité ARN, Viral Ribosomes/*metabolism Support
@article{,
title = {HIV-1 RNA dimerization initiation site is structurally similar to the ribosomal A site and binds aminoglycoside antibiotics},
author = {E Ennifar and J C Paillart and R Marquet and B Ehresmann and C Ehresmann and P Dumas and P Walter},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12435744},
isbn = {12435744},
year = {2003},
date = {2003-01-01},
journal = {J Biol Chem},
volume = {278},
number = {4},
pages = {2723-2730},
abstract = {Human immunodeficiency virus (HIV) genomic RNA is packaged into virions as a dimer. The first step of dimerization is the formation of a kissing-loop complex at the so-called dimerization initiation site (DIS). We found an unexpected and fortuitous resemblance between the HIV-1 DIS kissing-loop complex and the eubacterial 16 S ribosomal aminoacyl-tRNA site (A site), which is the target of aminoglycoside antibiotics. Similarities exist not only at the primary and secondary structure level but also at the tertiary structure level, as revealed by comparison of the respective DIS and A site crystal structures. Gel shift, inhibition of lead-induced cleavage, and footprinting experiments showed that paromomycin and neomycin specifically bind to the kissing-loop complex formed by the DIS, with an affinity and a geometry similar to that observed for the A site. Modeling of the aminoglycoside-DIS complex allowed us to identify antibiotic modifications likely to increase the affinity and/or the specificity for the DIS. This could be a starting point for designing antiviral drugs against HIV-1 RNA dimerization.},
note = {0021-9258
Journal Article},
keywords = {Anti-Bacterial Agents/*pharmacology Binding Sites Dimerization HIV-1/*metabolism Models, ENNIFAR, MARQUET, Molecular Neomycin/pharmacology Nucleic Acid Conformation Paromomycin/pharmacology Protein Binding RNA/metabolism *RNA, Non-U.S. Gov't Temperature Ultraviolet Rays, PAILLART, Unité ARN, Viral Ribosomes/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Goldschmidt V, Rigourd M, Ehresmann C, Grice S F Le, Ehresmann B, Marquet R
Direct and indirect contributions of RNA secondary structure elements to the initiation of HIV-1 reverse transcription Article de journal
Dans: J Biol Chem, vol. 277, no. 45, p. 43233-43242, 2002, ISBN: 12194974, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA Primers DNA Replication HIV-1/*genetics HIV-1 Reverse Transcriptase/*metabolism Human Kinetics Polymerase Chain Reaction RNA, Genetic, Lys/genetics RNA, MARQUET, Non-U.S. Gov't Transcription, Transfer, Unité ARN, Viral/*chemistry/*genetics/metabolism Support
@article{,
title = {Direct and indirect contributions of RNA secondary structure elements to the initiation of HIV-1 reverse transcription},
author = {V Goldschmidt and M Rigourd 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=12194974},
isbn = {12194974},
year = {2002},
date = {2002-01-01},
journal = {J Biol Chem},
volume = {277},
number = {45},
pages = {43233-43242},
abstract = {Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription requires specific recognition between the viral RNA (vRNA), tRNA(3)(Lys), which acts as primer, and reverse transcriptase (RT). The specificity of this ternary complex is mediated by intricate interactions between the HIV-1 RNA and tRNA(3)(Lys). Here, we compared the relative importance of the secondary structure elements of this complex in the initiation process. To this aim, we used the previously published three-dimensional model of the initiation complex to rationally introduce a series of deletions and substitutions in the vRNA. When necessary, we used chemical probing to check the structure of the tRNA(3)(Lys)-mutant vRNA complexes. For each of them, we measured the binding affinity of RT and the kinetics of initial extension of tRNA(3)(Lys) and of synthesis of the (-) strand strong stop DNA. Our results were overall in keeping with the three-dimensional model of the initiation complex. Surprisingly, we found that disruption of the intermolecular template-primer interactions, which are not directly recognized by RT, more severely affected reverse transcription than deletions or disruption of one of the intramolecular helices to which RT directly binds. Perturbations of the highly constrained junction between the intermolecular helix formed by the primer binding site and the 3' end of tRNA(3)(Lys) and the helix immediately upstream also had dramatic effects on the initiation of reverse transcription. Taken together, our results demonstrate the overwhelming importance of the overall three-dimensional structure of the initiation complex and identify structural elements that constitute promising targets for anti-initiation-specific drugs.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence DNA Primers DNA Replication HIV-1/*genetics HIV-1 Reverse Transcriptase/*metabolism Human Kinetics Polymerase Chain Reaction RNA, Genetic, Lys/genetics RNA, MARQUET, Non-U.S. Gov't Transcription, Transfer, Unité ARN, Viral/*chemistry/*genetics/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Fournier C, Cortay J C, Carbonnelle C, Ehresmann C, Marquet R, Boulanger P
The HIV-1 Nef protein enhances the affinity of reverse transcriptase for RNA in vitro Article de journal
Dans: Virus Genes, vol. 25, no. 3, p. 255-269, 2002, ISBN: 12881637, (0920-8569 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Binding Sites Electrophoretic Mobility Shift Assay Gene Products, MARQUET, nef/*metabolism HIV-1/*genetics/metabolism Human In Vitro Molecular Sequence Data Protein Footprinting RNA/genetics/*metabolism RNA-Directed DNA Polymerase/*metabolism Support, Non-U.S. Gov't, Unité ARN
@article{,
title = {The HIV-1 Nef protein enhances the affinity of reverse transcriptase for RNA in vitro},
author = {C Fournier and J C Cortay and C Carbonnelle and C Ehresmann and R Marquet and P Boulanger},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12881637},
isbn = {12881637},
year = {2002},
date = {2002-01-01},
journal = {Virus Genes},
volume = {25},
number = {3},
pages = {255-269},
abstract = {Several viral proteins, including nucleocapsid protein, integrase, Vif, Tat, and Nef have been proposed to act as cofactors of HIV-1 reverse transcription. Using two viral RNA probes, one overlapping the primer-binding site (PBS) and the other representing the ribosomal frameshifting signal (FS) of HIV-1 RNA, we found that recombinant full-length Nef protein (NefLAI) increased the affinity of reverse transcriptase (RT) for RNA in vitro, and interacted directly with RT in protein co-precipitation assays. The effect on RT-RNA binding and the capacity of Nef to interact with RT was also observed with N-terminal deletion mutant NefDelta57 and NefSF2, although to a lesser level. NefDelta57 corresponded to the processed Nef protein present in the internal core of mature virions, and lacked the N-myristoylated N-terminus and N-terminal region implicated in virus infectivity and pathogenicity in vivo. NefSF2, a Nef allele from a highly pathogenic strain of HIV-1, differed from NefLAI by the amino acid sequence and immunoreactivity of its N-terminal domain. The effect observed with NefSF2 and NefDelta57, and data from phage biopanning experiments suggested that the RT-binding region in Nef involved the C-terminal flexible loop of its C-terminal domain, but the function in RT-RNA binding was also influenced by its N-terminal domain.},
note = {0920-8569
Journal Article},
keywords = {Amino Acid Sequence Binding Sites Electrophoretic Mobility Shift Assay Gene Products, MARQUET, nef/*metabolism HIV-1/*genetics/metabolism Human In Vitro Molecular Sequence Data Protein Footprinting RNA/genetics/*metabolism RNA-Directed DNA Polymerase/*metabolism Support, Non-U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Brunel C, Marquet R, Romby P, Ehresmann C
RNA loop-loop interactions as dynamic functional motifs Article de journal
Dans: Biochimie, vol. 84, no. 9, p. 925-944, 2002, ISBN: 12458085, (0300-9084 Journal Article Review Review Literature).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Pairing Base Sequence Dimerization HIV-1/genetics Human Kinetics Molecular Sequence Data *Nucleic Acid Conformation RNA/genetics/*metabolism Support, MARQUET, Non-U.S. Gov't Thermodynamics, ROMBY, Unité ARN
@article{,
title = {RNA loop-loop interactions as dynamic functional motifs},
author = {C Brunel and R Marquet and P Romby and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12458085},
isbn = {12458085},
year = {2002},
date = {2002-01-01},
journal = {Biochimie},
volume = {84},
number = {9},
pages = {925-944},
abstract = {RNA loop-loop interactions are frequently used to trigger initial recognition between two RNA molecules. In this review, we present selected well-documented cases that illustrate the diversity of biological processes using RNA loop-loop recognition properties. The first one is related to natural antisense RNAs that play a variety of regulatory functions in bacteria and their extra-chromosomal elements. The second one concerns the dimerization of HIV-1 genomic RNA, which is responsible for the encapsidation of a diploid RNA genome. The third one concerns RNA interactions involving double-loop interactions. These are used by the bicoid mRNA to form dimers, a property that appears to be important for mRNA localization in drosophila embryo, and by bacteriophage phi29 pRNA which forms hexamers that participate in the translocation of the DNA genome through the portal vertex of the capsid. Despite the high diversity of systems and mechanisms, some common features can be highlighted. (1) Efficient recognition requires rapid bi-molecular binding rates, regardless of the RNA pairing scheme. (2) The initial recognition is favored by particular conformations of the loops enabling a proper presentation of nucleotides (generally a restricted number) that initiate the recognition process. (3) The fate of the initial reversible loop-loop complex is dictated by both functional and structural constraints. RNA structures have evolved either to "freeze" the initial complex, or to convert it into a more stable one, which involves propagation of intermolecular interactions along topologically feasible pathways. Stabilization of the initial complex may also be assisted by proteins and/or formation of additional contacts.},
note = {0300-9084
Journal Article
Review
Review Literature},
keywords = {Animals Base Pairing Base Sequence Dimerization HIV-1/genetics Human Kinetics Molecular Sequence Data *Nucleic Acid Conformation RNA/genetics/*metabolism Support, MARQUET, Non-U.S. Gov't Thermodynamics, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Brule F, Marquet R, Rong L, Wainberg M A, Roques B P, Grice S F Le, Ehresmann B, Ehresmann C
Structural and functional properties of the HIV-1 RNA-tRNA(Lys)3 primer complex annealed by the nucleocapsid protein: comparison with the heat-annealed complex Article de journal
Dans: RNA, vol. 8, no. 1, p. 8-15, 2002, ISBN: 11873759, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Genetic, Genetic Transcription, Lys/*chemistry/genetics/metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/*chemistry/genetics/metabolism Support
@article{,
title = {Structural and functional properties of the HIV-1 RNA-tRNA(Lys)3 primer complex annealed by the nucleocapsid protein: comparison with the heat-annealed complex},
author = {F Brule and R Marquet and L Rong and M A Wainberg and B P Roques and S F Le Grice and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11873759},
isbn = {11873759},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {1},
pages = {8-15},
abstract = {The conversion of the single-stranded RNA genome into double-stranded DNA by virus-coded reverse transcriptase (RT) is an essential step of the retrovirus life cycle. In human immunodeficiency virus type 1 (HIV-1), RT uses the cellular tRNA(Lys)3 to initiate the (-) strand DNA synthesis. Placement of the primer tRNA(Lys)3 involves binding of its 3'-terminal 18 nt to a complementary region of genomic RNA termed PBS. However, the PBS sequence is not the unique determinant of primer usage and additional contacts are important. This placement is believed to be achieved in vivo by the nucleocapsid domain of Gag or by the mature protein NCp. Up to now, structural information essentially arose from heat-annealed primer-template complexes (Isel et al., J Mol Biol, 1995, 247:236-250; Isel et al., EMBO J, 1999, 18:1038-1048). Here, we investigated the formation of the primer-template complex mediated by NCp and compared structural and functional properties of heat- and NCp-annealed complexes. We showed that both heat- and NCp-mediated procedures allow comparable high yields of annealing. Then, we investigated structural features of both kinds of complexes by enzymatic probing, and we compared their relative efficiency in (-) strong stop DNA synthesis. We did not find any significant differences between these complexes, suggesting that information derived from the heat-annealed complex can be transposed to the NCp-mediated complex and most likely to complexes formed in vivo.},
note = {1355-8382
Journal Article},
keywords = {Genetic, Genetic Transcription, Lys/*chemistry/genetics/metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/*chemistry/genetics/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Schuster C, Isel C, Imbert I, Ehresmann C, Marquet R, Kieny M P
Secondary structure of the 3' terminus of hepatitis C virus minus-strand RNA Article de journal
Dans: J Virol, vol. 76, no. 16, p. 8058-8068, 2002, ISBN: 12134011, (0022-538x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, MARQUET, Molecular Molecular Probe Techniques Molecular Sequence Data Nucleic Acid Conformation Plasmids/genetics RNA, Non-U.S. Gov't Virus Replication, Unité ARN, Viral/*chemistry/genetics Support, Viral/genetics Hepacivirus/*chemistry/genetics/physiology Human Models
@article{,
title = {Secondary structure of the 3' terminus of hepatitis C virus minus-strand RNA},
author = {C Schuster and C Isel and I Imbert and C Ehresmann and R Marquet and M P Kieny},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12134011},
isbn = {12134011},
year = {2002},
date = {2002-01-01},
journal = {J Virol},
volume = {76},
number = {16},
pages = {8058-8068},
abstract = {The 3'-terminal ends of both the positive and negative strands of the hepatitis C virus (HCV) RNA, the latter being the replicative intermediate, are most likely the initiation sites for replication by the viral RNA-dependent RNA polymerase, NS5B. The structural features of the very conserved 3' plus [(+)] strand untranslated region [3' (+) UTR] are well established (K. J. Blight and C. M. Rice, J. Virol. 71:7345-7352, 1997). However, little information is available concerning the 3' end of the minus [(-)] strand RNA. In the present work, we used chemical and enzymatic probing to investigate the conformation of that region, which is complementary to the 5' (+) UTR and the first 74 nucleotides of the HCV polyprotein coding sequence. By combining our experimental data with computer predictions, we have derived a secondary-structure model of this region. In our model, the last 220 nucleotides, where initiation of the (+) strand RNA synthesis presumably takes place, fold into five stable stem-loops, forming domain I. Domain I is linked to an overall less stable structure, named domain II, containing the sequences complementary to the pseudoknot of the internal ribosomal entry site in the 5' (+) UTR. Our results show that, even though the (-) strand 3'-terminal region has the antisense sequence of the 5' (+) UTR, it does not fold into its mirror image. Interestingly, comparison of the replication initiation sites on both strands reveals common structural features that may play key functions in the replication process.},
note = {0022-538x
Journal Article},
keywords = {Base Sequence DNA, MARQUET, Molecular Molecular Probe Techniques Molecular Sequence Data Nucleic Acid Conformation Plasmids/genetics RNA, Non-U.S. Gov't Virus Replication, Unité ARN, Viral/*chemistry/genetics Support, Viral/genetics Hepacivirus/*chemistry/genetics/physiology Human Models},
pubstate = {published},
tppubtype = {article}
}
Rigourd M, Ehresmann C, Parniak M A, Ehresmann B, Marquet R
Dans: J Biol Chem, vol. 277, no. 21, p. 18611-18618, 2002, ISBN: 11901149, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Comparative Study DNA Primers *DNA Replication Drug Resistance, MARQUET, Microbial HIV-1 Reverse Transcriptase/*drug effects Kinetics Reverse Transcriptase Inhibitors/*pharmacology Support, Non-U.S. Gov't Zidovudine/*pharmacology, Unité ARN
@article{,
title = {Primer unblocking and rescue of DNA synthesis by azidothymidine (AZT)-resistant HIV-1 reverse transcriptase: comparison between initiation and elongation of reverse transcription and between (-) and (+) strand DNA synthesis},
author = {M Rigourd and C Ehresmann and M A Parniak and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11901149},
isbn = {11901149},
year = {2002},
date = {2002-01-01},
journal = {J Biol Chem},
volume = {277},
number = {21},
pages = {18611-18618},
abstract = {Azidothymidine (AZT) is a widely used inhibitor of type 1 human immunodeficiency virus reverse transcriptase (RT) that acts as chain terminator. Upon treatment, mutations conferring AZT resistance to RT are gradually selected. It has been shown that resistant RT is able to unblock the AZT-terminated primer by an ATP-dependent mechanism. However, this resistance mechanism has only been demonstrated for DNA-dependent DNA elongation. Here, we compared the AZT resistance of mutant RT during DNA elongation on DNA and RNA templates. We showed that, during DNA elongation, primer unblocking and rescue of DNA synthesis take place with similar rate constants on DNA and RNA templates. However, the fraction of a primer eventually repaired during RNA-dependent DNA synthesis is 2x lower compared with that of DNA-dependent synthesis, leading to reduced resistance. We also compared the initiation of reverse transcription, which uses tRNA(3)(Lys) as a primer and displays characteristic kinetic features, and the subsequent RNA-dependent elongation. Unlike during elongation, resistant RT was unable to unblock the AZT-terminated primer during initiation of (-) DNA strand synthesis. Our results demonstrate that the efficiency of primer unblocking conferred by the AZT resistance mutations greatly vary during the different steps of the provirus synthesis. These results also suggest that inhibitors specifically targeting the initiation of reverse transcription might prove to be advantageous, as compared with elongation inhibitors.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence Comparative Study DNA Primers *DNA Replication Drug Resistance, MARQUET, Microbial HIV-1 Reverse Transcriptase/*drug effects Kinetics Reverse Transcriptase Inhibitors/*pharmacology Support, Non-U.S. Gov't Zidovudine/*pharmacology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Skripkin E, Ehresmann B, Ehresmann C, Marquet R
In vitro evidence for a long range pseudoknot in the 5'-untranslated and matrix coding regions of HIV-1 genomic RNA Article de journal
Dans: J Biol Chem, vol. 277, no. 8, p. 5995-6004, 2002, ISBN: 11744696, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 5' Untranslated Regions/*genetics Base Sequence Dimerization HIV-1/*genetics Human Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Oligodeoxyribonucleotides, Antisense/pharmacology Poly A/chemistry/genetics RNA, MARQUET, Non-U.S. Gov't Virus Replication/genetics, Nucleic Acid Support, PAILLART, Unité ARN, Viral/chemistry/drug effects/*genetics Sequence Alignment Sequence Homology
@article{,
title = {In vitro evidence for a long range pseudoknot in the 5'-untranslated and matrix coding regions of HIV-1 genomic 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=11744696},
isbn = {11744696},
year = {2002},
date = {2002-01-01},
journal = {J Biol Chem},
volume = {277},
number = {8},
pages = {5995-6004},
abstract = {The 5'-untranslated leader region of human immunodeficiency virus type 1 (HIV-1) RNA contains multiple signals that control distinct steps of the viral replication cycle such as transcription, reverse transcription, genomic RNA dimerization, splicing, and packaging. It is likely that fine tuned coordinated regulation of these functions is achieved through specific RNA-protein and RNA-RNA interactions. In a search for cis-acting elements important for the tertiary structure of the 5'-untranslated region of HIV-1 genomic RNA, we identified, by ladder selection experiments, a short stretch of nucleotides directly downstream of the poly(A) signal that interacts with a nucleotide sequence located in the matrix region. Confirmation of the sequence of the interacting sites was obtained by partial or complete inhibition of this interaction by antisense oligonucleotides and by nucleotide substitutions. In the wild type RNA, this long range interaction was intramolecular, since no intermolecular RNA association was detected by gel electrophoresis with an RNA mutated in the dimerization initiation site and containing both sequences involved in the tertiary interaction. Moreover, the functional importance of this interaction is supported by its conservation in all HIV-1 isolates as well as in HIV-2 and simian immunodeficiency virus. Our results raise the possibility that this long range RNA-RNA interaction might be involved in the full-length genomic RNA selection during packaging, repression of the 5' polyadenylation signal, and/or splicing regulation.},
note = {0021-9258
Journal Article},
keywords = {5' Untranslated Regions/*genetics Base Sequence Dimerization HIV-1/*genetics Human Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Oligodeoxyribonucleotides, Antisense/pharmacology Poly A/chemistry/genetics RNA, MARQUET, Non-U.S. Gov't Virus Replication/genetics, Nucleic Acid Support, PAILLART, Unité ARN, Viral/chemistry/drug effects/*genetics Sequence Alignment Sequence Homology},
pubstate = {published},
tppubtype = {article}
}
Tisne C, Rigourd M, Marquet R, Ehresmann C, Dardel F
Dans: RNA, vol. 6, no. 10, p. 1403-1412, 2000, ISBN: 11073216, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Biomolecular *Nucleic Acid Conformation RNA/*chemistry/genetics/metabolism RNA, Genetic Transcription, Genetic/*genetics Virus Replication, Lys/*chemistry/genetics/metabolism Structure-Activity Relationship Support, MARQUET, Molecular Molecular Sequence Data Mutation/genetics Nuclear Magnetic Resonance, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/biosynthesis/genetics Escherichia coli/genetics *Genetic Engineering HIV-1/*genetics/physiology Human Iodine/metabolism Models
@article{,
title = {NMR and biochemical characterization of recombinant human tRNA(Lys)3 expressed in Escherichia coli: identification of posttranscriptional nucleotide modifications required for efficient initiation of HIV-1 reverse transcription},
author = {C Tisne and M Rigourd and R Marquet and C Ehresmann and F Dardel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11073216},
isbn = {11073216},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {10},
pages = {1403-1412},
abstract = {Reverse transcription of HIV-1 viral RNA uses human tRNA(Lys)3 as a primer. Some of the modified nucleotides carried by this tRNA must play a key role in the initiation of this process, because unmodified tRNA produced in vitro is only marginally active as primer. To provide a better understanding of the contribution of base modifications in the initiation complex, we have designed a recombinant system that allows tRNA(Lys)3 expression in Escherichia coli. Because of their high level of overexpression, some modifications are incorporated at substoichiometric levels. We have purified the two major recombinant tRNA(Lys)3 subspecies, and their modified nucleotide contents have been characterized by a combination of NMR and biochemical techniques. Both species carry psis, Ds, T, t6A, and m7G. Differences are observed at position 34, within the anticodon. One fraction lacks the 5-methylaminomethyl group, whereas the other lacks the 2-thio group. Although the s2U34-containing recombinant tRNA is a less efficient primer, it presents most of the characteristics of the mammalian tRNA. On the other hand, the mnm5U34-containing tRNA has a strongly reduced activity. Our results demonstrate that the modifications that are absent in E. coli (m2G10, psi27, m5C48, m5C49, and m1A58) as well as the mnm5 group at position 34 are dispensable for initiation of reverse transcription. In contrast, the 2-thio group at position 34 seems to play an important part in this process.},
note = {1355-8382
Journal Article},
keywords = {Base Sequence DNA, Biomolecular *Nucleic Acid Conformation RNA/*chemistry/genetics/metabolism RNA, Genetic Transcription, Genetic/*genetics Virus Replication, Lys/*chemistry/genetics/metabolism Structure-Activity Relationship Support, MARQUET, Molecular Molecular Sequence Data Mutation/genetics Nuclear Magnetic Resonance, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/biosynthesis/genetics Escherichia coli/genetics *Genetic Engineering HIV-1/*genetics/physiology Human Iodine/metabolism Models},
pubstate = {published},
tppubtype = {article}
}
Rigourd M, Lanchy J M, Grice S F Le, Ehresmann B, Ehresmann C, Marquet R
Inhibition of the initiation of HIV-1 reverse transcription by 3'-azido-3'-deoxythymidine. Comparison with elongation Article de journal
Dans: J Biol Chem, vol. 275, no. 35, p. 26944-26951, 2000, ISBN: 10864929, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Comparative Study DNA Primers Diphosphates/metabolism HIV-1/*genetics HIV-1 Reverse Transcriptase/antagonists & inhibitors/metabolism Human Hydrolysis Kinetics Lymphocytes/drug effects/metabolism/virology Peptide Chain Elongation/*drug effects Support, Genetic/*drug effects Zidovudine/analogs & derivatives/metabolism/*pharmacology, MARQUET, Non-U.S. Gov't Thymine Nucleotides/metabolism Transcription, Unité ARN
@article{,
title = {Inhibition of the initiation of HIV-1 reverse transcription by 3'-azido-3'-deoxythymidine. Comparison with elongation},
author = {M Rigourd and J M Lanchy and S F Le Grice 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=10864929},
isbn = {10864929},
year = {2000},
date = {2000-01-01},
journal = {J Biol Chem},
volume = {275},
number = {35},
pages = {26944-26951},
abstract = {Initiation of human immunodeficiency virus-1 reverse transcription requires formation of a complex containing the viral RNA, primer tRNA(3)(Lys), and reverse transcriptase. Initiation, corresponding to addition of the first six nucleotides to tRNA(3)(Lys), is distinguished from elongation by its high specificity and low efficiency (processivity). Here, we compared the inhibition of initiation and elongation of reverse transcription by 3'-azido-3'-deoxythymidine 5'-triphosphate (AZTTP), the active form of 3'-azido-3'-deoxythymidine. We report the first detailed study of nucleotide binding, discrimination, and pyrophosphorolysis by the authentic initiation complex. We showed that the initiation and elongation complexes bound AZTTP and dTTP with the same affinity, while the polymerization rates were reduced by 148-160-fold during initiation. The pyrophosphorolysis rate of dTTP was reduced by the same extent, indicating that the polymerization equilibrium is the same in the two phases. The efficient unblocking of the 3'-azido-3'-deoxythymidine 5'-monophosphate (AZTMP)-terminated primer by pyrophosphorolysis significantly relieved inhibition of DNA synthesis during elongation in the presence of physiological pyrophosphate concentrations. Remarkably, although pyrophosphorolysis of dTMP and AZTMP were equally efficient during elongation, reverse transcriptase was almost totally unable to unblock the AZTMP-terminated primer during initiation. As a result, inhibition of reverse transcription by AZTTP was more efficient during initiation than elongation of reverse transcription, despite a reduced selectivity of incorporation.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence Comparative Study DNA Primers Diphosphates/metabolism HIV-1/*genetics HIV-1 Reverse Transcriptase/antagonists & inhibitors/metabolism Human Hydrolysis Kinetics Lymphocytes/drug effects/metabolism/virology Peptide Chain Elongation/*drug effects Support, Genetic/*drug effects Zidovudine/analogs & derivatives/metabolism/*pharmacology, MARQUET, Non-U.S. Gov't Thymine Nucleotides/metabolism Transcription, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lodmell J S, Ehresmann C, Ehresmann B, Marquet R
Convergence of natural and artificial evolution on an RNA loop-loop interaction: the HIV-1 dimerization initiation site Article de journal
Dans: RNA, vol. 6, no. 9, p. 1267-1276, 2000, ISBN: 10999604, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Codon, Initiator Dimerization Directed Molecular Evolution Evolution, MARQUET, Molecular HIV-1/*chemistry/genetics Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry/metabolism Support
@article{,
title = {Convergence of natural and artificial evolution on an RNA loop-loop interaction: the HIV-1 dimerization initiation site},
author = {J S Lodmell 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=10999604},
isbn = {10999604},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {9},
pages = {1267-1276},
abstract = {Loop-loop interactions among nucleic acids constitute an important form of molecular recognition in a variety of biological systems. In HIV-1, genomic dimerization involves an intermolecular RNA loop-loop interaction at the dimerization initiation site (DIS), a hairpin located in the 5' noncoding region that contains an autocomplementary sequence in the loop. Only two major DIS loop sequence variants are observed among natural viral isolates. To investigate sequence and structural constraints on genomic RNA dimerization as well as loop-loop interactions in general, we randomized several or all of the nucleotides in the DIS loop and selected in vitro for dimerization-competent sequences. Surprisingly, increasing interloop complementarity above a threshold of 6 bp did not enhance dimerization, although the combinations of nucleotides forming the theoretically most stable hexanucleotide duplexes were selected. Noncanonical interactions contributed significantly to the stability and/or specificity of the dimeric complexes as demonstrated by the overwhelming bias for noncanonical base pairs closing the loop and covariations between flanking and central loop nucleotides. Degeneration of the entire loop yielded a complex population of dimerization-competent sequences whose consensus sequence resembles that of wild-type HIV-1. We conclude from these findings that the DIS has evolved to satisfy simultaneous constraints for optimal dimerization affinity and the capacity for homodimerization. Furthermore, the most constrained features of the DIS identified by our experiments could be the basis for the rational design of DIS-targeted antiviral compounds.},
note = {1355-8382
Journal Article},
keywords = {Codon, Initiator Dimerization Directed Molecular Evolution Evolution, MARQUET, Molecular HIV-1/*chemistry/genetics Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry/metabolism Support},
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}
}
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}
}
Benas P, Bec G, Keith G, Marquet R, Ehresmann C, Ehresmann B, Dumas P
The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop Article de journal
Dans: RNA, vol. 6, no. 10, p. 1347-1355, 2000, ISBN: 11073212, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Anticodon/*chemistry/genetics Base Sequence Cattle Chickens/*genetics Crystallography, Biomolecular *Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Lys/*chemistry/genetics Rabbits Support, MARQUET, Molecular Molecular Sequence Data Nuclear Magnetic Resonance, Non-U.S. Gov't, Transfer, Unité ARN, X-Ray HIV-1/*genetics Models
@article{,
title = {The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop},
author = {P Benas and G Bec and G Keith and R Marquet and C Ehresmann and B Ehresmann and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11073212},
isbn = {11073212},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {10},
pages = {1347-1355},
abstract = {We have solved to 3.3 A resolution the crystal structure of the HIV reverse-transcription primer tRNA(Lys,3). The overall structure is exactly comparable to the well-known L-shape structure first revealed by yeast tRNA(Phe). In particular, it unambiguously shows a canonical anticodon loop. This contradicts previous results in short RNA fragment studies and leads us to conclude that neither frameshifting specificities of tRNA(Lys) nor tRNA(Lys,3) primer selection by HIV are due to a specific three-dimensional anticodon structure. Comparison of our structure with the results of an NMR study on a hairpin representing a nonmodified anticodon stem-loop makes plausible the conclusion that chemical modifications of the wobble base U34 to 5-methoxycarbonyl-methyl-2-thiouridine and of A37 to 2-methylthio-N-6-threonylcarbamoyl-adenosine would be responsible for a canonical 7-nt anticodon-loop structure, whereas the unmodified form would result in a noncanonical UUU short triloop. The hexagonal crystal packing is remarkable and shows tight dimers of tRNAs forming a right-handed double superhelix. Within the dimers, the tRNAs are associated head-to-tail such that the CCA end of one tRNA interacts with the anticodon of the symmetry-related tRNA. This provides us with a partial view of a codon-anticodon interaction and gives insights into the positioning of residue 37, and of its posttranscriptional modifications, relative to the first base of the codon.},
note = {1355-8382
Journal Article},
keywords = {Animals Anticodon/*chemistry/genetics Base Sequence Cattle Chickens/*genetics Crystallography, Biomolecular *Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Lys/*chemistry/genetics Rabbits Support, MARQUET, Molecular Molecular Sequence Data Nuclear Magnetic Resonance, Non-U.S. Gov't, Transfer, Unité ARN, X-Ray HIV-1/*genetics Models},
pubstate = {published},
tppubtype = {article}
}
Yusupov M, Walter P, Marquet R, Ehresmann C, Ehresmann B, Dumas P
Crystallization of the dimerization-initiation site of genomic HIV-1 RNA: preliminary crystallographic results Article de journal
Dans: Acta Crystallogr D Biol Crystallogr, vol. 55, no. Pt 1, p. 281-284, 1999, ISBN: 10089425, (0907-4449 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites Crystallization Crystallography, MARQUET, Non-U.S. Gov't, Unité ARN, Viral HIV-1/*chemistry/genetics Human Molecular Sequence Data Nucleic Acid Conformation RNA, Viral/*chemistry/genetics/isolation & purification Solutions Support, X-Ray Dimerization Genome
@article{,
title = {Crystallization of the dimerization-initiation site of genomic HIV-1 RNA: preliminary crystallographic results},
author = {M Yusupov and P Walter and R Marquet and C Ehresmann and B Ehresmann and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10089425},
isbn = {10089425},
year = {1999},
date = {1999-01-01},
journal = {Acta Crystallogr D Biol Crystallogr},
volume = {55},
number = {Pt 1},
pages = {281-284},
abstract = {The genomic RNA of all retroviruses is encapsidated in virions as a dimer of single-stranded chains held together near their 5'-end. For HIV-1, the initial site of dimerization has been shown to be a hairpin with a nine-residue loop containing a self-complementary sequence of six residues. This structure is proposed to promote dimerization by loop-loop interaction and formation of a so-called 'kissing complex'. A 23-nucleotide RNA strand containing the loop enclosed by a seven base-pair stem has been synthesized. This oligomer was crystallized by the vapour-diffusion method at 310 K, pH 6.5, with methyl-pentanediol as the precipitant agent in the presence of MgCl2, KCl and spermine. Quasi-complete diffraction data were obtained at 2.7 A resolution with a conventional X-ray source and at 2.3 A resolution on a synchrotron beamline. The space group is P3121 or its enantiomorph P3221, with cell parameters a = b = 60. 1},
note = {0907-4449
Journal Article},
keywords = {Base Sequence Binding Sites Crystallization Crystallography, MARQUET, Non-U.S. Gov't, Unité ARN, Viral HIV-1/*chemistry/genetics Human Molecular Sequence Data Nucleic Acid Conformation RNA, Viral/*chemistry/genetics/isolation & purification Solutions Support, X-Ray Dimerization Genome},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Westhof E, Ehresmann C, Ehresmann B, Marquet R
Non-canonical interactions in a kissing loop complex: the dimerization initiation site of HIV-1 genomic RNA Article de journal
Dans: J Mol Biol, vol. 270, no. 1, p. 36-49, 1997, ISBN: 9231899, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Dimerization HIV-1/*genetics Kinetics Models, MARQUET, Molecular Mutagenesis, Non-U.S. Gov't, PAILLART, Site-Directed Nucleic Acid Conformation Purines/chemistry RNA, Unité ARN, Viral/*chemistry/genetics/*metabolism Support
@article{,
title = {Non-canonical interactions in a kissing loop complex: the dimerization initiation site of HIV-1 genomic RNA},
author = {J C Paillart and E Westhof 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=9231899},
isbn = {9231899},
year = {1997},
date = {1997-01-01},
journal = {J Mol Biol},
volume = {270},
number = {1},
pages = {36-49},
abstract = {Retroviruses encapsidate two molecules of genomic RNA that are noncovalently linked close to their 5' ends in a region called the dimer linkage structure (DLS). The dimerization initiation site (DIS) of human immunodeficiency virus type 1 (HIV-1) constitutes the essential part of the DLS in vitro and is crucial for efficient HIV-1 replication in cell culture. We previously identified the DIS as a hairpin structure, located upstream of the major splice donor site, that contains in the loop a six-nucleotide self-complementary sequence preceded and followed by two and one purines, respectively. Two RNA monomers form a kissing loop complex via intermolecular interactions of the six nucleotide self-complementary sequence. Here, we introduced compensatory mutations in the self-complementary sequence and/or a mutation in the flanking purines. We determined the kinetics of dimerization, the thermal stabilities and the apparent equilibrium dissociation constants of wild-type and mutant dimers and used chemical probing to obtain structural information. Our results demonstrate the importance of the 5'-flanking purine and of the two central bases of the self-complementary sequence in the dimerization process. The experimental data are rationalized by triple interactions between these residues in the deep groove of the kissing helix and are incorporated into a three-dimensional model of the kissing loop dimer. In addition, chemical probing and molecular modeling favor the existence of a non-canonical interaction between the conserved adenine residues at the first and last positions in the DIS loop. Furthermore, we show that destabilization of the kissing loop complex at the DIS can be compensated by interactions involving sequences located downstream of the splice donor site of the HIV-1 genomic RNA.},
note = {0022-2836
Journal Article},
keywords = {Dimerization HIV-1/*genetics Kinetics Models, MARQUET, Molecular Mutagenesis, Non-U.S. Gov't, PAILLART, Site-Directed Nucleic Acid Conformation Purines/chemistry RNA, Unité ARN, Viral/*chemistry/genetics/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Isel C, Ehresmann C, Keith G, Ehresmann B, Marquet R
Two step synthesis of (-) strong-stop DNA by avian and murine reverse transcriptases in vitro Article de journal
Dans: Nucleic Acids Res, vol. 25, no. 3, p. 545-552, 1997, ISBN: 9016594, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Cattle DNA Primers DNA, Avian/*enzymology Rna RNA, MARQUET, Murine/*enzymology Mice Myeloblastosis Virus, Non-U.S. Gov't, Pro RNA, Transfer, Trp RNA-Directed DNA Polymerase/*metabolism Support, Unité ARN, Viral/*biosynthesis Leukemia Virus
@article{,
title = {Two step synthesis of (-) strong-stop DNA by avian and murine reverse transcriptases in vitro},
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=9016594},
isbn = {9016594},
year = {1997},
date = {1997-01-01},
journal = {Nucleic Acids Res},
volume = {25},
number = {3},
pages = {545-552},
abstract = {Retroviral reverses transcriptases (RTs) are RNA- and DNA-dependent DNA polymerases that use a tRNA bound at the so-called primer binding site (PBS) located near the 5'end of the genomic RNA as primer. Thus, RTs must be able to accommodate both RNA and DNA in the primer strand. To test whether the natural primer confers some advantages to the priming process, we compared initiation of reverse transcription of avian and murine retroviral RNAs, using either their natural tRNA primer, tRNATrp and tRNAPro, respectively, or synthetic 18mer oligodeoxyribonucleotides (ODNs) and oligoribonucleotides (ORNs) complementary to their PBS. In both retroviral systems, the initial extension of ODNs was fast and processive. The initial extension of ORNs, tRNATrp and tRNAPro was much slower and distributive, giving rise to the transient accumulation of short pausing products. Synthesis of (-) strong-stop DNA was delayed when using ORNs and tRNAs, compared to ODNs. Even though ORNs and tRNAs were initially extended at the same rate, the short pausing products were more rapidly extended when using the tRNA primers. As a consequence, synthesis of (-) strong-stop DNA was much more efficient with tRNA primers, compared to ORNs. Taken together, these results suggest that the tRNA-primed synthesis of (-) strong-stop DNA is a two-step process, as already observed for HIV-1. The initiation mode corresponds to the initial non-processive nucleotide addition and extension of the short pausing products. It is more efficient with the natural primers than with ORNs. Initiation is followed by a more processive and unspecific elongation mode. Elongation is observed when the primer strand is DNA, i.e. when using the ODNs as primers or when the ORN and tRNA primers have been extended by a sufficient number (depending on the retroviral system) of deoxyribonucleotides.},
note = {0305-1048
Journal Article},
keywords = {Animals Cattle DNA Primers DNA, Avian/*enzymology Rna RNA, MARQUET, Murine/*enzymology Mice Myeloblastosis Virus, Non-U.S. Gov't, Pro RNA, Transfer, Trp RNA-Directed DNA Polymerase/*metabolism Support, Unité ARN, Viral/*biosynthesis Leukemia Virus},
pubstate = {published},
tppubtype = {article}
}
Yusupova G, Lanchy J M, Yusupov M, Keith G, Grice S F Le, Ehresmann C, Ehresmann B, Marquet R
Primer selection by HIV-1 reverse transcriptase on RNA-tRNA(3Lys) and DNA-tRNA(3Lys) hybrids Article de journal
Dans: J Mol Biol, vol. 261, no. 3, p. 315-321, 1996, ISBN: 8780773, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Lys/genetics/*metabolism RNA, MARQUET, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN, Viral/genetics HIV-1/*enzymology/genetics HIV-1 Reverse Transcriptase Human Molecular Sequence Data *RNA Processing, Viral/genetics RNA-Directed DNA Polymerase/genetics/*metabolism Support
@article{,
title = {Primer selection by HIV-1 reverse transcriptase on RNA-tRNA(3Lys) and DNA-tRNA(3Lys) hybrids},
author = {G Yusupova and J M Lanchy and M Yusupov 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=8780773},
isbn = {8780773},
year = {1996},
date = {1996-01-01},
journal = {J Mol Biol},
volume = {261},
number = {3},
pages = {315-321},
abstract = {During reverse transcription of the genomic RNA of human immunodeficiency virus type 1 (HIV-1) into double-stranded DNA, reverse transcriptase (RT) must accommodate RNA-RNA, DNA-RNA, RNA-DNA and DNA-DNA hybrids as primer-template. In this study, we examined extension of RNA-tRNA3Lys, and DNA-tRNA3Lys complexes by HIV-1 RT. When the 3' end of tRNA3Lys is annealed to oligoribonucleotides, tRNA3Lys, but not the complementary RNAs, is extended by HIV-1 RT, indicating that tRNA3Lys is efficiently used as primer and RNA as template. An opposite primer usage is observed when tRNA3Lys is annealed to complementary oligodeoxyribonucleotides. In this case, the oligodeoxyribonucleotides are efficiently used as primer and tRNA3Lys as template. This result indicates that the nature of nucleic acid bound to tRNA3Lys determines which strand of the RNA-tRNA3Lys and DNA-tRNA3Lys hybrids is extended by HIV-1 RT. When an oligoribonucleotide is annealed to an unmodified transcript of tRNA3Lys, both nucleic acids are extended by HIV-1 RT, indicating that specific selection of tRNA3Lys as primer requires the post-transcriptional modifications of tRNA3Lys.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence DNA, Lys/genetics/*metabolism RNA, MARQUET, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN, Viral/genetics HIV-1/*enzymology/genetics HIV-1 Reverse Transcriptase Human Molecular Sequence Data *RNA Processing, Viral/genetics RNA-Directed DNA Polymerase/genetics/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Skripkin E, Paillart J C, Marquet R, Blumenfeld M, Ehresmann B, Ehresmann C
Mechanisms of inhibition of in vitro dimerization of HIV type I RNA by sense and antisense oligonucleotides Article de journal
Dans: J Biol Chem, vol. 271, no. 46, p. 28812-28817, 1996, ISBN: 8910525, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antisense/*pharmacology RNA, Biopolymers HIV-1/*genetics Nucleic Acid Conformation Oligonucleotides/*pharmacology Oligonucleotides, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*antagonists & inhibitors/chemistry Support
@article{,
title = {Mechanisms of inhibition of in vitro dimerization of HIV type I RNA by sense and antisense oligonucleotides},
author = {E Skripkin and J C Paillart and R Marquet and M Blumenfeld and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8910525},
isbn = {8910525},
year = {1996},
date = {1996-01-01},
journal = {J Biol Chem},
volume = {271},
number = {46},
pages = {28812-28817},
abstract = {Retroviruses display a strong selective pressure to maintain the dimeric nature of their genomic RNAs, suggesting that dimerization is essential for viral replication. Recently, we identified the cis-element required for initiation of human immunodeficiency virus type I (HIV-I) RNA dimerization in vitro. The dimerization initiation site (DIS) is a hairpin structure containing a self-complementary sequence in the loop. We proposed that dimerization is initiated by a loop-loop kissing interaction involving the self-complementary sequence present in each monomer. We tested the ability of sense and antisense oligonucleotides targeted against the DIS to interfere with a preformed viral RNA dimer. Self-dimerization and inhibition properties of the tested oligonucleotides are dictated by the nature of the loop. An RNA loop is absolutely required in the case of sense oligonucleotides, whereas the nature and the sequence of the stem is not important. They form reversible loop-loop interactions and act as competitive inhibitors. Antisense oligonucleotides are less efficient in self-dimerization and are more potent inhibitors than sense oligonucleotides. They are less sensitive to the nature of the loop than the antisense oligonucleotides. Antisense hairpins with either RNA or DNA stems are able to form highly stable and irreversible complexes with viral RNA, resulting from complete extension of base pairing initiated by loop-loop interaction.},
note = {0021-9258
Journal Article},
keywords = {Antisense/*pharmacology RNA, Biopolymers HIV-1/*genetics Nucleic Acid Conformation Oligonucleotides/*pharmacology Oligonucleotides, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*antagonists & inhibitors/chemistry Support},
pubstate = {published},
tppubtype = {article}
}
Skripkin E, Isel C, Marquet R, Ehresmann B, Ehresmann C
Psoralen crosslinking between human immunodeficiency virus type 1 RNA and primer tRNA3(Lys) Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 3, p. 509-514, 1996, ISBN: 8602365, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Cross-Linking Reagents/*metabolism Ficusin/*metabolism HIV-1/*genetics Human Molecular Sequence Data Molecular Structure RNA, Lys/*genetics/metabolism RNA, MARQUET, Non-U.S. Gov't, Transfer, Unité ARN, Viral/*genetics/metabolism Support
@article{,
title = {Psoralen crosslinking between human immunodeficiency virus type 1 RNA and primer tRNA3(Lys)},
author = {E Skripkin and C Isel and R Marquet and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8602365},
isbn = {8602365},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {3},
pages = {509-514},
abstract = {Initiation of reverse transcription is a crucial step of retroviral infection. In HIV-1, it involves hybridization of the 18 3'-terminal nucleotides of the primer tRNA3(Lys) to the primer binding site (PBS) of the viral RNA. Moreover, additional interactions between the two RNAs were recently evidenced [Isel et al. (1995) J. Mol. Biol. 247, 25269-25272]. To get further information on the topology of the viral RNA/tRNA3(Lys) complex, we used psoralen to induce RNA-RNA crosslinking. A defined intermolecular crosslinked complex was obtained. The crosslinked regions were characterized by RNase T1 digestion followed by bi-dimensional gel electrophoresis. The crosslinked residues (nucleotide mcm5S2U34 and U35 in the anticodon loop of tRNA3(Lys) and UCU154 in the viral RNA upstream of the PBS) were mapped using a retardation method coupled with random hydrolysis. The formation of this crosslink depends on the same elements that are required for the formation of the extended interactions between primer and template RNAs, i.e., the modified bases of the tRNA and a conserved A-rich loop located upstream of the PBS in the genomic RNA. Therefore, the present crosslinking data provide relevant information on the topology of the template/primer binary complex.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Cross-Linking Reagents/*metabolism Ficusin/*metabolism HIV-1/*genetics Human Molecular Sequence Data Molecular Structure RNA, Lys/*genetics/metabolism RNA, MARQUET, Non-U.S. Gov't, Transfer, Unité ARN, Viral/*genetics/metabolism Support},
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}
}
Paillart J C, Skripkin E, Ehresmann B, Ehresmann C, Marquet R
The use of chemical modification interference and inverse PCR mutagenesis to identify the dimerization initiation site of HIV-1 genomic RNA Article de journal
Dans: Pharm Acta Helv, vol. 71, no. 1, p. 21-28, 1996, ISBN: 8786995, (0031-6865 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence *Genome, MARQUET, Non-U.S. Gov't, PAILLART, Site-Directed Polymerase Chain Reaction RNA, Unité ARN, Viral HIV-1/*chemistry Human Molecular Sequence Data Mutagenesis, Viral/*chemistry Support
@article{,
title = {The use of chemical modification interference and inverse PCR mutagenesis to identify the dimerization initiation site of HIV-1 genomic 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=8786995},
isbn = {8786995},
year = {1996},
date = {1996-01-01},
journal = {Pharm Acta Helv},
volume = {71},
number = {1},
pages = {21-28},
abstract = {The retroviral genome consists of two identical RNA molecules physically linked together close to their 5' end, in a region called the Dimer Linkage Structure (DLS). Recent findings suggest that dimerization is involved in encapsidation, regulation of translation and reverse transcription. Previous in vitro studies localized the DLS of HIV-1 in a region downstream of the splice donor (SD) site. More recently, we showed that dimerization of HIV-1 RNA also involves sequences upstream of the SD site. Modification interference experiments and site-directed mutagenesis were used to identify the nucleotides required in the dimerization process of HIV-1 RNA. Our results point out a self-complementary sequence located in a hairpin loop, between the Primer Binding Site (PBS) and the SD site, as the Dimerization Initiation Site.},
note = {0031-6865
Journal Article},
keywords = {Base Sequence *Genome, MARQUET, Non-U.S. Gov't, PAILLART, Site-Directed Polymerase Chain Reaction RNA, Unité ARN, Viral HIV-1/*chemistry Human Molecular Sequence Data Mutagenesis, Viral/*chemistry Support},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Marquet R, Skripkin E, Ehresmann C, Ehresmann B
Dimerization of retroviral genomic RNAs: structural and functional implications Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 639-653, 1996, ISBN: 8955907, (0300-9084 Journal Article Review Review, Academic).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence HIV-1/genetics Human Microscopy, DNA Support, Electron Molecular Sequence Data *Nucleic Acid Conformation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry/metabolism Rats Retroviridae/*genetics Sequence Analysis
@article{,
title = {Dimerization of retroviral genomic RNAs: structural and functional implications},
author = {J C Paillart and R Marquet and E Skripkin and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955907},
isbn = {8955907},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {639-653},
abstract = {Retroviruses are a family of widespread small animal viruses at the origin of a diversity of diseases. They share common structural and functional properties such as reverse transcription of their RNA genome and integration of the proviral DNA into the host genome, and have the particularity of packaging a diploid genome. The genome of all retroviruses is composed of two homologous RNA molecules that are non-covalently linked near their 5' end in a region called the dimer linkage structure (DLS). There is now considerable evidence that a specific site (or sites) in the 5' leader region of all retroviruses, located either upstream or/and downstream of the major splice donor site, is involved in the dimer linkage. For MoMuLV and especially HIV-1, it was shown that dimerization is initiated at a stem-loop structure named the dimerization initiation site (DIS). The DIS of HIV-1 and related regions in other retroviruses corresponds to a highly conserved structure with a self-complementary loop sequence, that is involved in a typical loop-loop 'kissing' complex which can be further stabilized by long distance interactions or by conformational rearrangements. RNA interactions involved in the viral RNA dimer were postulated to regulate several key steps in retroviral cycle, such as: i) translation and encapsidation: the arrest of gag translation imposed by the highly structured DLS-encapsidation signal would leave the RNA genome available for the encapsidation machinery; and ii) recombination during reverse transcription: the presence of two RNA molecules in particles would be necessary for variability and viability of virus progeny and the ordered structure imposed by the DLS would be required for efficient reverse transcription.},
note = {0300-9084
Journal Article
Review
Review, Academic},
keywords = {Animals Base Sequence HIV-1/genetics Human Microscopy, DNA Support, Electron Molecular Sequence Data *Nucleic Acid Conformation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry/metabolism Rats Retroviridae/*genetics Sequence Analysis},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Berthoux L, Ottmann M, Darlix J L, Marquet R, Ehresmann B, Ehresmann C
A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis Article de journal
Dans: J Virol, vol. 70, no. 12, p. 8348-8354, 1996, ISBN: 8970954, (0022-538x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals COS Cells DNA, Genetic Virion *Virus Assembly, MARQUET, Non-U.S. Gov't Transcription, Nucleic Acid Support, PAILLART, Post-Translational Proviruses/genetics *RNA, Unité ARN, Viral *Regulatory Sequences, Viral HIV-1/*genetics/physiology Human Mutagenesis Protein Processing, Viral/*biosynthesis Gene Expression Genome
@article{,
title = {A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis},
author = {J C Paillart and L Berthoux and M Ottmann and J L Darlix and R Marquet and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8970954},
isbn = {8970954},
year = {1996},
date = {1996-01-01},
journal = {J Virol},
volume = {70},
number = {12},
pages = {8348-8354},
abstract = {In retroviruses, the genomic RNA is in the form of a 60S-70S complex composed of two identical genome-length RNA molecules tightly associated through numerous interactions. A major interaction, called the dimer linkage structure, has been found near the RNA 5' end and is probably involved in the control of translation, packaging, and recombination during proviral DNA synthesis. Recently, a small sequence corresponding to a stem-loop structure located in the 5' leader of human immunodeficiency virus type 1 (HIV-1) RNA was found to be required for the initiation of HIV-1 RNA dimerization in vitro and named the dimerization initiation site (E. Skripkin, J.-C. Paillart, R. Marquet, B. Ehresmann, and C. Ehresmann, Proc. Natl. Acad. Sci. USA 91: 4945-4949, 1994). To investigate the possible role of this 5' stem-loop in HIV-1 virion formation and infectivity, four mutant viruses were generated and analyzed in vivo. Results show that deletion of the stem-loop structure reduces infectivity by a factor of 10(3) whereas loop substitutions cause a decrease of 10- to 100-fold. The level of genomic RNA packaging was found to be decreased fivefold in mutants virions containing the stem-loop deletion and only twofold in the loop-substituted virions. Surprisingly, the second DNA strand transfer during reverse transcription was found to be severely impaired upon stem-loop deletion. Taken together, these results indicate that the stem-loop structure called the dimerization initiation site is a cis element acting on both genomic RNA packaging and synthesis of proviral DNA.},
note = {0022-538x
Journal Article},
keywords = {Animals COS Cells DNA, Genetic Virion *Virus Assembly, MARQUET, Non-U.S. Gov't Transcription, Nucleic Acid Support, PAILLART, Post-Translational Proviruses/genetics *RNA, Unité ARN, Viral *Regulatory Sequences, Viral HIV-1/*genetics/physiology Human Mutagenesis Protein Processing, Viral/*biosynthesis Gene Expression Genome},
pubstate = {published},
tppubtype = {article}
}
Marquet R, Paillart J C, Skripkin E, Ehresmann C, Ehresmann B
Localization of the dimerization initiation site of HIV-1 genomic RNA and mechanism of dimerization. Chapitre d'ouvrage
Dans: Sarma, R H; Sarma, M H (Ed.): Biological Structure and Dynamics: Proceedings of the Ninth Conversation in the Discipline Biomolecular Stereodynamics, held at the State University of New York at Albany, June 20-24, 1995, vol. 2, p. 61-72, Adenine Press, 1996.
Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@inbook{,
title = {Localization of the dimerization initiation site of HIV-1 genomic RNA and mechanism of dimerization.},
author = {R Marquet and J C Paillart and E Skripkin and C Ehresmann and B Ehresmann},
editor = {R H Sarma and M H Sarma},
url = {http://books.google.fr/books?hl=fr&id=SOpqAAAAMAAJ&q=Marquet#search_anchor},
year = {1996},
date = {1996-01-01},
booktitle = {Biological Structure and Dynamics: Proceedings of the Ninth Conversation in the Discipline Biomolecular Stereodynamics, held at the State University of New York at Albany, June 20-24, 1995},
volume = {2},
pages = {61-72},
publisher = {Adenine Press},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
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}
}
Paillart J C, Skripkin E, Ehresmann B, Ehresmann C, Marquet R
The use of chemical modification interference and inverse PCR mutagenesis to identify the dimerization initiation site of HIV-1 genomic RNA Article de journal
Dans: Pharm Acta Helv, vol. 71, no. 1, p. 21-28, 1996, ISBN: 8786995, (0031-6865 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence *Genome, MARQUET, Non-U.S. Gov't, PAILLART, Site-Directed Polymerase Chain Reaction RNA, Unité ARN, Viral HIV-1/*chemistry Human Molecular Sequence Data Mutagenesis, Viral/*chemistry Support
@article{,
title = {The use of chemical modification interference and inverse PCR mutagenesis to identify the dimerization initiation site of HIV-1 genomic 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=8786995},
isbn = {8786995},
year = {1996},
date = {1996-01-01},
journal = {Pharm Acta Helv},
volume = {71},
number = {1},
pages = {21-28},
abstract = {The retroviral genome consists of two identical RNA molecules physically linked together close to their 5' end, in a region called the Dimer Linkage Structure (DLS). Recent findings suggest that dimerization is involved in encapsidation, regulation of translation and reverse transcription. Previous in vitro studies localized the DLS of HIV-1 in a region downstream of the splice donor (SD) site. More recently, we showed that dimerization of HIV-1 RNA also involves sequences upstream of the SD site. Modification interference experiments and site-directed mutagenesis were used to identify the nucleotides required in the dimerization process of HIV-1 RNA. Our results point out a self-complementary sequence located in a hairpin loop, between the Primer Binding Site (PBS) and the SD site, as the Dimerization Initiation Site.},
note = {0031-6865
Journal Article},
keywords = {Base Sequence *Genome, MARQUET, Non-U.S. Gov't, PAILLART, Site-Directed Polymerase Chain Reaction RNA, Unité ARN, Viral HIV-1/*chemistry Human Molecular Sequence Data Mutagenesis, Viral/*chemistry Support},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Marquet R, Skripkin E, Ehresmann C, Ehresmann B
Dimerization of retroviral genomic RNAs: structural and functional implications Article de journal
Dans: Biochimie, vol. 78, no. 7, p. 639-653, 1996, ISBN: 8955907, (0300-9084 Journal Article Review Review, Academic).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence HIV-1/genetics Human Microscopy, DNA Support, Electron Molecular Sequence Data *Nucleic Acid Conformation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry/metabolism Rats Retroviridae/*genetics Sequence Analysis
@article{,
title = {Dimerization of retroviral genomic RNAs: structural and functional implications},
author = {J C Paillart and R Marquet and E Skripkin and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955907},
isbn = {8955907},
year = {1996},
date = {1996-01-01},
journal = {Biochimie},
volume = {78},
number = {7},
pages = {639-653},
abstract = {Retroviruses are a family of widespread small animal viruses at the origin of a diversity of diseases. They share common structural and functional properties such as reverse transcription of their RNA genome and integration of the proviral DNA into the host genome, and have the particularity of packaging a diploid genome. The genome of all retroviruses is composed of two homologous RNA molecules that are non-covalently linked near their 5' end in a region called the dimer linkage structure (DLS). There is now considerable evidence that a specific site (or sites) in the 5' leader region of all retroviruses, located either upstream or/and downstream of the major splice donor site, is involved in the dimer linkage. For MoMuLV and especially HIV-1, it was shown that dimerization is initiated at a stem-loop structure named the dimerization initiation site (DIS). The DIS of HIV-1 and related regions in other retroviruses corresponds to a highly conserved structure with a self-complementary loop sequence, that is involved in a typical loop-loop 'kissing' complex which can be further stabilized by long distance interactions or by conformational rearrangements. RNA interactions involved in the viral RNA dimer were postulated to regulate several key steps in retroviral cycle, such as: i) translation and encapsidation: the arrest of gag translation imposed by the highly structured DLS-encapsidation signal would leave the RNA genome available for the encapsidation machinery; and ii) recombination during reverse transcription: the presence of two RNA molecules in particles would be necessary for variability and viability of virus progeny and the ordered structure imposed by the DLS would be required for efficient reverse transcription.},
note = {0300-9084
Journal Article
Review
Review, Academic},
keywords = {Animals Base Sequence HIV-1/genetics Human Microscopy, DNA Support, Electron Molecular Sequence Data *Nucleic Acid Conformation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry/metabolism Rats Retroviridae/*genetics Sequence Analysis},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Berthoux L, Ottmann M, Darlix J L, Marquet R, Ehresmann B, Ehresmann C
A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis Article de journal
Dans: J Virol, vol. 70, no. 12, p. 8348-8354, 1996, ISBN: 8970954, (0022-538x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals COS Cells DNA, Genetic Virion *Virus Assembly, MARQUET, Non-U.S. Gov't Transcription, Nucleic Acid Support, PAILLART, Post-Translational Proviruses/genetics *RNA, Unité ARN, Viral *Regulatory Sequences, Viral HIV-1/*genetics/physiology Human Mutagenesis Protein Processing, Viral/*biosynthesis Gene Expression Genome
@article{,
title = {A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis},
author = {J C Paillart and L Berthoux and M Ottmann and J L Darlix and R Marquet and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8970954},
isbn = {8970954},
year = {1996},
date = {1996-01-01},
journal = {J Virol},
volume = {70},
number = {12},
pages = {8348-8354},
abstract = {In retroviruses, the genomic RNA is in the form of a 60S-70S complex composed of two identical genome-length RNA molecules tightly associated through numerous interactions. A major interaction, called the dimer linkage structure, has been found near the RNA 5' end and is probably involved in the control of translation, packaging, and recombination during proviral DNA synthesis. Recently, a small sequence corresponding to a stem-loop structure located in the 5' leader of human immunodeficiency virus type 1 (HIV-1) RNA was found to be required for the initiation of HIV-1 RNA dimerization in vitro and named the dimerization initiation site (E. Skripkin, J.-C. Paillart, R. Marquet, B. Ehresmann, and C. Ehresmann, Proc. Natl. Acad. Sci. USA 91: 4945-4949, 1994). To investigate the possible role of this 5' stem-loop in HIV-1 virion formation and infectivity, four mutant viruses were generated and analyzed in vivo. Results show that deletion of the stem-loop structure reduces infectivity by a factor of 10(3) whereas loop substitutions cause a decrease of 10- to 100-fold. The level of genomic RNA packaging was found to be decreased fivefold in mutants virions containing the stem-loop deletion and only twofold in the loop-substituted virions. Surprisingly, the second DNA strand transfer during reverse transcription was found to be severely impaired upon stem-loop deletion. Taken together, these results indicate that the stem-loop structure called the dimerization initiation site is a cis element acting on both genomic RNA packaging and synthesis of proviral DNA.},
note = {0022-538x
Journal Article},
keywords = {Animals COS Cells DNA, Genetic Virion *Virus Assembly, MARQUET, Non-U.S. Gov't Transcription, Nucleic Acid Support, PAILLART, Post-Translational Proviruses/genetics *RNA, Unité ARN, Viral *Regulatory Sequences, Viral HIV-1/*genetics/physiology Human Mutagenesis Protein Processing, Viral/*biosynthesis Gene Expression Genome},
pubstate = {published},
tppubtype = {article}
}
Marquet R, Paillart J C, Skripkin E, Ehresmann C, Ehresmann B
Localization of the dimerization initiation site of HIV-1 genomic RNA and mechanism of dimerization. Chapitre d'ouvrage
Dans: Sarma, R H; Sarma, M H (Ed.): Biological Structure and Dynamics: Proceedings of the Ninth Conversation in the Discipline Biomolecular Stereodynamics, held at the State University of New York at Albany, June 20-24, 1995, vol. 2, p. 61-72, Adenine Press, 1996.
Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@inbook{,
title = {Localization of the dimerization initiation site of HIV-1 genomic RNA and mechanism of dimerization.},
author = {R Marquet and J C Paillart and E Skripkin and C Ehresmann and B Ehresmann},
editor = {R H Sarma and M H Sarma},
url = {http://books.google.fr/books?hl=fr&id=SOpqAAAAMAAJ&q=Marquet#search_anchor},
year = {1996},
date = {1996-01-01},
booktitle = {Biological Structure and Dynamics: Proceedings of the Ninth Conversation in the Discipline Biomolecular Stereodynamics, held at the State University of New York at Albany, June 20-24, 1995},
volume = {2},
pages = {61-72},
publisher = {Adenine Press},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Marquet R
L'initiation de la transcription inverse du HIV-1: spécificités structurales et fonctionelles. Article de journal
Dans: Regard sur la Biochimie, vol. 4, p. 62-69, 1996, ISSN: 0336-1640.
Liens | BibTeX | Étiquettes: MARQUET, Unité ARN, Virus HIV1 Transcription inverse Initiation transcription Article synthèse Virus immunodéficience humaine Lentivirinae Retroviridae Virus
@article{,
title = {L'initiation de la transcription inverse du HIV-1: spécificités structurales et fonctionelles.},
author = {R Marquet},
url = {http://cat.inist.fr/?aModele=afficheN&cpsidt=2524109},
issn = {0336-1640},
year = {1996},
date = {1996-01-01},
journal = {Regard sur la Biochimie},
volume = {4},
pages = {62-69},
keywords = {MARQUET, Unité ARN, Virus HIV1 Transcription inverse Initiation transcription Article synthèse Virus immunodéficience humaine Lentivirinae Retroviridae Virus},
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}
}
Isel C, Lanchy J M, Grice S F Le, Ehresmann C, Ehresmann B, Marquet R
Specific initiation and switch to elongation of human immunodeficiency virus type 1 reverse transcription require the post-transcriptional modifications of primer tRNA3Lys Article de journal
Dans: EMBO J, vol. 15, no. 4, p. 917-924, 1996, ISBN: 8631312, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Cell-Free System Gene Expression Regulation, Genetic *Virus Replication, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral HIV-1/*genetics HIV-1 Reverse Transcriptase RNA, Viral/metabolism RNA-Directed DNA Polymerase/*metabolism Support
@article{,
title = {Specific initiation and switch to elongation of human immunodeficiency virus type 1 reverse transcription require the post-transcriptional modifications of primer tRNA3Lys},
author = {C Isel and J M Lanchy 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=8631312},
isbn = {8631312},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {4},
pages = {917-924},
abstract = {Initiation of RNA-dependent DNA synthesis by retroviral reverse transcriptases is generally considered as unspecific. In the case of human immunodeficiency virus type 1 (HIV-1), the natural primer is tRNA3Lys. We recently found evidence of complex interactions between tRNA3Lys and HIV-1 RNA that may be involved in the priming process. In this study, we compare the ability of natural and unmodified synthetic tRNA3Lys and 18mer oligoribo- and oligodeoxyribonucleotides complementary to the viral primer binding site to initiate replication of HIV-1 RNA using either homologous or heterologous reverse transcriptases. We show that HIV-1 RNA, HIV-1 reverse transcriptase and primer tRNA3Lys form a specific initiation complex that differs from the unspecific elongation complex formed when an oligodeoxyribonucleotide is used as primer. Modified nucleosides of tRNA3Lys are required for efficient initiation and transition to elongation. Transition from initiation to elongation, but not initiation of reverse transcription itself, is facilitated by extended primer-template interactions. Elongation, but not initiation of reverse transcription, is inhibited by Mn2+, which further differentiates these two different functional states of reverse transcriptase. These results define initiation of reverse transcription as a target to block viral replication.},
note = {0261-4189
Journal Article},
keywords = {Cell-Free System Gene Expression Regulation, Genetic *Virus Replication, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral HIV-1/*genetics HIV-1 Reverse Transcriptase RNA, Viral/metabolism RNA-Directed DNA Polymerase/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Isel C, Ehresmann C, Ehresmann B, Marquet R
Determining the conformation of RNAs in solution. Application to a retroviral system: structure of the HIV-1 primer binding site region and effect of tRNA(3Lys) binding Article de journal
Dans: Pharm Acta Helv, vol. 71, no. 1, p. 11-19, 1996, ISBN: 8786994, (0031-6865 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Binding Sites DNA Primers HIV-1/*chemistry Human Nucleic Acid Conformation RNA, Lys/*chemistry RNA, MARQUET, Non-U.S. Gov't, Transfer, Unité ARN, Viral/*chemistry Solutions Support
@article{,
title = {Determining the conformation of RNAs in solution. Application to a retroviral system: structure of the HIV-1 primer binding site region and effect of tRNA(3Lys) binding},
author = {C Isel 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=8786994},
isbn = {8786994},
year = {1996},
date = {1996-01-01},
journal = {Pharm Acta Helv},
volume = {71},
number = {1},
pages = {11-19},
abstract = {RNAs play a crucial and central role in a large variety of biological functions obviously linked to the wide variety of structures that they can adopt. Understanding the function of RNAs thus requires the knowledge of their two- and three-dimensional structures. We describe in detail the way to access the secondary structure of RNAs, by combining sequence comparison, secondary structure prediction by computer and, mainly, experimental data obtained by probing with chemicals and ribonucleases. These approaches were used to investigate secondary structure of the region containing the primer binding site of HIV-1 genomic RNA either free or involved in the binary complex with the replication primer tRNA(3Lys).},
note = {0031-6865
Journal Article},
keywords = {Amino Acid Sequence Binding Sites DNA Primers HIV-1/*chemistry Human Nucleic Acid Conformation RNA, Lys/*chemistry RNA, MARQUET, Non-U.S. Gov't, Transfer, Unité ARN, Viral/*chemistry Solutions Support},
pubstate = {published},
tppubtype = {article}
}
Gotte M, Marquet R, Isel C, Anderson V E, Keith G, Gross H J, Ehresmann C, Ehresmann B, Heumann H
Probing the higher order structure of RNA with peroxonitrous acid Article de journal
Dans: FEBS Lett, vol. 390, no. 2, p. 226-228, 1996, ISBN: 8706865, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Chelating Agents Edetic Acid Hydroxyl Radical/chemistry Molecular Probes Molecular Structure *Nitrates RNA, Fungal/chemistry RNA, Lys/chemistry RNA, MARQUET, Non-U.S. Gov't, Phe/chemistry Rabbits Saccharomyces cerevisiae/chemistry Support, Transfer, Transfer/*chemistry RNA, Unité ARN
@article{,
title = {Probing the higher order structure of RNA with peroxonitrous acid},
author = {M Gotte and R Marquet and C Isel and V E Anderson and G Keith and H J Gross and C Ehresmann and B Ehresmann and H Heumann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8706865},
isbn = {8706865},
year = {1996},
date = {1996-01-01},
journal = {FEBS Lett},
volume = {390},
number = {2},
pages = {226-228},
abstract = {Potassium peroxonitrite (ONOOK) and [Fe(EDTA)]2- were used to analyze the influence of chemically entirely different hydroxyl radical sources on tRNA cleavage profiles. [Fe(EDTA)]2- gives rise to hydroxyl radicals via a Fenton-like reaction during the oxidation of chelated Fe2+, while ONOOK generates hydroxyl radicals via its conjugate acid (ONOOH) when adding a stable alkaline solution of ONOOK in samples buffered at neutral pH. [Fe(EDTA)]2- is known to induce oxidative strand scission at sugar moieties thought to be solvent accessible, while those residues located in the 'inside' of structured RNAs are protected. Although ONOOH is neutral and significantly smaller than the metal complex, both reagents generate the same protection pattern on tRNAs, suggesting that access of the commonly formed hydroxyl radical, rather than access of its source, is the determining factor when probing the higher order structure of RNA. Strong difference in reactivity is only seen at the modified 2-thiouridine S34 of tRNA(Lys3) which shows hyperreactivity towards ONOOK treatment. This particular reaction may require interaction between the peroxonitrite anion and the thiocarbonyl group of the base, since hyperreactivity is not observed when probing the dethiolated tRNA(Lys3).},
note = {0014-5793
Journal Article},
keywords = {Animals Chelating Agents Edetic Acid Hydroxyl Radical/chemistry Molecular Probes Molecular Structure *Nitrates RNA, Fungal/chemistry RNA, Lys/chemistry RNA, MARQUET, Non-U.S. Gov't, Phe/chemistry Rabbits Saccharomyces cerevisiae/chemistry Support, Transfer, Transfer/*chemistry RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mely Y, de Rocquigny H, Sorinas-Jimeno M, Keith G, Roques B P, Marquet R, Gerard D
Binding of the HIV-1 nucleocapsid protein to the primer tRNA(3Lys), in vitro, is essentially not specific Article de journal
Dans: J Biol Chem, vol. 270, no. 4, p. 1650-1656, 1995, ISBN: 7829498, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Capsid/*chemistry/*metabolism *Capsid Proteins Escherichia coli Gene Products, Amino Acyl/biosynthesis/chemistry/*metabolism Substrate Specificity Support, gag/*chemistry/*metabolism HIV-1/*metabolism Hydrogen-Ion Concentration Kinetics Magnesium Chloride/pharmacology Mathematics Models, Genetic Zinc Fingers, MARQUET, Non-U.S. Gov't Transcription, Theoretical Molecular Sequence Data Nucleic Acid Conformation Osmolar Concentration Protein Binding RNA, Transfer, Unité ARN
@article{,
title = {Binding of the HIV-1 nucleocapsid protein to the primer tRNA(3Lys), in vitro, is essentially not specific},
author = {Y Mely and H de Rocquigny and M Sorinas-Jimeno and G Keith and B P Roques and R Marquet and D Gerard},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7829498},
isbn = {7829498},
year = {1995},
date = {1995-01-01},
journal = {J Biol Chem},
volume = {270},
number = {4},
pages = {1650-1656},
abstract = {The nucleocapsid protein NCp7 of human immunodeficiency virus, type 1, is a key component in the viral life cycle. Since, the first common step of all reported NCp7 activities corresponds to a nucleic acid-binding step, the NCp7 binding parameters to the natural primer tRNA(3Lys) were investigated. Using NCp7 intrinsic fluorescence, we found that (i) in 0.1 M NaCl, NCp7 bound noncooperatively to tRNA(3Lys) with a Kobs = 3.2 x 10(6) M-1 association constant and a n = 6 binding site size, (ii) four ionic interactions were formed in the NCp7.tRNA(3Lys) complex, and (iii) nonelectrostatic factors provided about 60% of the binding energy. These binding parameters were not significantly altered when the natural tRNA(3Lys) was replaced by either an in vitro synthetic tRNA(3Lys) transcript, the heterologous yeast tRNA(Phe) or the structurally unrelated 5 S RNA from Escherichia coli. Moreover, the environment of the intrinsic fluorescent reporters (Trp37 and Trp61) was similar in the various complexes. Finally, experiments performed at low protein concentration provide no evidence of high affinity binding sites. Taken together, our data strongly suggested an essentially nonspecific binding of NCp7 to tRNA(3Lys) and thus did not seem to support a direct role of NCp7, per se, in the selection of tRNA(3Lys) from the pool of cellular tRNAs.},
note = {0021-9258
Journal Article},
keywords = {Amino Acid Sequence Capsid/*chemistry/*metabolism *Capsid Proteins Escherichia coli Gene Products, Amino Acyl/biosynthesis/chemistry/*metabolism Substrate Specificity Support, gag/*chemistry/*metabolism HIV-1/*metabolism Hydrogen-Ion Concentration Kinetics Magnesium Chloride/pharmacology Mathematics Models, Genetic Zinc Fingers, MARQUET, Non-U.S. Gov't Transcription, Theoretical Molecular Sequence Data Nucleic Acid Conformation Osmolar Concentration Protein Binding RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Marquet R, Isel C, Ehresmann C, Ehresmann B
tRNAs as primer of reverse transcriptases Article de journal
Dans: Biochimie, vol. 77, no. 1-2, p. 113-124, 1995, ISBN: 7541250, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Binding Sites DNA Nucleotidylexotransferase/genetics/metabolism Hepadnaviridae/genetics Introns Plant Viruses/genetics Plasmids RNA/chemistry/*metabolism RNA, MARQUET, Non-U.S. Gov't, Transfer/chemistry/*metabolism RNA, Unité ARN, Viral/genetics/*metabolism RNA-Directed DNA Polymerase/*metabolism Retroelements/genetics Retroviridae/genetics Support
@article{,
title = {tRNAs as primer of reverse transcriptases},
author = {R Marquet and C Isel and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7541250},
isbn = {7541250},
year = {1995},
date = {1995-01-01},
journal = {Biochimie},
volume = {77},
number = {1-2},
pages = {113-124},
abstract = {Genetic elements coding for proteins that present amino acid identity with the conserved motifs of retroviral reverse transcriptases constitute the retroid family. With the exception of reverse transcriptases encoded by mitochondrial plasmids of Neurospora, all reverse transcriptases have an absolute requirement for a primer to initiate DNA synthesis. In retroviruses, plant pararetroviruses, and retrotransposons (transposons containing long terminal repeats), DNA synthesis is primed by specific tRNAs. All these retroelements contain a primer binding site presenting a Watson-Crick complementarity with the primer tRNA. The tRNAs most widely used as primers are tRNA(Trp), tRNA(Pro), tRNA(1,2Lys), tRNA(3Lys), tRNA(iMet). Other tRNAs such as tRNA(Gln), tRNA(Leu), tRNA(Ser), tRNA(Asn) and tRNA(Arg) are also occasionally used as primers. In the retroviruses and plant pararetroviruses, the primer binding site is complementary to the 3' end of the primer tRNA. In the case of retrotransposons, the primer binding site is either complementary to the 3' end or to an internal region of the primer tRNA. Additional interactions taking place between the primer tRNA and the retro-RNA outside of the primer binding site have been evidenced in the case of Rous sarcoma virus, human immunodeficiency virus type I, and yeast retrotransposon Ty1. A selective encapsidation of the primer tRNA, probably promoted by interactions with reverse transcriptase, occurs during the formation of virus or virus-like particles. Annealing of the primer tRNA to the primer binding site appears to be mediated by reverse transcriptase and/or the nucleocapsid protein. Modified nucleosides of the primer tRNA have been shown to be important for replication of the primer binding site, encapsidation of the primer (in the case of Rous sarcoma virus), and interaction with the genomic RNA (in the case of human immunodeficiency virus type I).},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Binding Sites DNA Nucleotidylexotransferase/genetics/metabolism Hepadnaviridae/genetics Introns Plant Viruses/genetics Plasmids RNA/chemistry/*metabolism RNA, MARQUET, Non-U.S. Gov't, Transfer/chemistry/*metabolism RNA, Unité ARN, Viral/genetics/*metabolism RNA-Directed DNA Polymerase/*metabolism Retroelements/genetics Retroviridae/genetics Support},
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}
}
Skripkin E, Paillart J C, Marquet R, Ehresmann B, Ehresmann C
Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 91, no. 11, p. 4945-4949, 1994, ISBN: 8197162, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites Biopolymers HIV-1/*genetics Molecular Sequence Data Nucleic Acid Conformation Nucleotides/chemistry RNA, MARQUET, Non-U.S. Gov't, Nucleic Acid Support, PAILLART, Unité ARN, Viral/*chemistry Repetitive Sequences
@article{,
title = {Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro},
author = {E Skripkin and J C Paillart and R Marquet and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8197162},
isbn = {8197162},
year = {1994},
date = {1994-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {91},
number = {11},
pages = {4945-4949},
abstract = {The diploid genome of all retroviruses is made of two homologous copies of RNA intimately associated near their 5' end, in a region called the dimer linkage structure. Dimerization of genomic RNA is thought to be important for crucial functions of the retroviral life cycle (reverse transcription, translation, encapsidation). Previous in vitro studies mapped the dimer linkage structure of human immunodeficiency virus type 1 (HIV-1) in a region downstream of the splice donor site, containing conserved purine tracts that were postulated to mediate dimerization, through purine quartets. However, we recently showed that dimerization of HIV-1 RNA also involves sequences upstream of the splice donor site. Here, we used chemical modification interference to identify nucleotides that are required in unmodified form for dimerization of a RNA fragment containing nucleotides 1-707 of HIV-1 RNA. These nucleotides map exclusively in a restricted area upstream of the splice donor site and downstream of the primer binding site. They are centered around a palindromic sequence (GUGCAC279) located in a hairpin loop. Our results support a model in which dimer formation is initiated by the annealing of the palindromic sequences, possibly by a loop-loop interaction between the two monomers. Further experiments show that the deletion of the stem-loop or base substitutions in the loop abolish dimerization, despite the presence of the previously postulated dimer linkage structure. On the other hand, deletions of the purine tracts downstream of the splice donor site do not prevent dimerization. Therefore, we conclude that the palindromic region represents the dimerization initiation site of genomic RNA.},
note = {0027-8424
Journal Article},
keywords = {Base Sequence Binding Sites Biopolymers HIV-1/*genetics Molecular Sequence Data Nucleic Acid Conformation Nucleotides/chemistry RNA, MARQUET, Non-U.S. Gov't, Nucleic Acid Support, PAILLART, Unité ARN, Viral/*chemistry Repetitive Sequences},
pubstate = {published},
tppubtype = {article}
}
Paillart J C, Marquet R, Skripkin E, Ehresmann B, Ehresmann C
Mutational analysis of the bipartite dimer linkage structure of human immunodeficiency virus type 1 genomic RNA Article de journal
Dans: J Biol Chem, vol. 269, no. 44, p. 27486-27493, 1994, ISBN: 7961663, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA Mutational Analysis HIV-1/*chemistry Heat Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry Structure-Activity Relationship Support
@article{,
title = {Mutational analysis of the bipartite dimer linkage structure of human immunodeficiency virus type 1 genomic RNA},
author = {J C Paillart and R Marquet and E Skripkin and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7961663},
isbn = {7961663},
year = {1994},
date = {1994-01-01},
journal = {J Biol Chem},
volume = {269},
number = {44},
pages = {27486-27493},
abstract = {The genome of all retroviruses consists in two homologous RNA molecules associated near their 5' end in a region called the dimer linkage structure. Dimerization of genomic RNA is thought to be important for several functions of the retroviral cycle such as encapsidation, reverse transcription, and translation. In human immunodeficiency virus type 1 (HIV-1), a region downstream of the splice donor site was initially postulated to mediate dimerization. However, we recently showed that the dimerization initiation site is located upstream of the splice donor site and suggested that dimerization may initiate through a loop-loop interaction. Here, we show that single base mutations in the palindromic loop of the dimerization initiation site completely abolish dimerization, while introduction of compensatory mutations restores the process. Furthermore, two single nucleotide mutants that are unable to form homodimers efficiently codimerize, while the wild type RNA and the compensatory mutant, which both form homodimers, are unable to codimerize. These results unambiguously prove the interaction between the palindromic loops of each monomer. By contrast, none of the deletions that we introduced downstream of the splice donor site abolishes dimerization. However, deletions of two purine tracts located in the vicinity of the initiation codon of the gag gene significantly decrease the thermal stability of the HIV-1 RNA dimer.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence DNA Mutational Analysis HIV-1/*chemistry Heat Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, MARQUET, Non-U.S. Gov't, PAILLART, Unité ARN, Viral/*chemistry Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
Marquet R, Paillart J C, Skripkin E, Ehresmann C, Ehresmann B
Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 2, p. 145-151, 1994, ISBN: 8121797, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Cations HIV-1/*genetics Kinetics Macromolecular Systems Magnesium Models, Chemical Models, Genetic Molecular Sequence Data RNA Splicing RNA, MARQUET, Non-U.S. Gov't Thermodynamics, PAILLART, Unité ARN, Viral/*chemistry Support
@article{,
title = {Dimerization of human immunodeficiency virus type 1 RNA involves sequences located upstream of the splice donor site},
author = {R Marquet and J C Paillart and E Skripkin and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8121797},
isbn = {8121797},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {2},
pages = {145-151},
abstract = {The retroviral genome consists of two homologous RNA molecules associated close to their 5' ends. We studied the spontaneous dimerization of four HIV-1 RNA fragments (RNAs 1-707, 1-615, 311-612, and 311-415) containing the previously defined dimerization domain, and a RNA fragment (RNA 1-311) corresponding to the upstream sequences. Significant dimerization of all RNAs is observed on agarose gels when magnesium is included in the electrophoresis buffer. In contrast to dimerization of RNAs 311-612 and 311-415, dimerization of RNAs 1-707, 1-615 and 1-311 strongly depends on the size of the monovalent cation present in the incubation buffer. Also, dimerization of RNAs 1-707, 1-615, and 1-311 is 10 times faster than that of RNAs 311-612 and 311-415. The dimers formed by the latter RNAs are substantially more stable than that of RNA 1-615, while RNA 1-311 dimer is 5-7 degrees C less stable than RNA 1-615 dimer. These results indicate that dimerization of HIV-1 genomic RNA involves elements located upstream of the splice donor site (position 305), i.e. outside of the previously defined dimerization domain.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Cations HIV-1/*genetics Kinetics Macromolecular Systems Magnesium Models, Chemical Models, Genetic Molecular Sequence Data RNA Splicing RNA, MARQUET, Non-U.S. Gov't Thermodynamics, PAILLART, Unité ARN, Viral/*chemistry Support},
pubstate = {published},
tppubtype = {article}
}