Publications
2003
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 Journal Article
In: Biochimie, vol. 85, no. 5, pp. 521-525, 2003, ISBN: 12763311, (0300-9084 Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
2002
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 Journal Article
In: J Biol Chem, vol. 277, no. 45, pp. 43233-43242, 2002, ISBN: 12194974, (0021-9258 Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
1997
Aphasizhev R, Senger B, Fasiolo F
Importance of structural features for tRNA(Met) identity Journal Article
In: RNA, vol. 3, no. 5, pp. 489-497, 1997, ISBN: 9149230, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Anticodon Base Sequence Electrophoresis, Genetic Variation (Genetics), Met/*biosynthesis/*chemistry/isolation & purification Saccharomyces cerevisiae/genetics/metabolism Support, Non-U.S. Gov't Transcription, Polyacrylamide Gel Kinetics Magnesium Chloride Models, Structural Molecular Sequence Data *Nucleic Acid Conformation RNA, Transfer, Unité ARN
@article{,
title = {Importance of structural features for tRNA(Met) identity},
author = {R Aphasizhev and B Senger and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9149230},
isbn = {9149230},
year = {1997},
date = {1997-01-01},
journal = {RNA},
volume = {3},
number = {5},
pages = {489-497},
abstract = {We showed previously that the tRNA tertiary structure makes an important contribution to the identity of yeast tRNA(Met) (Senger B, Aphasizhev R, Walter P, Fasiolo F, 1995, J Mol Biol 249:45-58). To learn more about the role played by the tRNA framework, we analyzed the effect of some phosphodiester cleavages and 2'OH groups in tRNA binding and aminoacylation. The tRNA is inactivated provided the break occurs in the central core region responsible for the tertiary fold or in the anticodon stem/loop region. We also show that, for tRNA(Met) to bind, the anticodon loop, but not the anticodon stem, requires a ribosephosphate backbone. A tertiary mutant of yeast tRNA(Met) involving interactions from the D- and T-loop unique to the initiator species fails to be aminoacylated, but still binds to yeast methionyl-tRNA synthetase. In the presence of 10 mM MgCl2, the mutant transcript has a 3D fold significantly stabilized by about 30 degrees C over a wild-type transcript as deduced from the measure of their T(m) values. The k(cat) defect of the tRNA(Met) mutant may arise from a failure to overcome an increase of the free energetic cost of distorting the more stable tRNA structure and/or a tRNA based MetRS conformational change required for formation of transition state of aminoacylation.},
note = {1355-8382
Journal Article},
keywords = {Anticodon Base Sequence Electrophoresis, Genetic Variation (Genetics), Met/*biosynthesis/*chemistry/isolation & purification Saccharomyces cerevisiae/genetics/metabolism Support, Non-U.S. Gov't Transcription, Polyacrylamide Gel Kinetics Magnesium Chloride Models, Structural Molecular Sequence Data *Nucleic Acid Conformation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1996
Paillart J C, Berthoux L, Ottmann M, Darlix J L, Marquet R, Ehresmann B, Ehresmann C
In: J Virol, vol. 70, no. 12, pp. 8348-8354, 1996, ISBN: 8970954, (0022-538x Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
Paillart J C, Berthoux L, Ottmann M, Darlix J L, Marquet R, Ehresmann B, Ehresmann C
In: J Virol, vol. 70, no. 12, pp. 8348-8354, 1996, ISBN: 8970954, (0022-538x Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
1995
Sturchler-Pierrat C, Hubert N, Totsuka T, Mizutani T, Carbon P, Krol A
Selenocysteylation in eukaryotes necessitates the uniquely long aminoacyl acceptor stem of selenocysteine tRNA(Sec) Journal Article
In: J Biol Chem, vol. 270, no. 31, pp. 18570-18574, 1995, ISBN: 7629188, (0021-9258 Journal Article).
Abstract | Links | BibTeX | Tags: Acylation Animals Base Composition Base Sequence Cattle Eukaryotic Cells Kinetics Molecular Sequence Data Mutagenesis, Amino Acid-Specific RNA, Amino Acyl/*biosynthesis/*genetics/metabolism Selenocysteine/*biosynthesis Sequence Deletion Serine-tRNA Ligase/*metabolism Structure-Activity Relationship Support, Genetic, Non-U.S. Gov't Transcription, Site-Directed Phylogeny *RNA, Transfer, Unité ARN
@article{,
title = {Selenocysteylation in eukaryotes necessitates the uniquely long aminoacyl acceptor stem of selenocysteine tRNA(Sec)},
author = {C Sturchler-Pierrat and N Hubert and T Totsuka and T Mizutani and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7629188},
isbn = {7629188},
year = {1995},
date = {1995-01-01},
journal = {J Biol Chem},
volume = {270},
number = {31},
pages = {18570-18574},
abstract = {Selenocysteine synthesis is achieved on a specific tRNA, tRNA(Sec), which is first charged with serine to yield seryl-tRNA(Sec). Eukaryotic tRNA(Sec) exhibits an aminoacyl acceptor stem with a unique length of 9 base pairs. Within this stem, two base pairs, G5a.U67b and U6.U67, drew our attention, whose non-Watson-Crick status is maintained in the course of evolution either through U6.U67 base conservation or base covariation at G5a.U67b. Single or double point mutations were performed, which modified the identity of either or both of the base pairs. Serylation by seryl-tRNA synthetase was unaffected by substitutions at either G5a.U67b or U6.U67. Instead, and quite surprisingly, changing G5a.U67b and U6.U67 to G5a-C67b/U6.G67 or G5a-C67b/C6-G67 gave rise to a tRNA(Sec) mutant exhibiting a gain of function in serylation. This finding sheds light on the negative influence born by a few base pairs in the acceptor stem of tRNA(Sec) on its serylation abilities. The tRNA(Sec) capacities to support selenocysteylation were next examined with regard to a possible role played by the two non-Watson-Crick base pairs and the unique length of the acceptor stem. It first emerges from our study that tRNA(Sec) transcribed in vitro is able to support selenocysteylation. Second, none of the point mutations engineered at G5a.U67b and/or U6.U67 significantly modified the selenocysteylation level. In contrast, reduction of the acceptor stem length to 8 base pairs led tRNA(Sec) to lose its ability to efficiently support selenocysteylation. Thus, our study provides strong evidence that the length of the acceptor stem is of prime importance for the serine to selenocysteine conversion step.},
note = {0021-9258
Journal Article},
keywords = {Acylation Animals Base Composition Base Sequence Cattle Eukaryotic Cells Kinetics Molecular Sequence Data Mutagenesis, Amino Acid-Specific RNA, Amino Acyl/*biosynthesis/*genetics/metabolism Selenocysteine/*biosynthesis Sequence Deletion Serine-tRNA Ligase/*metabolism Structure-Activity Relationship Support, Genetic, Non-U.S. Gov't Transcription, Site-Directed Phylogeny *RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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 Journal Article
In: J Biol Chem, vol. 270, no. 4, pp. 1650-1656, 1995, ISBN: 7829498, (0021-9258 Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
Heyman T, Agoutin B, Friant S, Wilhelm F X, Wilhelm M L
In: J Mol Biol, vol. 253, no. 2, pp. 291-303, 1995, ISBN: 7563090, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence Cloning, Fungal *Genes, Fungal/biosynthesis DNA, Genetic, Molecular DNA Primers *DNA Replication DNA, Non-U.S. Gov't Transcription, Nucleic Acid Restriction Mapping *Retroelements Saccharomyces cerevisiae/genetics/*virology Support, pol Genome, Unité ARN, Viral Molecular Sequence Data Poly C/analysis Polymerase Chain Reaction *Repetitive Sequences, Viral/*biosynthesis Genes
@article{,
title = {Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition},
author = {T Heyman and B Agoutin and S Friant and F X Wilhelm and M L Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7563090},
isbn = {7563090},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {253},
number = {2},
pages = {291-303},
abstract = {Long terminal repeat elements and retroviruses require primers for initiation of minus and plus-strand DNA synthesis by reverse transcriptase. Here we demonstrate genetically that plus-strand DNA synthesis of the yeast Ty1 element is initiated at two sites located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the pol gene in the integrase coding sequence (PPT2). A consequence of the presence of two PPTs is that Ty1 plus-strand DNA exists as segments at some time during replication. Three fragments have been identified: the plus-strand strong-stop DNA initiated at PPT1, a downstream fragment initiated at PPT2 and an upstream fragment spanning the 5'-terminal part of Ty1 and a portion of the TyB gene. Characterization of the 3' ends of the plus-strand DNA fragments reveals (1) that the upstream fragment is elongated beyond PPT2 creating a plus-strand overlap and (2) that the majority of plus-strand strong-stop DNA fragments bear a copy of the minus-strand primer binding site in agreement with the accepted model of retroviral genomic RNA reverse transcription. The two polypurine tracts, PPT1 and PPT2, have an identical sequence GGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Cloning, Fungal *Genes, Fungal/biosynthesis DNA, Genetic, Molecular DNA Primers *DNA Replication DNA, Non-U.S. Gov't Transcription, Nucleic Acid Restriction Mapping *Retroelements Saccharomyces cerevisiae/genetics/*virology Support, pol Genome, Unité ARN, Viral Molecular Sequence Data Poly C/analysis Polymerase Chain Reaction *Repetitive Sequences, Viral/*biosynthesis Genes},
pubstate = {published},
tppubtype = {article}
}
1994
Wilhelm M, Wilhelm F X, Keith G, Agoutin B, Heyman T
In: Nucleic Acids Res, vol. 22, no. 22, pp. 4560-4565, 1994, ISBN: 7527135, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Sequence Base Sequence Binding Sites Cloning, Fungal/*genetics RNA, Genetic, Met/*genetics Retroelements/*genetics/physiology Retroviridae/genetics Saccharomyces cerevisiae/*genetics Support, Molecular Molecular Sequence Data Mutation/physiology RNA/*genetics RNA, Non-U.S. Gov't Transcription, Transfer, Unité ARN
@article{,
title = {Yeast Ty1 retrotransposon: the minus-strand primer binding site and a cis-acting domain of the Ty1 RNA are both important for packaging of primer tRNA inside virus-like particles},
author = {M Wilhelm and F X Wilhelm and G Keith and B Agoutin and T Heyman},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7527135},
isbn = {7527135},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {22},
pages = {4560-4565},
abstract = {Reverse transcription of the yeast retrotransposon Ty1 is primed by the cytoplasmic initiator methionine tRNA (tRNA(iMet)). The primer tRNA(iMet) is packaged inside virus-like particles (VLPs) and binds to a 10 nucleotides minus-strand primer binding site, the (-)PBS, complementary to its 3' acceptor stem. We have found that three short sequences of the Ty1 RNA (box 1, box 2.1 and box 2.2) located 3' to the (-)PBS are complementary to other regions of the primer tRNA(iMet) (T psi C and DHU stems and loops). Reconstitution of reverse transcription in vitro with T7 transcribed Ty1 RNA species and tRNA(iMet) purified from yeast cells shows that the boxes do not affect the efficiency of reverse transcription. Thus the role of the boxes on packaging of the primer tRNA(iMet) into the VLPs was investigated by analysing the level of tRNA(iMet) packaged into mutant VLPs. Specific nucleotide changes in the (-)PBS or in the boxes that do not change the protein coding sequence but disrupt the complementarity with the primer tRNA(iMet) within the VLPs. We propose that base pairing between the primer tRNA(iMet) and the Ty1 RNA is of major importance for tRNA(iMet) packaging into the VLPs. Moreover the intactness of the boxes is essential for retrotransposition as shown by the transposition defect of a Ty1 element harboring an intact (-)PBS and mutated boxes.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid Sequence Base Sequence Binding Sites Cloning, Fungal/*genetics RNA, Genetic, Met/*genetics Retroelements/*genetics/physiology Retroviridae/genetics Saccharomyces cerevisiae/*genetics Support, Molecular Molecular Sequence Data Mutation/physiology RNA/*genetics RNA, Non-U.S. Gov't Transcription, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Benard L, Philippe C, Dondon L, Grunberg-Manago M, Ehresmann B, Ehresmann C, Portier C
Mutational analysis of the pseudoknot structure of the S15 translational operator from Escherichia coli Journal Article
In: Mol Microbiol, vol. 14, no. 1, pp. 31-40, 1994, ISBN: 7830558, (0950-382x Journal Article).
Abstract | Links | BibTeX | Tags: Bacterial Molecular Sequence Data *Nucleic Acid Conformation Plasmids Protein Binding RNA, Bacteriophage lambda/genetics Base Sequence Binding Sites Codon DNA Mutational Analysis Escherichia coli/*genetics/metabolism *Gene Expression Regulation, Genetic beta-Galactosidase/biosynthesis, Genetic Translation, Messenger/*chemistry/*metabolism Recombinant Fusion Proteins/biosynthesis Restriction Mapping Ribosomal Proteins/biosynthesis/*genetics/metabolism Support, Non-U.S. Gov't Transcription, Unité ARN
@article{,
title = {Mutational analysis of the pseudoknot structure of the S15 translational operator from Escherichia coli},
author = {L Benard and C Philippe and L Dondon and M Grunberg-Manago and B Ehresmann and C Ehresmann and C Portier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7830558},
isbn = {7830558},
year = {1994},
date = {1994-01-01},
journal = {Mol Microbiol},
volume = {14},
number = {1},
pages = {31-40},
abstract = {Expression of rpsO, the gene encoding the small ribosomal protein S15, is autoregulated at the translational level by S15, which binds to its mRNA in a region overlapping the ribosome-binding site. By measuring the effect of mutations on the expression of a translational rpsO-lacZ fusion and the S15 binding affinity for the translational operator, the formation of a pseudoknot in the operator site in vivo is fully demonstrated and appears to be a prerequisite for S15 binding. The mutational analysis suggests also that specific determinants for S15 binding are located in very limited regions of the structure formed by the pseudoknot. It is deduced that a specific pseudoknot conformation is a key element for autoregulation.},
note = {0950-382x
Journal Article},
keywords = {Bacterial Molecular Sequence Data *Nucleic Acid Conformation Plasmids Protein Binding RNA, Bacteriophage lambda/genetics Base Sequence Binding Sites Codon DNA Mutational Analysis Escherichia coli/*genetics/metabolism *Gene Expression Regulation, Genetic beta-Galactosidase/biosynthesis, Genetic Translation, Messenger/*chemistry/*metabolism Recombinant Fusion Proteins/biosynthesis Restriction Mapping Ribosomal Proteins/biosynthesis/*genetics/metabolism Support, Non-U.S. Gov't Transcription, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1993
Myslinski E, Schuster C, Krol A, Carbon P
Promoter strength and structure dictate module composition in RNA polymerase III transcriptional activator elements Journal Article
In: J Mol Biol, vol. 234, no. 2, pp. 311-318, 1993, ISBN: 7693950, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Animals Base Sequence Molecular Sequence Data Mutagenesis, Genetic/*physiology Xenopus laevis, Non-U.S. Gov't Transcription, Nucleic Acid/*physiology Selenocysteine/genetics Support, Site-Directed Oocytes/metabolism Promoter Regions (Genetics)/*genetics RNA/*genetics RNA Polymerase III/*metabolism RNA, Small Nuclear/genetics RNA, Transfer/genetics Regulatory Sequences, Unité ARN
@article{,
title = {Promoter strength and structure dictate module composition in RNA polymerase III transcriptional activator elements},
author = {E Myslinski and C Schuster and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7693950},
isbn = {7693950},
year = {1993},
date = {1993-01-01},
journal = {J Mol Biol},
volume = {234},
number = {2},
pages = {311-318},
abstract = {RNA polymerase III transcription of genes with external promoters only (e.g. U6 snRNA) or containing in addition an internal B box (selenocysteine tRNA(Sec)) is stimulated by upstream elements; a distal sequence element (DSE) for U6 or an activator element in the tRNA(Sec) gene. In contrast to the composite structure of the DSE which requires an octamer motif, the Xenopus tRNA(Sec) activator element contains an SPH motif only. In vivo transcription is optimally stimulated by SPH in an absolute octamer-independent manner since adding octamer does not induce superstimulation. Experiments performed in the work presented here led to the following observations. Co-operation between SPH and octamer motifs can be detected in two distinct cases: first when these motifs are placed in front of B box-less tRNA(Sec) or U6 external promoters and second, if either element of the external promoter (proximal sequence element or TATA element), or the SPH motif itself, are altered. Altogether, our data provide evidence that an SPH motif can function alone in an optimized promoter only. In contrast, an octamer becomes indispensable when the basal promoter is weak or disabled. It follows that module composition of Pol III transcriptional activator elements is dependent on the structure and strength of the promoter. This reveals the existence of cross-talk between activator and promoter elements, mediated by the bound transcription factors, which are thus able to compensate for each other in order to allow successful assembly of the transcription complex.},
note = {0022-2836
Journal Article},
keywords = {Animals Base Sequence Molecular Sequence Data Mutagenesis, Genetic/*physiology Xenopus laevis, Non-U.S. Gov't Transcription, Nucleic Acid/*physiology Selenocysteine/genetics Support, Site-Directed Oocytes/metabolism Promoter Regions (Genetics)/*genetics RNA/*genetics RNA Polymerase III/*metabolism RNA, Small Nuclear/genetics RNA, Transfer/genetics Regulatory Sequences, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1992
Senger B, Despons L, Walter P, Fasiolo F
The anticodon triplet is not sufficient to confer methionine acceptance to a transfer RNA Journal Article
In: Proc Natl Acad Sci U S A, vol. 89, no. 22, pp. 10768-10771, 1992, ISBN: 1438273, (0027-8424 Journal Article).
Abstract | Links | BibTeX | Tags: Anticodon/genetics/*metabolism Base Sequence Kinetics Methionine/*metabolism Models, Genetic, Met/genetics/*metabolism Saccharomyces cerevisiae/*genetics Support, Non-U.S. Gov't Transcription, Structural Molecular Sequence Data Nucleic Acid Conformation RNA, Transfer, Unité ARN
@article{,
title = {The anticodon triplet is not sufficient to confer methionine acceptance to a transfer RNA},
author = {B Senger and L Despons and P Walter and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1438273},
isbn = {1438273},
year = {1992},
date = {1992-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {89},
number = {22},
pages = {10768-10771},
abstract = {Previous work suggested that the presence of the anticodon CAU alone was enough to confer methionine acceptance to a tRNA. Conversions of Escherichia coli nonmethionine tRNAs to a methionine-accepting species were obtained by substitutions reconstructing the whole methionine anticodon loop together with preservation (or introduction) of the acceptor stem base A73. We show here that the CAU triplet alone is unable to confer methionine acceptance when transplanted into a yeast aspartic tRNA. Both non-anticodon bases of the anticodon loop of yeast tRNA(Met) and A73 are required in addition to CAU for methionine acceptance. The importance of these non-anticodon bases in other CAU-containing tRNA frameworks was also established. These specific non-anticodon base interactions make a substantial thermodynamic contribution to the methionine acceptance of a transfer RNA.},
note = {0027-8424
Journal Article},
keywords = {Anticodon/genetics/*metabolism Base Sequence Kinetics Methionine/*metabolism Models, Genetic, Met/genetics/*metabolism Saccharomyces cerevisiae/*genetics Support, Non-U.S. Gov't Transcription, Structural Molecular Sequence Data Nucleic Acid Conformation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lescure A, Murgo S, Carbon P, Krol A
The proximal promoter and the start site cooperate to specify correct U1 snRNA transcription initiation by RNA polymerase II Journal Article
In: Nucleic Acids Res, vol. 20, no. 7, pp. 1573-1578, 1992, ISBN: 1579449, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Animals Base Sequence DNA/metabolism DNA Mutational Analysis Molecular Sequence Data Promoter Regions (Genetics)/*genetics RNA Polymerase II/*metabolism RNA, Genetic/*genetics Xenopus laevis/genetics, KROL, LESCURE, Non-U.S. Gov't Transcription, Small Nuclear/*genetics Support, Unité ARN
@article{,
title = {The proximal promoter and the start site cooperate to specify correct U1 snRNA transcription initiation by RNA polymerase II},
author = {A Lescure and S Murgo and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1579449},
isbn = {1579449},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {7},
pages = {1573-1578},
abstract = {In this work, we attempted to gain insight into the detailed mechanism allowing correct transcription initiation of U1 snRNA genes by RNA polymerase II. Abolition of the CA motif residing at -1/+1 in the Xenopus U1 gene leads to a loss of the ability of the promoter to direct accurate initiation. A discrete site is selected only if a purine preceded by a pyrimidine is positioned at 58/57 bp downstream of the center of the PSE. The PSE alone is unable to designate a discrete initiation site. Rather, it serves to set the location of an initiation window without discriminating suitable from unsuitable initiation sites. The latter role is devoted to a PyPu sequence positioned at -1/+1. Therefore, it is the concomitant action of the PSE and an essential PyPu positioned at the proper distance from this promoter that specifies correct U1 snRNA transcription initiation by RNA polymerase II.},
note = {0305-1048
Journal Article},
keywords = {Animals Base Sequence DNA/metabolism DNA Mutational Analysis Molecular Sequence Data Promoter Regions (Genetics)/*genetics RNA Polymerase II/*metabolism RNA, Genetic/*genetics Xenopus laevis/genetics, KROL, LESCURE, Non-U.S. Gov't Transcription, Small Nuclear/*genetics Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lavignon M, Tounekti N, Rayner B, Imbach J L, Keith G, Paoletti J, Malvy C
Inhibition of murine leukemia viruses by nuclease-resistant alpha-oligonucleotides Journal Article
In: Antisense Res Dev, vol. 2, no. 4, pp. 315-324, 1992, ISBN: 1292779, (1050-5261 Journal Article).
Abstract | Links | BibTeX | Tags: 3T3 Cells Animals Base Sequence Binding Sites Culture Media Friend murine leukemia virus/*drug effects/genetics/physiology Mice Molecular Sequence Data Moloney murine leukemia virus/*drug effects/genetics/physiology Oligonucleotides, Antisense/metabolism/*pharmacology RNA, Genetic/drug effects, Genetic/drug effects Translation, Messenger/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Transcription, Unité ARN, Viral/chemistry/genetics/metabolism Support
@article{,
title = {Inhibition of murine leukemia viruses by nuclease-resistant alpha-oligonucleotides},
author = {M Lavignon and N Tounekti and B Rayner and J L Imbach and G Keith and J Paoletti and C Malvy},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1292779},
isbn = {1292779},
year = {1992},
date = {1992-01-01},
journal = {Antisense Res Dev},
volume = {2},
number = {4},
pages = {315-324},
abstract = {We studied the antiviral activity of nuclease-resistant alpha-anomeric oligonucleotides. An alpha-oligonucleotide (20-mer) targeted to the primer binding site (PBS) of murine retroviruses inhibited viral spreading. The inhibition only occurred when the cells had been electropermeabilized in the presence of the oligonucleotide. The PBS sequence is involved in reverse transcription and in translation. The data suggest that the oligonucleotide could perturb reverse transcription activity. Thus, either the oligonucleotide induced a decrease in initiation or it inhibited the extension of the minus or plus strands DNA during reverse transcription. These results show that reverse transcription may be an interesting target for antisense oligonucleotides.},
note = {1050-5261
Journal Article},
keywords = {3T3 Cells Animals Base Sequence Binding Sites Culture Media Friend murine leukemia virus/*drug effects/genetics/physiology Mice Molecular Sequence Data Moloney murine leukemia virus/*drug effects/genetics/physiology Oligonucleotides, Antisense/metabolism/*pharmacology RNA, Genetic/drug effects, Genetic/drug effects Translation, Messenger/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Transcription, Unité ARN, Viral/chemistry/genetics/metabolism Support},
pubstate = {published},
tppubtype = {article}
}