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}
}
Schaeffer C, Bardoni B, Mandel J L, Ehresmann B, Ehresmann C, Moine H
The fragile X mental retardation protein binds specifically to its mRNA via a purine quartet motif Article de journal
Dans: EMBO J, vol. 20, no. 17, p. 4803-4813, 2001, ISBN: 11532944, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Binding Sites Chickens Chimeric Proteins/chemistry/metabolism Fragile X Syndrome/genetics Gene Expression Regulation Human Kinetics Mental Retardation/*genetics Mice Molecular Sequence Data Nerve Tissue Proteins/*genetics/*metabolism RNA, Genetic Vertebrates Xenopus laevis, Messenger/chemistry/*genetics/*metabolism Rats Recombinant Fusion Proteins/chemistry/metabolism Sequence Alignment Sequence Homology, Non-U.S. Gov't *Translation, Nucleic Acid Support, Unité ARN
@article{,
title = {The fragile X mental retardation protein binds specifically to its mRNA via a purine quartet motif},
author = {C Schaeffer and B Bardoni and J L Mandel and B Ehresmann and C Ehresmann and H Moine},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11532944},
isbn = {11532944},
year = {2001},
date = {2001-01-01},
journal = {EMBO J},
volume = {20},
number = {17},
pages = {4803-4813},
abstract = {Fragile X syndrome is caused by the absence of protein FMRP, the function of which is still poorly understood. Previous studies have suggested that FMRP may be involved in various aspects of mRNA metabolism, including transport, stability and/or translatability. FMRP was shown to interact with a subset of brain mRNAs as well as with its own mRNA; however, no specific RNA-binding site could be identified precisely. Here, we report the identification and characterization of a specific and high affinity binding site for FMRP in the RGG-coding region of its own mRNA. This site contains a purine quartet motif that is essential for FMRP binding and can be substituted by a heterologous quartet-forming motif. The specific binding of FMRP to its target site was confirmed further in a reticulocyte lysate through its ability to repress translation of a reporter gene harboring the RNA target site in the 5'-untranslated region. Our data address interesting questions concerning the role of FMRP in the post-transcriptional control of its own gene and possibly other target genes.},
note = {0261-4189
Journal Article},
keywords = {Animals Base Sequence Binding Sites Chickens Chimeric Proteins/chemistry/metabolism Fragile X Syndrome/genetics Gene Expression Regulation Human Kinetics Mental Retardation/*genetics Mice Molecular Sequence Data Nerve Tissue Proteins/*genetics/*metabolism RNA, Genetic Vertebrates Xenopus laevis, Messenger/chemistry/*genetics/*metabolism Rats Recombinant Fusion Proteins/chemistry/metabolism Sequence Alignment Sequence Homology, Non-U.S. Gov't *Translation, Nucleic Acid Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Massire C, Jaeger L, Westhof E
Phylogenetic evidence for a new tertiary interaction in bacterial RNase P RNAs Article de journal
Dans: RNA, vol. 3, no. 6, p. 553-556, 1997, ISBN: 9174090, (1355-8382 Letter).
Liens | BibTeX | Étiquettes: Bacterial/*chemistry RNA, Base Sequence Comparative Study Databases, Catalytic/*chemistry Ribonuclease P Sequence Homology, Factual Endoribonucleases/*chemistry Molecular Sequence Data *Nucleic Acid Conformation Phylogeny RNA, Non-U.S. Gov't Variation (Genetics), Nucleic Acid Support, Unité ARN
@article{,
title = {Phylogenetic evidence for a new tertiary interaction in bacterial RNase P RNAs},
author = {C Massire and L Jaeger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9174090},
isbn = {9174090},
year = {1997},
date = {1997-01-01},
journal = {RNA},
volume = {3},
number = {6},
pages = {553-556},
note = {1355-8382
Letter},
keywords = {Bacterial/*chemistry RNA, Base Sequence Comparative Study Databases, Catalytic/*chemistry Ribonuclease P Sequence Homology, Factual Endoribonucleases/*chemistry Molecular Sequence Data *Nucleic Acid Conformation Phylogeny RNA, Non-U.S. Gov't Variation (Genetics), Nucleic Acid Support, Unité ARN},
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}
}
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}
}
Tanner N K, Schaff S, Thill G, Petit-Koskas E, Crain-Denoyelle A M, Westhof E
A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses Article de journal
Dans: Curr Biol, vol. 4, no. 6, p. 488-498, 1994, ISBN: 7922369, (0960-9822 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Catalytic/*chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Nucleic Acid Support, Site-Directed Nucleic Acid Conformation RNA, Unité ARN, Viral/chemistry/genetics/metabolism Sequence Homology, Viral/genetics Hepatitis Delta Virus/*enzymology/genetics Human Kinetics Models
@article{,
title = {A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses},
author = {N K Tanner and S Schaff and G Thill and E Petit-Koskas and A M Crain-Denoyelle and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7922369},
isbn = {7922369},
year = {1994},
date = {1994-01-01},
journal = {Curr Biol},
volume = {4},
number = {6},
pages = {488-498},
abstract = {BACKGROUND: Hepatitis delta virus (HDV), which has a single-stranded RNA genome about 1700 nucleotides long, is a satellite virus of hepatitis B, and is associated with a high incidence of fulminant hepatitis and death in infected humans. Like certain pathogenic subviral RNAs that infect plants, HDV RNA features a closed-circular conformation, a rolling-circle mechanism of replication and RNA-catalyzed self-cleaving reactions of both genomic and anti-genomic strands in vitro. The catalytic domains cannot be folded into either the hammerhead or hairpin secondary-structure motifs that have been found in other self-cleaving RNAs. RESULTS: A pseudoknot secondary-structure model has been suggested for the catalytic domain (ribozyme) of HDV RNA. We conducted extensive mutational analyses of regions of the HDV ribozyme predicted in this model to be single stranded, and found that several of them are important for catalytic activity. We used these data, sequence comparisons between different isolates and previously published structural analyses to produce a computer graphic model of the three-dimensional architecture of the HDV ribozyme. CONCLUSIONS: Our model supports the pseudoknotted structure and rationalizes several observations relating to the lengths of the various stems and the sequence requirements of the single-stranded regions. It also provides insight into the catalytic mechanism of the HDV ribozyme. We specifically propose that residues C75, U20 and C21 form the basis of the catalytic region and are close to the cleavable phosphate.},
note = {0960-9822
Journal Article},
keywords = {Base Sequence DNA, Catalytic/*chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Nucleic Acid Support, Site-Directed Nucleic Acid Conformation RNA, Unité ARN, Viral/chemistry/genetics/metabolism Sequence Homology, Viral/genetics Hepatitis Delta Virus/*enzymology/genetics Human Kinetics Models},
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}
}
Xue H, Shen W, Giege R, Wong J T
Identity elements of tRNA(Trp). Identification and evolutionary conservation Article de journal
Dans: J Biol Chem, vol. 268, no. 13, p. 9316-9322, 1993, ISBN: 8486627, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Bacillus subtilis/*genetics Base Sequence Cattle Cloning, Bacterial Halobacterium/genetics Kinetics Liver/physiology Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Molecular Comparative Study Escherichia coli/*genetics *Evolution Genes, Non-U.S. Gov't Triticum/genetics Tryptophan-tRNA Ligase/metabolism, Nucleic Acid Support, Structural, Transfer, Trp/chemistry/*genetics/metabolism Saccharomyces cerevisiae/genetics Sequence Homology, Unité ARN
@article{,
title = {Identity elements of tRNA(Trp). Identification and evolutionary conservation},
author = {H Xue and W Shen and R Giege and J T Wong},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8486627},
isbn = {8486627},
year = {1993},
date = {1993-01-01},
journal = {J Biol Chem},
volume = {268},
number = {13},
pages = {9316-9322},
abstract = {In this study, the varying reactivities of Bacillus subtilis tryptophanyl-tRNA synthetase toward prokaryotic, eukaryotic, and halophile tRNAs were employed to define the potential identity elements on tRNA(Trp). On this basis mutagenesis was performed to obtain, through in vivo heterologous expression in Escherichia coli and in vitro transcription with T7 RNA polymerase, mutant B. subtilis tRNA(Trp) for comparison with the wild-type. These comparisons served to establish G73 and the anticodon as major identity elements, and A1-U72, G5-C68, and A9 as minor identity elements. While the tryptophanyl-tRNA synthetase from B. subtilis and E. coli require G73 to function, replacement of G73 by A73 favors the enzyme from yeast. This change points to the variation of the identity elements for the same amino acid among different organisms. The similarity in these elements between B. subtilis and E. coli tryptophanyl-tRNA synthetase, however, suggests that identity elements on tRNA, like the active centers on enzymes, undergo evolutionary change at slower rates than less essential portions of the macromolecule.},
note = {0021-9258
Journal Article},
keywords = {Animals Bacillus subtilis/*genetics Base Sequence Cattle Cloning, Bacterial Halobacterium/genetics Kinetics Liver/physiology Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Denaturation RNA, Molecular Comparative Study Escherichia coli/*genetics *Evolution Genes, Non-U.S. Gov't Triticum/genetics Tryptophan-tRNA Ligase/metabolism, Nucleic Acid Support, Structural, Transfer, Trp/chemistry/*genetics/metabolism Saccharomyces cerevisiae/genetics Sequence Homology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mougel M, Tounekti N, Darlix J L, Paoletti J, Ehresmann B, Ehresmann C
Conformational analysis of the 5' leader and the gag initiation site of Mo-MuLV RNA and allosteric transitions induced by dimerization Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 20, p. 4677-4684, 1993, ISBN: 8233816, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Allosteric Regulation Base Sequence Biopolymers *Genes, gag Molecular Sequence Data Moloney murine leukemia virus/*genetics *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Unité ARN, Viral/*chemistry/genetics Sequence Homology
@article{,
title = {Conformational analysis of the 5' leader and the gag initiation site of Mo-MuLV RNA and allosteric transitions induced by dimerization},
author = {M Mougel and N Tounekti and J L Darlix and J Paoletti and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8233816},
isbn = {8233816},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {20},
pages = {4677-4684},
abstract = {Dimerization of genomic RNA is a key step in the retroviral life cycle and has been postulated to be involved in the regulation of translation, encapsidation and reverse transcription. Here, we have derived a secondary structure model of nucleotides upstream from psi and of the gag initiation region of Mo-MuLV RNA in monomeric and dimeric forms, using chemical probing, sequence comparison and computer prediction. The 5' domain is extensively base-paired and interactions take place between U5 and 5' leader sequences. The U5-PBS subdomain can fold in two mutually exclusive conformations: a very stable and extended helical structure (E form) in which 17 of the 18 nucleotides of the PBS are paired, or an irregular three-branch structure (B form) in which 10 nucleotides of the PBS are paired. The dimeric RNA adopts the B conformation. The monomeric RNA can switch from the E to the B conformation by a thermal treatment. If the E to B transition is associated to dimerization, it may facilitate annealing of the primer tRNAPro to the PBS by lowering the free energy required for melting the PBS. Furthermore, dimerization induces allosteric rearrangements around the SD site and the gag initiation region.},
note = {0305-1048
Journal Article},
keywords = {Allosteric Regulation Base Sequence Biopolymers *Genes, gag Molecular Sequence Data Moloney murine leukemia virus/*genetics *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Unité ARN, Viral/*chemistry/genetics Sequence Homology},
pubstate = {published},
tppubtype = {article}
}
Baron C, Westhof E, Bock A, Giege R
Solution structure of selenocysteine-inserting tRNA(Sec) from Escherichia coli. Comparison with canonical tRNA(Ser) Article de journal
Dans: J Mol Biol, vol. 231, no. 2, p. 274-292, 1993, ISBN: 8510147, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Adenine/chemistry Aspergillus Nuclease S1/pharmacology Base Sequence Comparative Study Escherichia coli/*chemistry Guanine/chemistry Lead/pharmacology Models, Amino Acid-Specific/*chemistry/drug effects RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Ser/*chemistry/drug effects Selenocysteine/*metabolism Sequence Homology, Transfer, Unité ARN
@article{,
title = {Solution structure of selenocysteine-inserting tRNA(Sec) from Escherichia coli. Comparison with canonical tRNA(Ser)},
author = {C Baron and E Westhof and A Bock and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8510147},
isbn = {8510147},
year = {1993},
date = {1993-01-01},
journal = {J Mol Biol},
volume = {231},
number = {2},
pages = {274-292},
abstract = {Selenocysteine-inserting tRNAs (or tRNA(Sec)) are structurally untypical tRNAs that are charged by seryl-tRNA synthetase before being recognized by the selenocysteine synthase that converts serine into selenocysteine. tRNA(Sec) from Escherichia coli contains 95 nucleotides and is the longest tRNA known to date, in contrast to canonical tRNA(Ser), 88 nucleotides-long. We have studied its solution conformation by chemical and enzymatic probing. Global structural features were obtained by cobra venom and S1 nuclease mapping, as well as by probing with Pb2+. Accessibilities of phosphate groups were measured by ethylnitrosourea probing. Information about positions in bases involved in Watson-Crick pairing, in stacking or in tertiary interactions were obtained by chemical probing with dimethylsulfate, diethylpyrocarbonate, kethoxal and carbodiimide. On the basis of these chemical data, a three-dimensional model was constructed by computer modeling and compared to that of canonical tRNA(Ser). tRNA(Sec) resembles tRNA(Ser) at the level of its T-arm and anticodon-arm conformations, as well as at the joining of the D- and T-loops by a tertiary Watson-Crick G19-C56 interaction. Its extra-long variable arm is a double-stranded structure closed by a four nucleotide loop that is linked to the body of the tRNA in a way different from that found in tRNA(Ser). As anticipated from the peculiar features of the sequence in the D-loop and at the junction of amino acid and D-arms, tRNA(Sec) possesses a novel but restricted set of tertiary interactions in the core of its three-dimensional structure: a G8-A21-U14 triple pair and a novel interaction between C16 of the D-loop and C59 of the T-loop. A third triple interaction involving C15-G20a-G48 is suggested but some experimental evidence for it is still lacking. It is furthermore concluded that the D-arm has six base-pairs instead of three, as in canonical class II tRNA(Ser), with the D-loop containing only four nucleotides. Finally, the amino acid accepting arm forms a stack of eight Watson-Crick base-pairs (instead of 7 in other tRNAs). The biological relevance of this model with regard to interaction with seryl-tRNA synthetase and enzymes from the selenocysteine metabolism is discussed.},
note = {0022-2836
Journal Article},
keywords = {Adenine/chemistry Aspergillus Nuclease S1/pharmacology Base Sequence Comparative Study Escherichia coli/*chemistry Guanine/chemistry Lead/pharmacology Models, Amino Acid-Specific/*chemistry/drug effects RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Ser/*chemistry/drug effects Selenocysteine/*metabolism Sequence Homology, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Murgo S, Krol A, Carbon P
The differential transcriptional activity of two amphibian U1 small-nuclear RNA genes correlates with structural differences in the proximal sequence element Article de journal
Dans: Eur J Biochem, vol. 203, no. 3, p. 443-447, 1992, ISBN: 1735429, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Ambystoma Animals Base Sequence Microinjections Molecular Sequence Data Mutagenesis, Genetic Xenopus laevis, Non-U.S. Gov't *Transcription, Nucleic Acid Sequence Homology, Nucleic Acid Support, Site-Directed Phylogeny RNA, Small Nuclear/*genetics *Regulatory Sequences, Unité ARN
@article{,
title = {The differential transcriptional activity of two amphibian U1 small-nuclear RNA genes correlates with structural differences in the proximal sequence element},
author = {S Murgo and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1735429},
isbn = {1735429},
year = {1992},
date = {1992-01-01},
journal = {Eur J Biochem},
volume = {203},
number = {3},
pages = {443-447},
abstract = {We previously analyzed the transcription of an axolotl U1 small-nuclear RNA (snRNA) gene (AmU1) by microinjection into Xenopus laevis oocytes. In such an assay, AmU1 showed a low template activity compared to that of an X. laevis U1 snRNA gene (XlU1B2). Swapping the proximal sequence element (PSE) with that of XlU1B2 was required for AmU1 to acquire a transcription level equal to that of XlU1B2. In the present work, we examine the functional importance of the nucleotides that are common or different in both PSEs with the aim of identifying which nucleotides within the Xenopus U1 PSE are critical for this enhancement of Ambystoma mexicanum U1 snRNA transcription. The PSE mutation analysis showed that the central, phylogenetically conserved C-58/C-57 doublet is absolutely required for U1 promoter activity. In the 3' portion of this element, a CGC to ATG change (positions -54/-52) which partially restores the XlU1B2 PSE sequence, enables the AmU1 gene to gain the same transcriptional activity as XlU1B2. Remarkably, in this clustered point mutation, the sole C-54 to A-54 change is sufficient to obtain this increased level. Therefore, the activity of the AmU1 gene in injected Xenopus oocytes is strongly affected by a single sequence difference between AmU1 and XlU1B2 PSEs. This finding underscores the crucial importance of the nucleotide identity at position -54 to the function of the Xenopus U1 PSE.},
note = {0014-2956
Journal Article},
keywords = {Ambystoma Animals Base Sequence Microinjections Molecular Sequence Data Mutagenesis, Genetic Xenopus laevis, Non-U.S. Gov't *Transcription, Nucleic Acid Sequence Homology, Nucleic Acid Support, Site-Directed Phylogeny RNA, Small Nuclear/*genetics *Regulatory Sequences, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lescure A, Tebb G, Mattaj I W, Krol A, Carbon P
A factor with Sp1 DNA-binding specificity stimulates Xenopus U6 snRNA in vivo transcription by RNA polymerase III Article de journal
Dans: J Mol Biol, vol. 228, no. 2, p. 387-394, 1992, ISBN: 1453450, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Binding Sites Dna Molecular Sequence Data RNA Polymerase III/*metabolism RNA, Genetic Xenopus, LESCURE, Non-U.S. Gov't Transcription Factor, Nucleic Acid Support, Small Nuclear/*genetics *Regulatory Sequences, Sp1/metabolism *Transcription, Unité ARN
@article{,
title = {A factor with Sp1 DNA-binding specificity stimulates Xenopus U6 snRNA in vivo transcription by RNA polymerase III},
author = {A Lescure and G Tebb and I W Mattaj and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1453450},
isbn = {1453450},
year = {1992},
date = {1992-01-01},
journal = {J Mol Biol},
volume = {228},
number = {2},
pages = {387-394},
abstract = {We have previously shown that transcription of the Xenopus U6 snRNA gene by RNA polymerase III is stimulated in injected Xenopus oocytes by an activator element termed the DSE, which contains an octamer sequence. Data presented here reveal that the DSE contains, in addition, a GC-rich sequence capable of binding Sp1. Both elements are required to obtain wild-type levels of U6 transcription in vivo. The Xenopus U6 DSE exhibits optimal activation properties only when positioned at its normal location upstream from the start site. The U6 Sp1 motif binds the mammalian Sp1 transcriptional activator independently of the Oct-1 protein in vitro. Those mutations that lead to a reduced transcription level in vivo abolish the binding of Sp1 in vitro. Thus, transcriptional stimulation through the Xenopus U6 Sp1 motif is likely to be mediated by a protein with DNA-binding specificity identical to mammalian Sp1. These findings support the notion that RNA polymerase II and III transcription complexes share transactivators.},
note = {0022-2836
Journal Article},
keywords = {Animals Base Sequence Binding Sites Dna Molecular Sequence Data RNA Polymerase III/*metabolism RNA, Genetic Xenopus, LESCURE, Non-U.S. Gov't Transcription Factor, Nucleic Acid Support, Small Nuclear/*genetics *Regulatory Sequences, Sp1/metabolism *Transcription, Unité ARN},
pubstate = {published},
tppubtype = {article}
}