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1994
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}
}
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.
1992
Sturchler C, Carbon P, Krol A
An additional long-range interaction in human U1 snRNA Article de journal
Dans: Nucleic Acids Res, vol. 20, no. 6, p. 1215-1221, 1992, ISBN: 1532853, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites Hela Cells Human Molecular Sequence Data Mutagenesis, Site-Directed Nucleic Acid Conformation RNA, Small Nuclear, Small Nuclear/*chemistry/metabolism Ribonucleases/metabolism Ribonucleoproteins/metabolism Ribonucleoproteins, Unité ARN
@article{,
title = {An additional long-range interaction in human U1 snRNA},
author = {C Sturchler and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1532853},
isbn = {1532853},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {6},
pages = {1215-1221},
abstract = {We present evidence for the existence of an additional long-range interaction in vertebrate U1 snRNAs. By submitting human U1 snRNP, HeLa nuclear extracts, authentic human or X. laevis in vitro transcribed U1 snRNAs to RNase V1, a nuclease specific for double-stranded regions, cleavages occurred in the sequence psi psi ACC (positions 5-9) residing in the 5' terminal region of the RNA. The RNase V1 sensitive region is insensitive to single-stranded probes, something unexpected knowing that it was considered single-stranded in order to base-pair to pre-mRNA 5' splice site. We have identified the sequence GGUAG (positions 132-136) as the only possible 3' partner. Mutants, either abolishing or restoring the interaction between the partners, coupled to an RNase V1 assay, served to substantiate this base-pairing model. The presence of this additional helix, even detected in nuclear extracts under in vitro splicing conditions, implies that a conformational change must occur to release a free U1 snRNA 5' end.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Binding Sites Hela Cells Human Molecular Sequence Data Mutagenesis, Site-Directed Nucleic Acid Conformation RNA, Small Nuclear, Small Nuclear/*chemistry/metabolism Ribonucleases/metabolism Ribonucleoproteins/metabolism Ribonucleoproteins, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
We present evidence for the existence of an additional long-range interaction in vertebrate U1 snRNAs. By submitting human U1 snRNP, HeLa nuclear extracts, authentic human or X. laevis in vitro transcribed U1 snRNAs to RNase V1, a nuclease specific for double-stranded regions, cleavages occurred in the sequence psi psi ACC (positions 5-9) residing in the 5' terminal region of the RNA. The RNase V1 sensitive region is insensitive to single-stranded probes, something unexpected knowing that it was considered single-stranded in order to base-pair to pre-mRNA 5' splice site. We have identified the sequence GGUAG (positions 132-136) as the only possible 3' partner. Mutants, either abolishing or restoring the interaction between the partners, coupled to an RNase V1 assay, served to substantiate this base-pairing model. The presence of this additional helix, even detected in nuclear extracts under in vitro splicing conditions, implies that a conformational change must occur to release a free U1 snRNA 5' end.
