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RNA architecture and reactivity
Publications
1992
Wilhelm M L, Baranowski W, Keith G, Wilhelm F X
Rapid transfer of small RNAs from a polyacrylamide gel onto a nylon membrane using a gel dryer Journal Article
In: Nucleic Acids Res, vol. 20, no. 15, pp. 4106, 1992, ISBN: 1508703, (0305-1048 Journal Article).
Links | BibTeX | Tags: 5S/*isolation & purification RNA, Acrylic Resins Human Nylons RNA, Ribosomal, Small Nuclear/*isolation & purification RNA, Transfer/*isolation & purification Yeasts/genetics, Unité ARN
@article{,
title = {Rapid transfer of small RNAs from a polyacrylamide gel onto a nylon membrane using a gel dryer},
author = {M L Wilhelm and W Baranowski and G Keith and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1508703},
isbn = {1508703},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {15},
pages = {4106},
note = {0305-1048
Journal Article},
keywords = {5S/*isolation & purification RNA, Acrylic Resins Human Nylons RNA, Ribosomal, Small Nuclear/*isolation & purification RNA, Transfer/*isolation & purification Yeasts/genetics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Michel F
Some tertiary motifs of RNA foldings Book Chapter
In: Lilley, D M J; Heumann, H; Suck, D (Ed.): Structural Tools for the Analysis of Protein-Nucleic Acid Complexes (Advances in Life Sciences), pp. 255-267, Birkhauser Verlag, Basel, 1992.
Links | BibTeX | Tags: Unité ARN
@inbook{,
title = {Some tertiary motifs of RNA foldings},
author = {E Westhof and F Michel},
editor = {D M J Lilley and H Heumann and D Suck},
url = {http://www.amazon.com/Structural-Analysis-Protein-Nucleic-Complexes-Advances/dp/0817627766},
year = {1992},
date = {1992-01-01},
booktitle = {Structural Tools for the Analysis of Protein-Nucleic Acid Complexes (Advances in Life Sciences)},
pages = {255-267},
publisher = {Birkhauser Verlag, Basel},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Westhof E, Jaeger L
RNA pseudoknots Journal Article
In: Curr Opin Struct Biol, vol. 2, no. 3, pp. 327-333, 1992.
Abstract | Links | BibTeX | Tags: Unité ARN
@article{,
title = {RNA pseudoknots},
author = {E Westhof and L Jaeger},
url = {http://www.sciencedirect.com/science/article/pii/0959440X9290221R},
doi = {10.1016/0959-440X(92)90221-R},
year = {1992},
date = {1992-01-01},
journal = {Curr Opin Struct Biol},
volume = {2},
number = {3},
pages = {327-333},
abstract = {RNA pseudoknots result from Watson-Crick base pairing involving a stretch of bases located between paired strands and a distal single-stranded region. Recently, significant advances in our understanding of their structural and functional aspects have been accomplished. At the structural level, modelling and NMR studies have shown that a defined subset of pseudoknots may be considered as tertiary motifs in RNA foldings. At the functional level, there is evidence that the realm of functions encompassed by RNA pseudoknots extends from the control of translation in prokaryotes, retroviruses and coronaviruses to the control of catalytic activity in ribozymes and the control of replication in some plant viruses.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
RNA pseudoknots result from Watson-Crick base pairing involving a stretch of bases located between paired strands and a distal single-stranded region. Recently, significant advances in our understanding of their structural and functional aspects have been accomplished. At the structural level, modelling and NMR studies have shown that a defined subset of pseudoknots may be considered as tertiary motifs in RNA foldings. At the functional level, there is evidence that the realm of functions encompassed by RNA pseudoknots extends from the control of translation in prokaryotes, retroviruses and coronaviruses to the control of catalytic activity in ribozymes and the control of replication in some plant viruses.
Westhof E
Westhof's rule Journal Article
In: Nature, vol. 358, no. 6386, pp. 459-460, 1992, ISBN: 1641036, (0028-0836 Letter).
Links | BibTeX | Tags: *Hydrogen Bonding *Nucleic Acid Conformation, Unité ARN, WESTHOF
@article{,
title = {Westhof's rule},
author = {E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1641036},
isbn = {1641036},
year = {1992},
date = {1992-01-01},
journal = {Nature},
volume = {358},
number = {6386},
pages = {459-460},
note = {0028-0836
Letter},
keywords = {*Hydrogen Bonding *Nucleic Acid Conformation, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Tounekti N, Mougel M, Roy C, Marquet R, Darlix J L, Paoletti J, Ehresmann B, Ehresmann C
Effect of dimerization on the conformation of the encapsidation Psi domain of Moloney murine leukemia virus RNA Journal Article
In: J Mol Biol, vol. 223, no. 1, pp. 205-220, 1992, ISBN: 1731069, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence Comparative Study Hydrogen Bonding Macromolecular Systems Molecular Sequence Data Molecular Structure Moloney murine leukemia virus/*ultrastructure Nucleic Acid Conformation Phylogeny RNA, MARQUET, Non-U.S. Gov't, Unité ARN, Viral/chemistry/*ultrastructure Sequence Alignment Support
@article{,
title = {Effect of dimerization on the conformation of the encapsidation Psi domain of Moloney murine leukemia virus RNA},
author = {N Tounekti and M Mougel and C Roy and R Marquet 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=1731069},
isbn = {1731069},
year = {1992},
date = {1992-01-01},
journal = {J Mol Biol},
volume = {223},
number = {1},
pages = {205-220},
abstract = {In Moloney murine leukemia virus, the encapsidation Psi element was shown to be necessary and sufficient to promote packaging of viral RNA, and to be required for dimerization. The conformation of the Psi domain (nucleotides 215 to 565) was investigated in solution by chemical probing. The four bases were monitored at one of their Watson-Crick positions with dimethylsulfate at cytosine N3 and adenosine N1, and with a carbodiimide derivative at guanosine N1 and uridine N3. Position N7 of adenine residues was probed with diethylpyrocarbonate. The analyses were conducted on in vitro transcribed fragments corresponding either to the isolated Psi domain or to the 5'-terminal 725 nucleotides. The RNA fragments were analyzed in their monomeric and dimeric forms. A secondary structure model was derived from probing data, computer prediction and sequence analysis of related murine retroviruses. One major result is that Psi forms an independent and highly structured domain. Dimerization induces an extensive reduction of reactivity in region 278 to 309 that can be interpreted as the result of intermolecular interactions and/or intramolecular conformational rearrangements. A second region (around position 215) was shown to display discrete reactivity changes upon dimerization. These two regions represent likely elements of dimerization. More unexpectedly, reactivity changes (essentially enhancement of reactivity) were also detected in another part of Psi (around position 480) not believed to contain elements of dimerization. These reactivity changes could be interpreted as dimerization-induced allosteric transitions.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Comparative Study Hydrogen Bonding Macromolecular Systems Molecular Sequence Data Molecular Structure Moloney murine leukemia virus/*ultrastructure Nucleic Acid Conformation Phylogeny RNA, MARQUET, Non-U.S. Gov't, Unité ARN, Viral/chemistry/*ultrastructure Sequence Alignment Support},
pubstate = {published},
tppubtype = {article}
}
In Moloney murine leukemia virus, the encapsidation Psi element was shown to be necessary and sufficient to promote packaging of viral RNA, and to be required for dimerization. The conformation of the Psi domain (nucleotides 215 to 565) was investigated in solution by chemical probing. The four bases were monitored at one of their Watson-Crick positions with dimethylsulfate at cytosine N3 and adenosine N1, and with a carbodiimide derivative at guanosine N1 and uridine N3. Position N7 of adenine residues was probed with diethylpyrocarbonate. The analyses were conducted on in vitro transcribed fragments corresponding either to the isolated Psi domain or to the 5'-terminal 725 nucleotides. The RNA fragments were analyzed in their monomeric and dimeric forms. A secondary structure model was derived from probing data, computer prediction and sequence analysis of related murine retroviruses. One major result is that Psi forms an independent and highly structured domain. Dimerization induces an extensive reduction of reactivity in region 278 to 309 that can be interpreted as the result of intermolecular interactions and/or intramolecular conformational rearrangements. A second region (around position 215) was shown to display discrete reactivity changes upon dimerization. These two regions represent likely elements of dimerization. More unexpectedly, reactivity changes (essentially enhancement of reactivity) were also detected in another part of Psi (around position 480) not believed to contain elements of dimerization. These reactivity changes could be interpreted as dimerization-induced allosteric transitions.
Sturchler C, Carbon P, Krol A
An additional long-range interaction in human U1 snRNA Journal Article
In: Nucleic Acids Res, vol. 20, no. 6, pp. 1215-1221, 1992, ISBN: 1532853, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: 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.
Skouri M, Munch J P, Lorber B, Giege R, Candau S
Interaction between lysozyme molecules under precrystallization conditions studied by light scattering. Journal Article
In: J Crystal Growth, vol. 122, no. 1-4, pp. 14-20, 1992, ISBN: 10.1016/0022-0248(92)90221-4.
Abstract | Links | BibTeX | Tags: Unité ARN
@article{,
title = {Interaction between lysozyme molecules under precrystallization conditions studied by light scattering.},
author = {M Skouri and J P Munch and B Lorber and R Giege and S Candau},
url = {http://www.sciencedirect.com/science/article/pii/0022024892902214},
isbn = {10.1016/0022-0248(92)90221-4},
year = {1992},
date = {1992-01-01},
journal = {J Crystal Growth},
volume = {122},
number = {1-4},
pages = {14-20},
abstract = {Lightscattering experiments were undertaken on lysozymeunder various solvent conditions. When the protein is undersaturated, attractive interparticular interactions are detected. They are enhanced when the temperature is decreased, but are much weaker in NaCl solutions in which the protein crystallizes than in ammonium sulfate solutions in which it forms amorphous precipitates. When the protein in a NaCl solution is brought to supersaturation by a temperature decrease, lightscattering measurements indicate the simultaneous presence of two scatter populations which can be assimilated to individual lysozymemolecules and to large particles. Kinetic experiments in which the temperature is quenched rapidly indicate that the apparent hydrodynamic radius of the large particles increases regularly with time up to a plateau value of about 2600A˚.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lightscattering experiments were undertaken on lysozymeunder various solvent conditions. When the protein is undersaturated, attractive interparticular interactions are detected. They are enhanced when the temperature is decreased, but are much weaker in NaCl solutions in which the protein crystallizes than in ammonium sulfate solutions in which it forms amorphous precipitates. When the protein in a NaCl solution is brought to supersaturation by a temperature decrease, lightscattering measurements indicate the simultaneous presence of two scatter populations which can be assimilated to individual lysozymemolecules and to large particles. Kinetic experiments in which the temperature is quenched rapidly indicate that the apparent hydrodynamic radius of the large particles increases regularly with time up to a plateau value of about 2600A˚.
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}
}
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.
Rudinger J, Puglisi J D, Putz J, Schatz D, Eckstein F, Florentz C, Giege R
Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase Journal Article
In: Proc Natl Acad Sci U S A, vol. 89, no. 13, pp. 5882-5886, 1992, ISBN: 1631068, (0027-8424 Journal Article).
Abstract | Links | BibTeX | Tags: Asp/chemistry/*metabolism Saccharomyces cerevisiae/enzymology Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*metabolism Base Sequence Binding Sites DNA Mutational Analysis Fungal Proteins/metabolism Molecular Sequence Data Protein Binding RNA, FLORENTZ, Fungal/chemistry/metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase},
author = {J Rudinger and J D Puglisi and J Putz and D Schatz and F Eckstein and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1631068},
isbn = {1631068},
year = {1992},
date = {1992-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {89},
number = {13},
pages = {5882-5886},
abstract = {The interaction of wild-type and mutant yeast tRNA(Asp) transcripts with yeast aspartyl-tRNA synthetase (AspRS; EC 6.1.1.12) has been probed by using iodine cleavage of phosphorothioate-substituted transcripts. AspRS protects phosphates in the anticodon (G34, U35), D-stem (U25), and acceptor end (G73) that correspond to determinant nucleotides for aspartylation. This protection, as well as that in anticodon stem (C29, U40, G41) and D-stem (U11 to U13), is consistent with direct interaction of AspRS at these phosphates. Other protection, in the variable loop (G45), D-loop (G18, G19), and T-stem and loop (G53, U54, U55), as well as enhanced reactivity at G37, may result from conformational changes of the transcript upon binding to AspRS. Transcripts mutated at determinant positions showed a loss of phosphate protection in the region of the mutation while maintaining the global protection pattern. The ensemble of results suggests that aspartylation specificity arises from both protein-base and protein-phosphate contacts and that different regions of tRNA(Asp) interact independently with AspRS. A mutant transcript of yeast tRNA(Phe) that contains the set of identity nucleotides for specific aspartylation gave a phosphate protection pattern strikingly similar to that of wild-type tRNA(Asp). This confirms that a small number of nucleotides within a different tRNA sequence context can direct specific interaction with synthetase.},
note = {0027-8424
Journal Article},
keywords = {Asp/chemistry/*metabolism Saccharomyces cerevisiae/enzymology Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*metabolism Base Sequence Binding Sites DNA Mutational Analysis Fungal Proteins/metabolism Molecular Sequence Data Protein Binding RNA, FLORENTZ, Fungal/chemistry/metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The interaction of wild-type and mutant yeast tRNA(Asp) transcripts with yeast aspartyl-tRNA synthetase (AspRS; EC 6.1.1.12) has been probed by using iodine cleavage of phosphorothioate-substituted transcripts. AspRS protects phosphates in the anticodon (G34, U35), D-stem (U25), and acceptor end (G73) that correspond to determinant nucleotides for aspartylation. This protection, as well as that in anticodon stem (C29, U40, G41) and D-stem (U11 to U13), is consistent with direct interaction of AspRS at these phosphates. Other protection, in the variable loop (G45), D-loop (G18, G19), and T-stem and loop (G53, U54, U55), as well as enhanced reactivity at G37, may result from conformational changes of the transcript upon binding to AspRS. Transcripts mutated at determinant positions showed a loss of phosphate protection in the region of the mutation while maintaining the global protection pattern. The ensemble of results suggests that aspartylation specificity arises from both protein-base and protein-phosphate contacts and that different regions of tRNA(Asp) interact independently with AspRS. A mutant transcript of yeast tRNA(Phe) that contains the set of identity nucleotides for specific aspartylation gave a phosphate protection pattern strikingly similar to that of wild-type tRNA(Asp). This confirms that a small number of nucleotides within a different tRNA sequence context can direct specific interaction with synthetase.
Rudinger J, Florentz C, Dreher T, Giege R
In: Nucleic Acids Res, vol. 20, no. 8, pp. 1865-1870, 1992, ISBN: 1579487, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence Codon/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data Mosaic Viruses/enzymology/genetics/*metabolism Mutation/genetics Nucleic Acid Conformation RNA, FLORENTZ, His/*metabolism RNA, Non-P.H.S. Yeasts/enzymology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN, Viral/*metabolism Support
@article{,
title = {Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA},
author = {J Rudinger and C Florentz and T Dreher and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1579487},
isbn = {1579487},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {8},
pages = {1865-1870},
abstract = {Mischarging of the valine specific tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA has been tested in the presence of purified arginyl-, aspartyl-, histidinyl-, and phenylalanyl-tRNA synthetases from bakers' yeast. Important mischarging of a 264 nucleotide-long transcript was found with histidinyl-tRNA synthetase which can acylate this fragment up to a level of 25% with a loss of specificity (expressed as Vmax/KM ratios) of only 100 fold as compared to a yeast tRNA(His) transcript. Experiments on transcripts of various lengths indicate that the minimal valylatable fragment (n = 88) is the most efficient substrate for histidinyl-tRNA synthetase, with kinetic characteristics similar to those found for the control tRNA(His) transcript. Mutations in the anticodon or adjacent to the 3' CCA that severely affect the valylation capacity of the 264 nucleotide long TYMV fragment are without negative effect on its mischarging, and for some cases even improve its efficiency. A short fragment (n = 42) of the viral RNA containing the pseudoknot and corresponding to the amino acid accepting branch of the molecule is an efficient histidine acceptor.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Codon/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data Mosaic Viruses/enzymology/genetics/*metabolism Mutation/genetics Nucleic Acid Conformation RNA, FLORENTZ, His/*metabolism RNA, Non-P.H.S. Yeasts/enzymology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN, Viral/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Mischarging of the valine specific tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA has been tested in the presence of purified arginyl-, aspartyl-, histidinyl-, and phenylalanyl-tRNA synthetases from bakers' yeast. Important mischarging of a 264 nucleotide-long transcript was found with histidinyl-tRNA synthetase which can acylate this fragment up to a level of 25% with a loss of specificity (expressed as Vmax/KM ratios) of only 100 fold as compared to a yeast tRNA(His) transcript. Experiments on transcripts of various lengths indicate that the minimal valylatable fragment (n = 88) is the most efficient substrate for histidinyl-tRNA synthetase, with kinetic characteristics similar to those found for the control tRNA(His) transcript. Mutations in the anticodon or adjacent to the 3' CCA that severely affect the valylation capacity of the 264 nucleotide long TYMV fragment are without negative effect on its mischarging, and for some cases even improve its efficiency. A short fragment (n = 42) of the viral RNA containing the pseudoknot and corresponding to the amino acid accepting branch of the molecule is an efficient histidine acceptor.
Romby P, Brunel C, Caillet J, Springer M, Grunberg-Manago M, Westhof E, Ehresmann C, Ehresmann B
In: Nucleic Acids Res, vol. 20, no. 21, pp. 5633-5640, 1992, ISBN: 1280807, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Acylation Anticodon Base Sequence Binding, Bacterial Methionine-tRNA Ligase/metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/metabolism RNA, Competitive Escherichia coli/enzymology/*genetics *Gene Expression Regulation, Genetic, Met/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/antagonists & inhibitors/*genetics/metabolism Translation, ROMBY, Thr/metabolism Repressor Proteins/*metabolism Ribosomes/metabolism Support, Transfer, Transfer/*metabolism RNA, Unité ARN
@article{,
title = {Molecular mimicry in translational control of E. coli threonyl-tRNA synthetase gene. Competitive inhibition in tRNA aminoacylation and operator-repressor recognition switch using tRNA identity rules},
author = {P Romby and C Brunel and J Caillet and M Springer and M Grunberg-Manago and E Westhof and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1280807},
isbn = {1280807},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {21},
pages = {5633-5640},
abstract = {We previously showed that: (i) E.coli threonyl-tRNA synthetase (ThrRS) binds to the leader of its mRNA and represses translation by preventing ribosome binding to its loading site; (ii) the translational operator shares sequence and structure similarities with tRNA(Thr); (iii) it is possible to switch the specificity of the translational control from ThrRS to methionyl-tRNA synthetase (MetRS) by changing the CGU anticodon-like sequence to CAU, the tRNA(Met) anticodon. Here, we show that the wild type (CGU) and the mutated (CAU) operators act as competitive inhibitors of tRNA(Thr) and tRNA(fMet) for aminoacylation catalyzed by E.coli ThrRS and MetRS, respectively. The apparent Kd of the MetRS/CAU operator complex is one order magnitude higher than that of the ThrRS/CGU operator complex. Although ThrRS and MetRS shield the anticodon- and acceptor-like domains of their respective operators, the relative contribution of these two domains differs significantly. As in the threonine system, the interaction of MetRS with the CAU operator occludes ribosome binding to its loading site. The present data demonstrate that the anticodon-like sequence is one major determinant for the identity of the operator and the regulation specificity. It further shows that the tRNA-like operator obeys to tRNA identity rules.},
note = {0305-1048
Journal Article},
keywords = {Acylation Anticodon Base Sequence Binding, Bacterial Methionine-tRNA Ligase/metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/metabolism RNA, Competitive Escherichia coli/enzymology/*genetics *Gene Expression Regulation, Genetic, Met/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/antagonists & inhibitors/*genetics/metabolism Translation, ROMBY, Thr/metabolism Repressor Proteins/*metabolism Ribosomes/metabolism Support, Transfer, Transfer/*metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
We previously showed that: (i) E.coli threonyl-tRNA synthetase (ThrRS) binds to the leader of its mRNA and represses translation by preventing ribosome binding to its loading site; (ii) the translational operator shares sequence and structure similarities with tRNA(Thr); (iii) it is possible to switch the specificity of the translational control from ThrRS to methionyl-tRNA synthetase (MetRS) by changing the CGU anticodon-like sequence to CAU, the tRNA(Met) anticodon. Here, we show that the wild type (CGU) and the mutated (CAU) operators act as competitive inhibitors of tRNA(Thr) and tRNA(fMet) for aminoacylation catalyzed by E.coli ThrRS and MetRS, respectively. The apparent Kd of the MetRS/CAU operator complex is one order magnitude higher than that of the ThrRS/CGU operator complex. Although ThrRS and MetRS shield the anticodon- and acceptor-like domains of their respective operators, the relative contribution of these two domains differs significantly. As in the threonine system, the interaction of MetRS with the CAU operator occludes ribosome binding to its loading site. The present data demonstrate that the anticodon-like sequence is one major determinant for the identity of the operator and the regulation specificity. It further shows that the tRNA-like operator obeys to tRNA identity rules.
Rippe K, Fritsch V, Westhof E, Jovin T M
Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex Journal Article
In: EMBO J, vol. 11, no. 10, pp. 3777-3786, 1992, ISBN: 1396571, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence Circular Dichroism DNA/*chemistry Hydrogen Bonding Hydrogen-Ion Concentration Indicators and Reagents Magnesium Chloride Models, Fluorescence Spectrophotometry, MARQUET, Molecular Molecular Sequence Data *Nucleic Acid Conformation Oligodeoxyribonucleotides/*chemistry Spectrometry, PAILLART, Ultraviolet Structure-Activity Relationship Thermodynamics, Unité ARN, WESTHOF
@article{,
title = {Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex},
author = {K Rippe and V Fritsch and E Westhof and T M Jovin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1396571},
isbn = {1396571},
year = {1992},
date = {1992-01-01},
journal = {EMBO J},
volume = {11},
number = {10},
pages = {3777-3786},
abstract = {The oligonucleotides d[(G-A)7G] and d[(G-A)12G] self-associate under physiological conditions (10 mM MgCl2, neutral pH) into a stable double-helical structure (psRR-DNA) in which the two polypurine strands are in a parallel orientation in contrast to the antiparallel disposition of conventional B-DNA. We have characterized psRR-DNA by gel electrophoresis, UV absorption, vacuum UV circular dichroism, monomer-excimer fluorescence of oligonucleotides end-labelled with pyrene, and chemical probing with diethyl pyrocarbonate and dimethyl sulfate. The duplex is stable at pH 4-9, suggesting that the structure is compatible with, but does not require, protonation of the A residues. The data support a model derived from force-field analysis in which the parallel-stranded d(G-A)n helix is right-handed and constituted of alternating, symmetrical Gsyn.Gsyn and Aanti.Aanti base pairs with N1H.O6 and N6H.N7 hydrogen bonds, respectively. This dinucleotide structure may be the source of a negative peak observed at 190 nm in the vacuum UV CD spectrum, a feature previously reported only for left-handed Z-DNA. The related sequence d[(GAAGGA)4G] also forms a parallel-stranded duplex but one that is less stable and probably involves a slightly different secondary structure. We discuss the potential intervention of psRR-DNA in recombination, gene expression and the stabilization of genomic structure.},
note = {0261-4189
Journal Article},
keywords = {Base Sequence Circular Dichroism DNA/*chemistry Hydrogen Bonding Hydrogen-Ion Concentration Indicators and Reagents Magnesium Chloride Models, Fluorescence Spectrophotometry, MARQUET, Molecular Molecular Sequence Data *Nucleic Acid Conformation Oligodeoxyribonucleotides/*chemistry Spectrometry, PAILLART, Ultraviolet Structure-Activity Relationship Thermodynamics, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
The oligonucleotides d[(G-A)7G] and d[(G-A)12G] self-associate under physiological conditions (10 mM MgCl2, neutral pH) into a stable double-helical structure (psRR-DNA) in which the two polypurine strands are in a parallel orientation in contrast to the antiparallel disposition of conventional B-DNA. We have characterized psRR-DNA by gel electrophoresis, UV absorption, vacuum UV circular dichroism, monomer-excimer fluorescence of oligonucleotides end-labelled with pyrene, and chemical probing with diethyl pyrocarbonate and dimethyl sulfate. The duplex is stable at pH 4-9, suggesting that the structure is compatible with, but does not require, protonation of the A residues. The data support a model derived from force-field analysis in which the parallel-stranded d(G-A)n helix is right-handed and constituted of alternating, symmetrical Gsyn.Gsyn and Aanti.Aanti base pairs with N1H.O6 and N6H.N7 hydrogen bonds, respectively. This dinucleotide structure may be the source of a negative peak observed at 190 nm in the vacuum UV CD spectrum, a feature previously reported only for left-handed Z-DNA. The related sequence d[(GAAGGA)4G] also forms a parallel-stranded duplex but one that is less stable and probably involves a slightly different secondary structure. We discuss the potential intervention of psRR-DNA in recombination, gene expression and the stabilization of genomic structure.
Przykorska A, el Adlouni C, Keith G, Szarkowski J W, Dirheimer G
Structural specificity of Rn nuclease I as probed on yeast tRNA(Phe) and tRNA(Asp) Journal Article
In: Nucleic Acids Res, vol. 20, no. 4, pp. 659-663, 1992, ISBN: 1542562, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Asp/chemistry/genetics/*metabolism RNA, Base Composition Base Sequence Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Yeasts/genetics, Pancreatic/*metabolism Secale cereale Substrate Specificity Support, Phe/chemistry/genetics/*metabolism Ribonuclease, Transfer, Unité ARN
@article{,
title = {Structural specificity of Rn nuclease I as probed on yeast tRNA(Phe) and tRNA(Asp)},
author = {A Przykorska and C el Adlouni and G Keith and J W Szarkowski and G Dirheimer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1542562},
isbn = {1542562},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {4},
pages = {659-663},
abstract = {A single-strand-specific nuclease from rye germ (Rn nuclease I) was characterized as a tool for secondary and tertiary structure investigation of RNAs. To test the procedure, yeast tRNA(Phe) and tRNA(Asp) for which the tertiary structures are known, as well as the 3'-half of tRNA(Asp) were used as substrates. In tRNA(Phe) the nuclease introduced main primary cuts at positions U33 and A35 of the anticodon loop and G18 and G19 of the D loop. No primary cuts were observed within the double stranded stems. In tRNA(Asp) the main cuts occurred at positions U33, G34, U35, C36 of the anticodon loop and G18 and C20:1 positions in the D loop. No cuts were observed in the T loop in intact tRNA(Asp) but strong primary cleavages occurred at positions psi 55, C56, A57 within that loop in the absence of the tertiary interactions between T and D loops (use of 3'-half tRNA(Asp)). These results show that Rn nuclease I is specific for exposed single-stranded regions.},
note = {0305-1048
Journal Article},
keywords = {Asp/chemistry/genetics/*metabolism RNA, Base Composition Base Sequence Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Yeasts/genetics, Pancreatic/*metabolism Secale cereale Substrate Specificity Support, Phe/chemistry/genetics/*metabolism Ribonuclease, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A single-strand-specific nuclease from rye germ (Rn nuclease I) was characterized as a tool for secondary and tertiary structure investigation of RNAs. To test the procedure, yeast tRNA(Phe) and tRNA(Asp) for which the tertiary structures are known, as well as the 3'-half of tRNA(Asp) were used as substrates. In tRNA(Phe) the nuclease introduced main primary cuts at positions U33 and A35 of the anticodon loop and G18 and G19 of the D loop. No primary cuts were observed within the double stranded stems. In tRNA(Asp) the main cuts occurred at positions U33, G34, U35, C36 of the anticodon loop and G18 and C20:1 positions in the D loop. No cuts were observed in the T loop in intact tRNA(Asp) but strong primary cleavages occurred at positions psi 55, C56, A57 within that loop in the absence of the tertiary interactions between T and D loops (use of 3'-half tRNA(Asp)). These results show that Rn nuclease I is specific for exposed single-stranded regions.
Perret V, Florentz C, Puglisi J D, Giege R
Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities Journal Article
In: J Mol Biol, vol. 226, no. 2, pp. 323-333, 1992, ISBN: 1640453, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Activation Aspartate-tRNA Ligase/*metabolism Base Sequence Molecular Sequence Data Nucleic Acid Conformation Phenylalanine-tRNA Ligase/*metabolism RNA, Asp/metabolism/*ultrastructure RNA, FLORENTZ, Fungal/metabolism/ultrastructure RNA, Non-U.S. Gov't, Phe/metabolism/*ultrastructure Saccharomyces cerevisiae Structure-Activity Relationship Substrate Specificity Support, Transfer, Unité ARN
@article{,
title = {Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities},
author = {V Perret and C Florentz and J D Puglisi and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1640453},
isbn = {1640453},
year = {1992},
date = {1992-01-01},
journal = {J Mol Biol},
volume = {226},
number = {2},
pages = {323-333},
abstract = {The structure and function of in vitro transcribed tRNA(Asp) variants with inserted conformational features characteristic of yeast tRNA(Phe), such as the length of the variable region or the arrangement of the conserved residues in the D-loop, have been investigated. Although they exhibit significant conformational alterations as revealed by Pb2+ treatment, these variants are still efficiently aspartylated by yeast aspartyl-tRNA synthetase. Thus, this synthetase can accommodate a variety of tRNA conformers. In a second series of variants, the identity determinants of yeast tRNA(Phe) were transplanted into the previous structural variants of tRNA(Asp). The phenylalanine acceptance of these variants improves with increasing the number of structural characteristics of tRNA(Phe), suggesting that phenylalanyl-tRNA synthetase is sensitive to the conformational frame embedding the cognate identity nucleotides. These results contrast with the efficient transplantation of tRNA(Asp) identity elements into yeast tRNA(Phe). This indicates that synthetases respond differently to the detailed conformation of their tRNA substrates. Efficient aminoacylation is not only dependent on the presence of the set of identity nucleotides, but also on a precise conformation of the tRNA.},
note = {0022-2836
Journal Article},
keywords = {Amino Acid Activation Aspartate-tRNA Ligase/*metabolism Base Sequence Molecular Sequence Data Nucleic Acid Conformation Phenylalanine-tRNA Ligase/*metabolism RNA, Asp/metabolism/*ultrastructure RNA, FLORENTZ, Fungal/metabolism/ultrastructure RNA, Non-U.S. Gov't, Phe/metabolism/*ultrastructure Saccharomyces cerevisiae Structure-Activity Relationship Substrate Specificity Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The structure and function of in vitro transcribed tRNA(Asp) variants with inserted conformational features characteristic of yeast tRNA(Phe), such as the length of the variable region or the arrangement of the conserved residues in the D-loop, have been investigated. Although they exhibit significant conformational alterations as revealed by Pb2+ treatment, these variants are still efficiently aspartylated by yeast aspartyl-tRNA synthetase. Thus, this synthetase can accommodate a variety of tRNA conformers. In a second series of variants, the identity determinants of yeast tRNA(Phe) were transplanted into the previous structural variants of tRNA(Asp). The phenylalanine acceptance of these variants improves with increasing the number of structural characteristics of tRNA(Phe), suggesting that phenylalanyl-tRNA synthetase is sensitive to the conformational frame embedding the cognate identity nucleotides. These results contrast with the efficient transplantation of tRNA(Asp) identity elements into yeast tRNA(Phe). This indicates that synthetases respond differently to the detailed conformation of their tRNA substrates. Efficient aminoacylation is not only dependent on the presence of the set of identity nucleotides, but also on a precise conformation of the tRNA.
Pauly M, Treger M, Westhof E, Chambon P
The initiation accuracy of the SV40 early transcription is determined by the functional domains of two TATA elements Journal Article
In: Nucleic Acids Res, vol. 20, no. 5, pp. 975-982, 1992, ISBN: 1312710, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence DNA Mutational Analysis DNA, Genetic/*genetics, Non-U.S. Gov't TATA Box/*genetics Transcription, Unité ARN, Viral/*genetics Hela Cells Human Molecular Sequence Data Nucleic Acid Conformation Simian virus 40/*genetics Support, Viral/chemistry/genetics Electrophoresis Genes, WESTHOF
@article{,
title = {The initiation accuracy of the SV40 early transcription is determined by the functional domains of two TATA elements},
author = {M Pauly and M Treger and E Westhof and P Chambon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1312710},
isbn = {1312710},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {5},
pages = {975-982},
abstract = {To locate the boundaries of the TATA element in the SV40 early promoter, point mutations have been constructed such as to cover the whole T + A-rich region of the replication origin. The effects of these mutations on the rate of transcription in vivo show that this region actually contains two TATA elements I and II, each independently directing the accurate initiation of transcription from a specified set of start sites, EES1 and EES2, respectively. The sequence of TATA element I fits best with the compiled 'consensus' sequence found in eukaryotic gene promoters and is the most efficient in directing transcription initiation. Mutations which improve this fit can still increase the rate of transcription, confirming the theory of a correlation between the nucleotide sequence of a TATA element and its functional efficiency. Moreover, some mutations which simultaneously modify the angle of DNA curvature in the T + A-rich promoter region and the rate of transcription reveal a correlation between DNA bending and transcription initiation.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence DNA Mutational Analysis DNA, Genetic/*genetics, Non-U.S. Gov't TATA Box/*genetics Transcription, Unité ARN, Viral/*genetics Hela Cells Human Molecular Sequence Data Nucleic Acid Conformation Simian virus 40/*genetics Support, Viral/chemistry/genetics Electrophoresis Genes, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
To locate the boundaries of the TATA element in the SV40 early promoter, point mutations have been constructed such as to cover the whole T + A-rich region of the replication origin. The effects of these mutations on the rate of transcription in vivo show that this region actually contains two TATA elements I and II, each independently directing the accurate initiation of transcription from a specified set of start sites, EES1 and EES2, respectively. The sequence of TATA element I fits best with the compiled 'consensus' sequence found in eukaryotic gene promoters and is the most efficient in directing transcription initiation. Mutations which improve this fit can still increase the rate of transcription, confirming the theory of a correlation between the nucleotide sequence of a TATA element and its functional efficiency. Moreover, some mutations which simultaneously modify the angle of DNA curvature in the T + A-rich promoter region and the rate of transcription reveal a correlation between DNA bending and transcription initiation.
Nothwang H G, Coux O, Keith G, Silva-Pereira I, Scherrer K
The major RNA in prosomes of HeLa cells and duck erythroblasts is tRNA(Lys,3) Journal Article
In: Nucleic Acids Res, vol. 20, no. 8, pp. 1959-1965, 1992, ISBN: 1579498, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Animals Base Sequence Blotting, Gel, Lys/*analysis/metabolism Ribonucleoproteins/*chemistry/drug effects Support, Non-U.S. Gov't Zinc/pharmacology, Northern Ducks Electrophoresis, Transfer, Two-Dimensional Erythroblasts Hela Cells Human Molecular Sequence Data RNA Nucleotidyltransferases/metabolism RNA, Unité ARN
@article{,
title = {The major RNA in prosomes of HeLa cells and duck erythroblasts is tRNA(Lys,3)},
author = {H G Nothwang and O Coux and G Keith and I Silva-Pereira and K Scherrer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1579498},
isbn = {1579498},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {8},
pages = {1959-1965},
abstract = {Two-dimensional gel electrophoresis of HeLa cell prosomal RNAs, 3'-end labeled by RNA ligase, revealed one prominent spot. Determination of a partial sequence at the 3'-end indicated full homology to the 18 nucleotides at the 3'-end of tRNA(Lys,3) from rabbit, the bovine and the human species. An oligonucleotide complementary to the 3'-end of tRNA(Lys,3) hybridized on Northern blots with prosomal RNA from both HeLa cells and duck erythroblasts. In two-dimensional PAGE, the major pRNA of HeLa cells co-migrated with bovine tRNA(Lys,3). Reconstitution of the CCA 3'-end of RNA from both human and duck prosomes, by tRNA-nucleotidyl-transferase, confirmed the tRNA character of this type of RNA. Furthermore, it revealed at least one additional tRNA band about 85 nt long among the prosomal RNA from both species. Finally, confirming an original property of prosomal RNA, we show that in vitro synthesized tRNA(Lys,3) hybridizes stably to duck globin mRNA, and to poly(A)(+)- and poly(A)(-)-RNA from HeLa cells.},
note = {0305-1048
Journal Article},
keywords = {Animals Base Sequence Blotting, Gel, Lys/*analysis/metabolism Ribonucleoproteins/*chemistry/drug effects Support, Non-U.S. Gov't Zinc/pharmacology, Northern Ducks Electrophoresis, Transfer, Two-Dimensional Erythroblasts Hela Cells Human Molecular Sequence Data RNA Nucleotidyltransferases/metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Two-dimensional gel electrophoresis of HeLa cell prosomal RNAs, 3'-end labeled by RNA ligase, revealed one prominent spot. Determination of a partial sequence at the 3'-end indicated full homology to the 18 nucleotides at the 3'-end of tRNA(Lys,3) from rabbit, the bovine and the human species. An oligonucleotide complementary to the 3'-end of tRNA(Lys,3) hybridized on Northern blots with prosomal RNA from both HeLa cells and duck erythroblasts. In two-dimensional PAGE, the major pRNA of HeLa cells co-migrated with bovine tRNA(Lys,3). Reconstitution of the CCA 3'-end of RNA from both human and duck prosomes, by tRNA-nucleotidyl-transferase, confirmed the tRNA character of this type of RNA. Furthermore, it revealed at least one additional tRNA band about 85 nt long among the prosomal RNA from both species. Finally, confirming an original property of prosomal RNA, we show that in vitro synthesized tRNA(Lys,3) hybridizes stably to duck globin mRNA, and to poly(A)(+)- and poly(A)(-)-RNA from HeLa cells.
Myslinski E, Krol A, Carbon P
Optimal tRNA((Ser)Sec) gene activity requires an upstream SPH motif Journal Article
In: Nucleic Acids Res, vol. 20, no. 2, pp. 203-209, 1992, ISBN: 1311068, (0305-1048 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid-Specific/*genetics Recombinant Fusion Proteins/genetics/metabolism Simian virus 40/*genetics Support, Animals Base Sequence DNA Mutational Analysis DNA-Binding Proteins/genetics Enhancer Elements (Genetics)/*genetics/physiology Gene Expression Regulation/*genetics Molecular Sequence Data Promoter Regions (Genetics)/genetics RNA, Non-U.S. Gov't TATA Box/genetics Xenopus laevis/*genetics, Small Nuclear/genetics RNA, Transfer, Unité ARN
@article{,
title = {Optimal tRNA((Ser)Sec) gene activity requires an upstream SPH motif},
author = {E Myslinski and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1311068},
isbn = {1311068},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {2},
pages = {203-209},
abstract = {The X. laevis tRNA((Ser)Sec) gene is different from the other tRNA genes in that its promoter contains two external elements, a PSE and a TATA box functionally equivalent to those of the U6 snRNA gene. Of the two internal promoters governing classical tRNA gene transcription, only subsists the internal B box. In this report, we show that the tRNA((Ser)Sec) contains in addition an activator element (AE) which we have mapped by extensive mutagenesis. Activation is only dependent on a 15 bp fragment residing between -209 and -195 and containing an SPH motif. In vitro, this element forms a complex with a nuclear protein which is different from the TEF-1 transcriptional activator that binds the SV40 Sph motifs. This AE is versatile since it shows capacity of activating a variety of genes in vivo, including U1 and U6 snRNAs and HSV thymidine kinase. Unexpectedly for an snRNA-related gene, the tRNA((Ser)Sec) is deprived of octamer or octamer-like motifs. The X.laevis tRNA((Ser)Sec) gene represents the first example of a Pol III snRNA-type gene whose activation of transcription is completely octamer-independent.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/*genetics Recombinant Fusion Proteins/genetics/metabolism Simian virus 40/*genetics Support, Animals Base Sequence DNA Mutational Analysis DNA-Binding Proteins/genetics Enhancer Elements (Genetics)/*genetics/physiology Gene Expression Regulation/*genetics Molecular Sequence Data Promoter Regions (Genetics)/genetics RNA, Non-U.S. Gov't TATA Box/genetics Xenopus laevis/*genetics, Small Nuclear/genetics RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The X. laevis tRNA((Ser)Sec) gene is different from the other tRNA genes in that its promoter contains two external elements, a PSE and a TATA box functionally equivalent to those of the U6 snRNA gene. Of the two internal promoters governing classical tRNA gene transcription, only subsists the internal B box. In this report, we show that the tRNA((Ser)Sec) contains in addition an activator element (AE) which we have mapped by extensive mutagenesis. Activation is only dependent on a 15 bp fragment residing between -209 and -195 and containing an SPH motif. In vitro, this element forms a complex with a nuclear protein which is different from the TEF-1 transcriptional activator that binds the SV40 Sph motifs. This AE is versatile since it shows capacity of activating a variety of genes in vivo, including U1 and U6 snRNAs and HSV thymidine kinase. Unexpectedly for an snRNA-related gene, the tRNA((Ser)Sec) is deprived of octamer or octamer-like motifs. The X.laevis tRNA((Ser)Sec) gene represents the first example of a Pol III snRNA-type gene whose activation of transcription is completely octamer-independent.
Murgo S, Krol A, Carbon P
In: Eur J Biochem, vol. 203, no. 3, pp. 443-447, 1992, ISBN: 1735429, (0014-2956 Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
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.
Michel F, Jaeger L, Westhof E, Kuras R, Tihy F, Xu M Q, Shub D A
Activation of the catalytic core of a group I intron by a remote 3' splice junction Journal Article
In: Genes Dev, vol. 6, no. 8, pp. 1373-1385, 1992, ISBN: 1644285, (0890-9369 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence DNA Mutational Analysis Escherichia coli/genetics Genes, Catalytic/genetics/*metabolism RNA, Messenger/genetics/*metabolism Support, P.H.S. T-Phages/genetics, U.S. Gov't, Unité ARN, Viral/*genetics Introns/genetics/*physiology Magnesium/metabolism Molecular Sequence Data Mutation/genetics Nucleic Acid Conformation Plasmids/genetics RNA Splicing/*genetics RNA
@article{,
title = {Activation of the catalytic core of a group I intron by a remote 3' splice junction},
author = {F Michel and L Jaeger and E Westhof and R Kuras and F Tihy and M Q Xu and D A Shub},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1644285},
isbn = {1644285},
year = {1992},
date = {1992-01-01},
journal = {Genes Dev},
volume = {6},
number = {8},
pages = {1373-1385},
abstract = {Over 1000 nucleotides may separate the ribozyme core of some group I introns from their 3' splice junctions. Using the sunY intron of bacteriophage T4 as a model system, we have investigated the mechanisms by which proximal splicing events are suppressed in vitro, as well as in vivo. Exon ligation as well as cleavage at the 5' splice site are shown to require long-range pairing between one of the peripheral components of the ribozyme core and some of the nucleotides preceding the authentic 3' splice junction. Consistent with our three-dimensional modeling of the entire sunY ribozyme, we propose that this novel interaction is necessary to drive 5' exon-core transcripts into an active conformation. A requirement for additional stabilizing interactions, either RNA-based or mediated by proteins, appears to be a general feature of group I self-splicing. A role for these interactions in mediating putative alternative splicing events is discussed.},
note = {0890-9369
Journal Article},
keywords = {Base Sequence DNA Mutational Analysis Escherichia coli/genetics Genes, Catalytic/genetics/*metabolism RNA, Messenger/genetics/*metabolism Support, P.H.S. T-Phages/genetics, U.S. Gov't, Unité ARN, Viral/*genetics Introns/genetics/*physiology Magnesium/metabolism Molecular Sequence Data Mutation/genetics Nucleic Acid Conformation Plasmids/genetics RNA Splicing/*genetics RNA},
pubstate = {published},
tppubtype = {article}
}
Over 1000 nucleotides may separate the ribozyme core of some group I introns from their 3' splice junctions. Using the sunY intron of bacteriophage T4 as a model system, we have investigated the mechanisms by which proximal splicing events are suppressed in vitro, as well as in vivo. Exon ligation as well as cleavage at the 5' splice site are shown to require long-range pairing between one of the peripheral components of the ribozyme core and some of the nucleotides preceding the authentic 3' splice junction. Consistent with our three-dimensional modeling of the entire sunY ribozyme, we propose that this novel interaction is necessary to drive 5' exon-core transcripts into an active conformation. A requirement for additional stabilizing interactions, either RNA-based or mediated by proteins, appears to be a general feature of group I self-splicing. A role for these interactions in mediating putative alternative splicing events is discussed.
Meng Q C, King S J, Branham K E, DeLucas L J, Lorber B, Oparil S
Preparative isolation of angiotensin-converting enzyme from human lung. Journal Article
In: J Chromatogr, vol. 579, no. 1, pp. 63-71, 1992.
Abstract | Links | BibTeX | Tags: Unité ARN
@article{,
title = {Preparative isolation of angiotensin-converting enzyme from human lung.},
author = {Q C Meng and S J King and K E Branham and L J DeLucas and B Lorber and S Oparil},
url = {http://www.ncbi.nlm.nih.gov/pubmed/1332983},
year = {1992},
date = {1992-01-01},
journal = {J Chromatogr},
volume = {579},
number = {1},
pages = {63-71},
abstract = {Angiotensin-converting enzyme from human lung was purified to apparent homogeneity using a five-step purification procedure consisting of ammonium sulfate precipitation, ion-exchange chromatography on DEAE Sephadex A-50, gel permeation on Sephadex G-200, chromatofocusing on a polybuffer exchange (PBE 94) column and high-performance liquid chromatographic gel permeation on a Bio-Sil TSK-250 column. This procedure gave an approximately 700-fold purification with a 20% yield compared to a 550-fold purification and a 1% yield with an affinity chromatography-based procedure. The 20-fold greater yield of the five-step procedure offers a major advantage for preparative use in the structural characterization of angiotensin-converting enzyme.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Angiotensin-converting enzyme from human lung was purified to apparent homogeneity using a five-step purification procedure consisting of ammonium sulfate precipitation, ion-exchange chromatography on DEAE Sephadex A-50, gel permeation on Sephadex G-200, chromatofocusing on a polybuffer exchange (PBE 94) column and high-performance liquid chromatographic gel permeation on a Bio-Sil TSK-250 column. This procedure gave an approximately 700-fold purification with a 20% yield compared to a 550-fold purification and a 1% yield with an affinity chromatography-based procedure. The 20-fold greater yield of the five-step procedure offers a major advantage for preparative use in the structural characterization of angiotensin-converting enzyme.
Lorber B, Giege R
Preparation and handling of biological macromolecules for crystallization. Book Chapter
In: Ducruix, A; Giegé, R (Ed.): Crystallization of Nucleic Acids and Proteins: A Practical Approach, pp. 19-45, Oxford University Press, USA, 1992.
Links | BibTeX | Tags: Unité ARN
@inbook{,
title = {Preparation and handling of biological macromolecules for crystallization.},
author = {B Lorber and R Giege},
editor = {A Ducruix and R Giegé},
url = {http://www.worldcat.org/title/crystallization-of-nucleic-acids-and-proteins-a-practical-approach/oclc/24009434},
year = {1992},
date = {1992-01-01},
booktitle = {Crystallization of Nucleic Acids and Proteins: A Practical Approach},
pages = {19-45},
publisher = {Oxford University Press, USA},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Lorber B, Giege R
A versatile reactor for temperature controlled crystallization of biological macromolecules. Journal Article
In: J Crystal Growth, vol. 122, no. 1-4, pp. 168-175, 1992, ISBN: 10.1016/0022-0248(92)90240-J.
Abstract | Links | BibTeX | Tags: FRUGIER, Unité ARN
@article{,
title = {A versatile reactor for temperature controlled crystallization of biological macromolecules.},
author = {B Lorber and R Giege},
url = {http://www.sciencedirect.com/science/article/pii/002202489290240J},
isbn = {10.1016/0022-0248(92)90240-J},
year = {1992},
date = {1992-01-01},
journal = {J Crystal Growth},
volume = {122},
number = {1-4},
pages = {168-175},
abstract = {Accurate control of crystallization conditions, and accordingly reproducibility of experiments, is often hampered by the lack of adequate instrumentation in the laboratory. A versatile and inexpensive crystallization reactor allowing crystal growth by vapor phase equilibration (sitting, hanging or sandwiched drops) or by the batch technique is described here. In this reactor, temperature is controlled accurately by a Peltier device and the crystallization process monitored by a time-lapse video recorder. An application for evaluating the growth kinetics of tetragonal lysozyme crystals as a function of temperature is given. It was observed that the apparent growth rate decreased when temperature was lowered, although under such conditions supersaturation was increased and crystals appeared sooner.},
keywords = {FRUGIER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Accurate control of crystallization conditions, and accordingly reproducibility of experiments, is often hampered by the lack of adequate instrumentation in the laboratory. A versatile and inexpensive crystallization reactor allowing crystal growth by vapor phase equilibration (sitting, hanging or sandwiched drops) or by the batch technique is described here. In this reactor, temperature is controlled accurately by a Peltier device and the crystallization process monitored by a time-lapse video recorder. An application for evaluating the growth kinetics of tetragonal lysozyme crystals as a function of temperature is given. It was observed that the apparent growth rate decreased when temperature was lowered, although under such conditions supersaturation was increased and crystals appeared sooner.
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 Journal Article
In: J Mol Biol, vol. 228, no. 2, pp. 387-394, 1992, ISBN: 1453450, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
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.
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}
}
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.
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}
}
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.
Heitzler J, Marechal-Drouard L, Dirheimer G, Keith G
Use of a dot blot hybridization method for identification of pure tRNA species on different membranes Journal Article
In: Biochim Biophys Acta-Gene Regul Mech, vol. 1129, no. 3, pp. 273-277, 1992, ISBN: 1536878, (0006-3002 Journal Article).
Abstract | Links | BibTeX | Tags: Artificial Nucleic Acid Hybridization RNA, Autoradiography *Membranes, Fungal/genetics RNA, Met/genetics Saccharomyces cerevisiae/genetics Support, Non-U.S. Gov't, Transfer, Transfer/*genetics RNA, Unité ARN
@article{,
title = {Use of a dot blot hybridization method for identification of pure tRNA species on different membranes},
author = {J Heitzler and L Marechal-Drouard and G Dirheimer and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1536878},
isbn = {1536878},
year = {1992},
date = {1992-01-01},
journal = {Biochim Biophys Acta-Gene Regul Mech},
volume = {1129},
number = {3},
pages = {273-277},
abstract = {The characterization of a tRNA in purification procedures usually involves aminoacylation assays but recently, the hybridization by dot blot with specific oligonucleotides as probes has been used for the tRNA identification. We present here an optimization of a dot blot hybridization method for the tRNA detection by comparing the efficiency of eight different nylon membranes. Neutral 0.22 microns porosity membranes (Nytran, Biodine A) give the best detection efficiency when small quantities of material (less than 40 ng of tRNA) are dotted on filter; by contrast, neutral 0.45 microns porosity membranes (such as Hybond N) are the most efficient when larger quantities of tRNA are dotted on the filter. The described technique allows to detect less than 20 pg of a pure tRNA species. Its use in the identification of Saccharomyces cerevisiae initiator tRNA(Met) in counter-current distribution fractions is shown.},
note = {0006-3002
Journal Article},
keywords = {Artificial Nucleic Acid Hybridization RNA, Autoradiography *Membranes, Fungal/genetics RNA, Met/genetics Saccharomyces cerevisiae/genetics Support, Non-U.S. Gov't, Transfer, Transfer/*genetics RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The characterization of a tRNA in purification procedures usually involves aminoacylation assays but recently, the hybridization by dot blot with specific oligonucleotides as probes has been used for the tRNA identification. We present here an optimization of a dot blot hybridization method for the tRNA detection by comparing the efficiency of eight different nylon membranes. Neutral 0.22 microns porosity membranes (Nytran, Biodine A) give the best detection efficiency when small quantities of material (less than 40 ng of tRNA) are dotted on filter; by contrast, neutral 0.45 microns porosity membranes (such as Hybond N) are the most efficient when larger quantities of tRNA are dotted on the filter. The described technique allows to detect less than 20 pg of a pure tRNA species. Its use in the identification of Saccharomyces cerevisiae initiator tRNA(Met) in counter-current distribution fractions is shown.
Graffe M, Dondon J, Caillet J, Romby P, Ehresmann C, Ehresmann B, Springer M
The specificity of translational control switched with transfer RNA identity rules Journal Article
In: Science, vol. 255, no. 5047, pp. 994-996, 1992, ISBN: 1372129, (0036-8075 Journal Article).
Abstract | Links | BibTeX | Tags: Bacterial Genes, Bacterial Molecular Sequence Data Nucleic Acid Conformation RNA, Bacterial Proteins/metabolism Base Sequence DNA Mutational Analysis *Gene Expression Regulation, Bacterial/metabolism RNA, Genetic, Messenger/*metabolism/ultrastructure RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics/metabolism *Translation, ROMBY, Structural, Thr/*metabolism Support, Transfer, Unité ARN
@article{,
title = {The specificity of translational control switched with transfer RNA identity rules},
author = {M Graffe and J Dondon and J Caillet and P Romby and C Ehresmann and B Ehresmann and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1372129},
isbn = {1372129},
year = {1992},
date = {1992-01-01},
journal = {Science},
volume = {255},
number = {5047},
pages = {994-996},
abstract = {The interaction of Escherichia coli threonyl-transfer RNA (tRNA) synthetase with the leader sequence of its own messenger RNA inhibits ribosome binding, resulting in negative translational feedback regulation. The leader sequence resembles the substrate (tRNA(Thr)) of the enzyme, and the nucleotides that mediate the correct recognition of the leader and the tRNA may be the same. A mutation suggested by tRNA identity rules that switches the resemblance of the leader sequence from tRNA(Thr) to tRNA(Met) causes the translation of the threonyl-tRNA synthetase messenger RNA to become regulated by methionyl-tRNA synthetase. This identity swap in the leader messenger RNA indicates that tRNA identity rules may be extended to interactions of synthetases with other RNAs.},
note = {0036-8075
Journal Article},
keywords = {Bacterial Genes, Bacterial Molecular Sequence Data Nucleic Acid Conformation RNA, Bacterial Proteins/metabolism Base Sequence DNA Mutational Analysis *Gene Expression Regulation, Bacterial/metabolism RNA, Genetic, Messenger/*metabolism/ultrastructure RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics/metabolism *Translation, ROMBY, Structural, Thr/*metabolism Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The interaction of Escherichia coli threonyl-transfer RNA (tRNA) synthetase with the leader sequence of its own messenger RNA inhibits ribosome binding, resulting in negative translational feedback regulation. The leader sequence resembles the substrate (tRNA(Thr)) of the enzyme, and the nucleotides that mediate the correct recognition of the leader and the tRNA may be the same. A mutation suggested by tRNA identity rules that switches the resemblance of the leader sequence from tRNA(Thr) to tRNA(Met) causes the translation of the threonyl-tRNA synthetase messenger RNA to become regulated by methionyl-tRNA synthetase. This identity swap in the leader messenger RNA indicates that tRNA identity rules may be extended to interactions of synthetases with other RNAs.
Glasser A L, el Adlouni C, Keith G, Sochacka E, Malkiewicz A, Santos M, Tuite M F, Desgres J
In: FEBS Lett, vol. 314, no. 3, pp. 381-385, 1992, ISBN: 1468572, (0014-5793 Journal Article).
Abstract | Links | BibTeX | Tags: *Anticodon Chromatography, Fungal/genetics RNA, High Pressure Liquid Fungal Proteins/biosynthesis Molecular Structure RNA, Leu/*genetics Saccharomyces cerevisiae/*genetics Spectrophotometry, Mass Support, Non-U.S. Gov't Uridine/*analogs & derivatives/analysis/chemistry/genetics, Transfer, Ultraviolet Spectrum Analysis, Unité ARN
@article{,
title = {Presence and coding properties of 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um) in the wobble position of the anticodon of tRNA(Leu) (U*AA) from brewer's yeast},
author = {A L Glasser and C el Adlouni and G Keith and E Sochacka and A Malkiewicz and M Santos and M F Tuite and J Desgres},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1468572},
isbn = {1468572},
year = {1992},
date = {1992-01-01},
journal = {FEBS Lett},
volume = {314},
number = {3},
pages = {381-385},
abstract = {The unknown modified nucleoside U* has been isolated by enzymatic and HPLC protocols from tRNA(Leu) (U*AA) recently discovered in brewer's yeast. The pure U* nucleoside has been characterized by electron impact mass spectroscopy, and comparison of its chromatographic and UV-absorption properties with those of appropriate synthetic compounds. The structure of U* was established as 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um). The yeast tRNA(Leu) (U*AA) is the only tRNA so far sequenced which has been shown to contain ncm5Um. The location of such a modified uridine at the first position of the anticodon restricts the decoding property to A of the leucine UUA codon.},
note = {0014-5793
Journal Article},
keywords = {*Anticodon Chromatography, Fungal/genetics RNA, High Pressure Liquid Fungal Proteins/biosynthesis Molecular Structure RNA, Leu/*genetics Saccharomyces cerevisiae/*genetics Spectrophotometry, Mass Support, Non-U.S. Gov't Uridine/*analogs & derivatives/analysis/chemistry/genetics, Transfer, Ultraviolet Spectrum Analysis, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The unknown modified nucleoside U* has been isolated by enzymatic and HPLC protocols from tRNA(Leu) (U*AA) recently discovered in brewer's yeast. The pure U* nucleoside has been characterized by electron impact mass spectroscopy, and comparison of its chromatographic and UV-absorption properties with those of appropriate synthetic compounds. The structure of U* was established as 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um). The yeast tRNA(Leu) (U*AA) is the only tRNA so far sequenced which has been shown to contain ncm5Um. The location of such a modified uridine at the first position of the anticodon restricts the decoding property to A of the leucine UUA codon.
Garcia A, Giege R
Footprinting evidence for close contacts of the yeast tRNA(Asp) anticodon region with aspartyl-tRNA synthetase Journal Article
In: Biochem Biophys Res Commun, vol. 186, no. 2, pp. 956-962, 1992, ISBN: 1497679, (0006-291x Journal Article).
Abstract | Links | BibTeX | Tags: Alkylation Anticodon/*metabolism Aspartate-tRNA Ligase/*metabolism Base Sequence Molecular Sequence Data Nucleic Acid Conformation Protein Binding RNA, Asp/genetics/isolation & purification/*metabolism Saccharomyces cerevisiae/enzymology/*genetics Sulfuric Acid Esters/metabolism/pharmacology Support, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Footprinting evidence for close contacts of the yeast tRNA(Asp) anticodon region with aspartyl-tRNA synthetase},
author = {A Garcia and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1497679},
isbn = {1497679},
year = {1992},
date = {1992-01-01},
journal = {Biochem Biophys Res Commun},
volume = {186},
number = {2},
pages = {956-962},
abstract = {Chemical footprinting experiments on brewer's yeast tRNA(Asp) complexed to its cognate aspartyl-tRNA synthetase are reported: they demonstrate that bases of the anticodon loop, including the anticodon itself, are in close proximity with the synthetase. Contacts were determined using dimethylsulfate as the probe for testing reactivity of guanine and cytosine residues in free and complexed tRNA. Results correlate with the decrease in aspartylation activity of yeast tRNA(Asp) molecules mutated at these contact positions and will be compared with other structural data arising from solution and crystallographic studies on the aspartic acid complex.},
note = {0006-291x
Journal Article},
keywords = {Alkylation Anticodon/*metabolism Aspartate-tRNA Ligase/*metabolism Base Sequence Molecular Sequence Data Nucleic Acid Conformation Protein Binding RNA, Asp/genetics/isolation & purification/*metabolism Saccharomyces cerevisiae/enzymology/*genetics Sulfuric Acid Esters/metabolism/pharmacology Support, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Chemical footprinting experiments on brewer's yeast tRNA(Asp) complexed to its cognate aspartyl-tRNA synthetase are reported: they demonstrate that bases of the anticodon loop, including the anticodon itself, are in close proximity with the synthetase. Contacts were determined using dimethylsulfate as the probe for testing reactivity of guanine and cytosine residues in free and complexed tRNA. Results correlate with the decrease in aspartylation activity of yeast tRNA(Asp) molecules mutated at these contact positions and will be compared with other structural data arising from solution and crystallographic studies on the aspartic acid complex.
Frugier M, Florentz C, Giege R
Anticodon-independent aminoacylation of an RNA minihelix with valine Journal Article
In: Proc Natl Acad Sci U S A, vol. 89, no. 9, pp. 3990-3994, 1992, ISBN: 1570324, (0027-8424 Journal Article).
Abstract | Links | BibTeX | Tags: *Amino Acid Activation Anticodon Base Sequence Hydrogen Bonding In Vitro Molecular Sequence Data RNA, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Valine-tRNA Ligase/*metabolism, Transfer, Unité ARN, Val/chemistry/*metabolism Saccharomyces cerevisiae Structure-Activity Relationship Support
@article{,
title = {Anticodon-independent aminoacylation of an RNA minihelix with valine},
author = {M Frugier and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1570324},
isbn = {1570324},
year = {1992},
date = {1992-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {89},
number = {9},
pages = {3990-3994},
abstract = {Minihelices mimicking the amino acid acceptor and anticodon branches of yeast tRNA(Val) have been synthesized by in vitro transcription of synthetic templates. It is shown that a minihelix corresponding to the amino acid acceptor branch and containing solely a valine-specific identity nucleotide can be aminoacylated by yeast valyl-tRNA synthetase. Its charging ability is lost after mutating this nucleotide. This ability is stimulated somewhat by the addition of a second hairpin helix that mimicks the anticodon arm, which suggests that information originating from the anticodon stem-loop can be transmitted to the active site of the enzyme by the core of the protein.},
note = {0027-8424
Journal Article},
keywords = {*Amino Acid Activation Anticodon Base Sequence Hydrogen Bonding In Vitro Molecular Sequence Data RNA, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Valine-tRNA Ligase/*metabolism, Transfer, Unité ARN, Val/chemistry/*metabolism Saccharomyces cerevisiae Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
Minihelices mimicking the amino acid acceptor and anticodon branches of yeast tRNA(Val) have been synthesized by in vitro transcription of synthetic templates. It is shown that a minihelix corresponding to the amino acid acceptor branch and containing solely a valine-specific identity nucleotide can be aminoacylated by yeast valyl-tRNA synthetase. Its charging ability is lost after mutating this nucleotide. This ability is stimulated somewhat by the addition of a second hairpin helix that mimicks the anticodon arm, which suggests that information originating from the anticodon stem-loop can be transmitted to the active site of the enzyme by the core of the protein.
Eiler S, Boeglin M, Martin F, Eriani G, Gangloff J, Thierry J C, Moras D
Crystallization of aspartyl-tRNA synthetase-tRNA(Asp) complex from Escherichia coli and first crystallographic results Journal Article
In: J Mol Biol, vol. 224, no. 4, pp. 1171-1173, 1992, ISBN: 1569573, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Asp/*ultrastructure X-Ray Diffraction, Aspartate-tRNA Ligase/*ultrastructure Crystallography Escherichia coli/enzymology RNA, ERIANI, Transfer, Unité ARN
@article{,
title = {Crystallization of aspartyl-tRNA synthetase-tRNA(Asp) complex from Escherichia coli and first crystallographic results},
author = {S Eiler and M Boeglin and F Martin and G Eriani and J Gangloff and J C Thierry and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1569573},
isbn = {1569573},
year = {1992},
date = {1992-01-01},
journal = {J Mol Biol},
volume = {224},
number = {4},
pages = {1171-1173},
abstract = {Crystals of the dimeric aspartyl-tRNA synthetase from Escherichia coli (molecular mass 132,000 Da) complexed with its cognate tRNA (molecular mass 25,000 Da) have been grown using ammonium sulfate as precipitant. The crystals belong to the orthorhombic space group C222(1) with unit cell parameters a = 102.75 A},
note = {0022-2836
Journal Article},
keywords = {Asp/*ultrastructure X-Ray Diffraction, Aspartate-tRNA Ligase/*ultrastructure Crystallography Escherichia coli/enzymology RNA, ERIANI, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Crystals of the dimeric aspartyl-tRNA synthetase from Escherichia coli (molecular mass 132,000 Da) complexed with its cognate tRNA (molecular mass 25,000 Da) have been grown using ammonium sulfate as precipitant. The crystals belong to the orthorhombic space group C222(1) with unit cell parameters a = 102.75 A
Ducruix A, Giege R (Ed.)
Crystallization of Nucleic Acids and Proteins: A Practical Approach Series (1nd edition). Book
Oxford University Press, USA, 1992, ISSN: ISSN.
Links | BibTeX | Tags: Unité ARN
@book{,
title = {Crystallization of Nucleic Acids and Proteins: A Practical Approach Series (1nd edition).},
editor = {A Ducruix and R Giege},
url = {http://www.worldcat.org/title/crystallization-of-nucleic-acids-and-proteins-a-practical-approach/oclc/24009434},
issn = {ISSN},
year = {1992},
date = {1992-01-01},
publisher = {Oxford University Press},
address = {USA},
series = {The practical approach series},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {book}
}
Dreher T W, Tsai C H, Florentz C, Giege R
Specific valylation of turnip yellow mosaic virus RNA by wheat germ valyl-tRNA synthetase determined by three anticodon loop nucleotides Journal Article
In: Biochemistry, vol. 31, no. 38, pp. 9183-9189, 1992, ISBN: 1390705, (0006-2960 Journal Article).
Abstract | Links | BibTeX | Tags: Anticodon/genetics/*metabolism Bacteriophage T7/enzymology Base Sequence DNA-Directed RNA Polymerases/metabolism Kinetics Molecular Sequence Data Mosaic Viruses/genetics/*metabolism Nucleic Acid Conformation RNA, FLORENTZ, Genetic Triticum/*enzymology Valine-tRNA Ligase/*metabolism Variation (Genetics), Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. Transcription, Transfer/chemistry/metabolism RNA, U.S. Gov't, Unité ARN, Viral/chemistry/genetics/*metabolism Seeds/enzymology Support
@article{,
title = {Specific valylation of turnip yellow mosaic virus RNA by wheat germ valyl-tRNA synthetase determined by three anticodon loop nucleotides},
author = {T W Dreher and C H Tsai and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1390705},
isbn = {1390705},
year = {1992},
date = {1992-01-01},
journal = {Biochemistry},
volume = {31},
number = {38},
pages = {9183-9189},
abstract = {The valylation by wheat germ valyl-tRNA synthetase of anticodon loop mutants of turnip yellow mosaic virus RNA has been studied. RNA substrates 264 nucleotides long were made by T7 RNA polymerase from cDNA encompassing the 3' tRNA-like region of genomic RNA. Substitution singly, or in combination, of three nucleotides in the anticodon loop resulted in very poor valylation (Vmax/KM less than 10(-3) relative to wild type). These nucleotides thus represent the major valine identity determinants recognized by wheat germ valyl-tRNA synthetase; their relative contribution to valine identity, in descending order, was as follows: the middle nucleotide of the anticodon (A56 in TYMV RNA), the 3' anticodon nucleotide (C55), and the 3'-most anticodon loop nucleotide (C53). Substitutions in the wobble position (C57) had no significant effect on valylation kinetics, while substitutions of the discriminator base (A4) resulted in small decreases in Vmax/Km. Mutations in the major identity nucleotides resulted in large increases in KM, suggesting that wheat germ valyl-tRNA synthetase has a lowered affinity for variant substrates with low valine identity. Comparison with other studies using valyl-tRNA synthetases from Escherichia coli and yeast indicates that the anticodon has been phylogenetically conserved as the dominant valine identity region, while the identity contribution of the discriminator base has been less conserved. The mechanism by which anticodon mutations are discriminated also appears to vary, being affinity-based for the wheat germ enzyme, and kinetically-based for the yeast enzyme [Florentz et al. (1991) Eur. J. Biochem. 195, 229-234].},
note = {0006-2960
Journal Article},
keywords = {Anticodon/genetics/*metabolism Bacteriophage T7/enzymology Base Sequence DNA-Directed RNA Polymerases/metabolism Kinetics Molecular Sequence Data Mosaic Viruses/genetics/*metabolism Nucleic Acid Conformation RNA, FLORENTZ, Genetic Triticum/*enzymology Valine-tRNA Ligase/*metabolism Variation (Genetics), Non-P.H.S. Support, Non-U.S. Gov't Support, P.H.S. Transcription, Transfer/chemistry/metabolism RNA, U.S. Gov't, Unité ARN, Viral/chemistry/genetics/*metabolism Seeds/enzymology Support},
pubstate = {published},
tppubtype = {article}
}
The valylation by wheat germ valyl-tRNA synthetase of anticodon loop mutants of turnip yellow mosaic virus RNA has been studied. RNA substrates 264 nucleotides long were made by T7 RNA polymerase from cDNA encompassing the 3' tRNA-like region of genomic RNA. Substitution singly, or in combination, of three nucleotides in the anticodon loop resulted in very poor valylation (Vmax/KM less than 10(-3) relative to wild type). These nucleotides thus represent the major valine identity determinants recognized by wheat germ valyl-tRNA synthetase; their relative contribution to valine identity, in descending order, was as follows: the middle nucleotide of the anticodon (A56 in TYMV RNA), the 3' anticodon nucleotide (C55), and the 3'-most anticodon loop nucleotide (C53). Substitutions in the wobble position (C57) had no significant effect on valylation kinetics, while substitutions of the discriminator base (A4) resulted in small decreases in Vmax/Km. Mutations in the major identity nucleotides resulted in large increases in KM, suggesting that wheat germ valyl-tRNA synthetase has a lowered affinity for variant substrates with low valine identity. Comparison with other studies using valyl-tRNA synthetases from Escherichia coli and yeast indicates that the anticodon has been phylogenetically conserved as the dominant valine identity region, while the identity contribution of the discriminator base has been less conserved. The mechanism by which anticodon mutations are discriminated also appears to vary, being affinity-based for the wheat germ enzyme, and kinetically-based for the yeast enzyme [Florentz et al. (1991) Eur. J. Biochem. 195, 229-234].
Despons L, Senger B, Fasiolo F, Walter P
Binding of the yeast tRNA(Met) anticodon by the cognate methionyl-tRNA synthetase involves at least two independent peptide regions Journal Article
In: J Mol Biol, vol. 225, no. 3, pp. 897-907, 1992, ISBN: 1602489, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Sequence Anticodon/*metabolism Binding Sites Kinetics Methionine-tRNA Ligase/*metabolism Models, Met/*metabolism Saccharomyces cerevisiae/enzymology Structure-Activity Relationship Support, Molecular Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Site-Directed Protein Conformation RNA, Transfer, Unité ARN
@article{,
title = {Binding of the yeast tRNA(Met) anticodon by the cognate methionyl-tRNA synthetase involves at least two independent peptide regions},
author = {L Despons and B Senger and F Fasiolo and P Walter},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1602489},
isbn = {1602489},
year = {1992},
date = {1992-01-01},
journal = {J Mol Biol},
volume = {225},
number = {3},
pages = {897-907},
abstract = {As for Escherichia coli methionine tRNAs, the anticodon triplet of yeast tRNA(Met) plays an important role in the recognition by the yeast methionyl-tRNA synthetase (MetRS), indicating that this determinant for methionine identity is conserved in yeast. Efficient aminoacylation of the E. coli tRNA(Met) transcript by the heterologous yeast methionine enzyme also suggests conservation of the protein determinants that interact with the CAU anticodon sequence. We have analysed by site-directed mutagenesis the peptide region 655 to 663 of the yeast MetRS that is equivalent to the anticodon binding region of the E. coli methionine enzyme. Only one change, converting Leu658 into Ala significantly reduced tRNA aminoacylation. Semi-conservative substitutions of L658 allow a correlation to be drawn between side-chain volume of the hydrophobic residue at this site and activity. The analysis of the L658A mutant shows that Km is mainly affected. This suggests that the peptide region 655 to 663 contributes partially to the binding of the anticodon, since separate mutational analysis of the anticodon bases shows that kcat is the most critical parameter in the recognition of tRNA(Met) by the yeast synthetase. We have analysed the role of peptide region (583-GNLVNR-588) that is spatially close to the region 655 to 663. Replacements of residues N584 and R588 reduces significantly the kcat of aminoacylation. The peptide region 583-GNLVNR-588 is highly conserved in all MetRS so far sequenced. We therefore propose that the hydrogen donor/acceptor amino acid residues within this region are the most critical protein determinants for the positive selection of the methionine tRNAs.},
note = {0022-2836
Journal Article},
keywords = {Amino Acid Sequence Anticodon/*metabolism Binding Sites Kinetics Methionine-tRNA Ligase/*metabolism Models, Met/*metabolism Saccharomyces cerevisiae/enzymology Structure-Activity Relationship Support, Molecular Molecular Sequence Data Mutagenesis, Non-U.S. Gov't, Site-Directed Protein Conformation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
As for Escherichia coli methionine tRNAs, the anticodon triplet of yeast tRNA(Met) plays an important role in the recognition by the yeast methionyl-tRNA synthetase (MetRS), indicating that this determinant for methionine identity is conserved in yeast. Efficient aminoacylation of the E. coli tRNA(Met) transcript by the heterologous yeast methionine enzyme also suggests conservation of the protein determinants that interact with the CAU anticodon sequence. We have analysed by site-directed mutagenesis the peptide region 655 to 663 of the yeast MetRS that is equivalent to the anticodon binding region of the E. coli methionine enzyme. Only one change, converting Leu658 into Ala significantly reduced tRNA aminoacylation. Semi-conservative substitutions of L658 allow a correlation to be drawn between side-chain volume of the hydrophobic residue at this site and activity. The analysis of the L658A mutant shows that Km is mainly affected. This suggests that the peptide region 655 to 663 contributes partially to the binding of the anticodon, since separate mutational analysis of the anticodon bases shows that kcat is the most critical parameter in the recognition of tRNA(Met) by the yeast synthetase. We have analysed the role of peptide region (583-GNLVNR-588) that is spatially close to the region 655 to 663. Replacements of residues N584 and R588 reduces significantly the kcat of aminoacylation. The peptide region 583-GNLVNR-588 is highly conserved in all MetRS so far sequenced. We therefore propose that the hydrogen donor/acceptor amino acid residues within this region are the most critical protein determinants for the positive selection of the methionine tRNAs.
Brunel C, Caillet J, Lesage P, Graffe M, Dondon J, Moine H, Romby P, Ehresmann C, Ehresmann B, Grunberg-Manago M, Springer M
Domains of the Escherichia coli threonyl-tRNA synthetase translational operator and their relation to threonine tRNA isoacceptors Journal Article
In: J Mol Biol, vol. 227, no. 3, pp. 621-634, 1992, ISBN: 1383551, (0022-2836).
Abstract | Links | BibTeX | Tags: Bacterial/genetics Gene Expression Regulation, Bacterial/genetics RNA, Base Sequence Escherichia coli/genetics Gene Expression Regulation, Enzymologic/*genetics Molecular Sequence Data Mutagenesis, Genetic/*genetics, Messenger/*genetics/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics/metabolism Translation, ROMBY, Site-Directed/genetics Nucleic Acid Conformation RNA, Thr/*genetics/metabolism Recombinant Fusion Proteins/genetics Support, Transfer, Unité ARN
@article{,
title = {Domains of the Escherichia coli threonyl-tRNA synthetase translational operator and their relation to threonine tRNA isoacceptors},
author = {C Brunel and J Caillet and P Lesage and M Graffe and J Dondon and H Moine and P Romby and C Ehresmann and B Ehresmann and M Grunberg-Manago and M Springer},
url = {http://www.ncbi.nlm.nih.gov/pubmed/1383551},
doi = {10.1016/0022-2836(92)90212-3},
isbn = {1383551},
year = {1992},
date = {1992-01-01},
journal = {J Mol Biol},
volume = {227},
number = {3},
pages = {621-634},
abstract = {The expression of the gene for threonyl-tRNA synthetase (thrS) is negatively autoregulated at the translational level in Escherichia coli. The synthetase binds to a region of the thrS leader mRNA upstream from the ribosomal binding site inhibiting subsequent translation. The leader mRNA consists of four structural domains. The present work shows that mutations in these four domains affect expression and/or regulation in different ways. Domain 1, the 3' end of the leader, contains the ribosomal binding site, which appears not to be essential for synthetase binding. Mutations in this domain probably affect regulation by changing the competition between the ribosome and the synthetase for binding to the leader. Domain 2, 3' from the ribosomal binding site, is a stem and loop with structural similarities to the tRNA(Thr) anticodon arm. In tRNAs the anticodon loop is seven nucleotides long, mutations that increase or decrease the length of the anticodon-like loop of domain 2 from seven nucleotides abolish control. The nucleotides in the second and third positions of the anticodon-like sequence are essential for recognition and the nucleotide in the wobble position is not, again like tRNA(Thr). The effect of mutations in domain 3 indicate that it acts as an articulation between domains 2 and 4. Domain 4 is a stable arm that has similarities to the acceptor arm of tRNA(Thr) and is shown to be necessary for regulation. Based on this mutational analysis and previous footprinting experiments, it appears that domains 2 and 4, those analogous to tRNA(Thr), are involved in binding the synthetase which inhibits translation probably by interfering with ribosome loading at the nearby translation initiation site.},
note = {0022-2836},
keywords = {Bacterial/genetics Gene Expression Regulation, Bacterial/genetics RNA, Base Sequence Escherichia coli/genetics Gene Expression Regulation, Enzymologic/*genetics Molecular Sequence Data Mutagenesis, Genetic/*genetics, Messenger/*genetics/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/*genetics/metabolism Translation, ROMBY, Site-Directed/genetics Nucleic Acid Conformation RNA, Thr/*genetics/metabolism Recombinant Fusion Proteins/genetics Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The expression of the gene for threonyl-tRNA synthetase (thrS) is negatively autoregulated at the translational level in Escherichia coli. The synthetase binds to a region of the thrS leader mRNA upstream from the ribosomal binding site inhibiting subsequent translation. The leader mRNA consists of four structural domains. The present work shows that mutations in these four domains affect expression and/or regulation in different ways. Domain 1, the 3' end of the leader, contains the ribosomal binding site, which appears not to be essential for synthetase binding. Mutations in this domain probably affect regulation by changing the competition between the ribosome and the synthetase for binding to the leader. Domain 2, 3' from the ribosomal binding site, is a stem and loop with structural similarities to the tRNA(Thr) anticodon arm. In tRNAs the anticodon loop is seven nucleotides long, mutations that increase or decrease the length of the anticodon-like loop of domain 2 from seven nucleotides abolish control. The nucleotides in the second and third positions of the anticodon-like sequence are essential for recognition and the nucleotide in the wobble position is not, again like tRNA(Thr). The effect of mutations in domain 3 indicate that it acts as an articulation between domains 2 and 4. Domain 4 is a stable arm that has similarities to the acceptor arm of tRNA(Thr) and is shown to be necessary for regulation. Based on this mutational analysis and previous footprinting experiments, it appears that domains 2 and 4, those analogous to tRNA(Thr), are involved in binding the synthetase which inhibits translation probably by interfering with ribosome loading at the nearby translation initiation site.