Rudinger-Thirion J, Giege R
The peculiar architectural framework of tRNASec is fully recognized by yeast AspRS Article de journal
Dans: RNA, vol. 5, no. 4, p. 495-502, 1999, ISBN: 10199566, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*genetics RNA, Amino Acyl-tRNA Ligases/*genetics/metabolism Anticodon/genetics Aspartic Acid/genetics/metabolism Base Sequence Escherichia coli/genetics Fungi/*enzymology/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Asp/genetics Selenocysteine/genetics/metabolism Support, Bacterial/genetics RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {The peculiar architectural framework of tRNASec is fully recognized by yeast AspRS},
author = {J Rudinger-Thirion and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10199566},
isbn = {10199566},
year = {1999},
date = {1999-01-01},
journal = {RNA},
volume = {5},
number = {4},
pages = {495-502},
abstract = {The wild-type transcript of Escherichia coli tRNASec, characterized by a peculiar core architecture and a large variable region, was shown to be aspartylatable by yeast AspRS. Similar activities were found for tRNASec mutants with methionine, leucine, and tryptophan anticodons. The charging efficiency of these molecules was found comparable to that of a minihelix derived from tRNAAsp and is accounted for by the presence of the discriminator residue G73, which is a major aspartate identity determinant. Introducing the aspartate identity elements from the anticodon loop (G34, U35, C36, C38) into tRNASec transforms this molecule into an aspartate acceptor with kinetic properties identical to tRNAAsp. Expression of the aspartate identity set in tRNASec is independent of the size of its variable region. The functional study was completed by footprinting experiments with four different nucleases as structural probes. Protection patterns by AspRS of transplanted tRNASec and tRNAAsp were found similar. They are modified, particularly in the anticodon loop, upon changing the aspartate anticodon into that of methionine. Altogether, it appears that recognition of a tRNA by AspRS is more governed by the presence of the aspartate identity set than by the structural framework that carries this set.},
note = {1355-8382
Journal Article},
keywords = {Amino Acid-Specific/*genetics RNA, Amino Acyl-tRNA Ligases/*genetics/metabolism Anticodon/genetics Aspartic Acid/genetics/metabolism Base Sequence Escherichia coli/genetics Fungi/*enzymology/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Asp/genetics Selenocysteine/genetics/metabolism Support, Bacterial/genetics RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Philippe C, Eyermann F, Benard L, Portier C, Ehresmann B, Ehresmann C
Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 90, no. 10, p. 4394-4398, 1993, ISBN: 7685101, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial Molecular Sequence Data Nucleic Acid Conformation Operator Regions (Genetics) *Peptide Chain Initiation RNA, Bacterial/genetics RNA, Base Sequence Escherichia coli/*genetics *Gene Expression Regulation, Messenger/genetics RNA, Met/metabolism Ribosomal Proteins/*genetics Ribosomes/*metabolism Structure-Activity Relationship Support, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site},
author = {C Philippe and F Eyermann and L Benard and C Portier and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7685101},
isbn = {7685101},
year = {1993},
date = {1993-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {90},
number = {10},
pages = {4394-4398},
abstract = {From genetic and biochemical evidence, we previously proposed that S15 inhibits its own translation by binding to its mRNA in a region overlapping the ribosome loading site. This binding was postulated to stabilize a pseudoknot structure that exists in equilibrium with two stem-loops. Here, we use "toeprint" experiments with Moloney murine leukemia virus reverse transcriptase to analyze the effect of S15 on the formation of the ternary mRNA-30S-tRNA(fMet) complex. We show that the binding of the 30S subunit on the mRNA stops reverse transcriptase near position +10, corresponding to the 3' terminus of the pseudoknot, most likely by stabilizing the pseudoknot conformation. Furthermore, S15 is found to stabilize the binary 30S-mRNA complex. When the ternary 30S-mRNA-tRNA(fMet) complex is formed, a toeprint is observed at position +17. This toeprint progressively disappears when the ternary complex is formed in the presence of increasing concentrations of S15, while a shift from position +17 to position +10 is observed. Beside, RNase T1 footprinting experiments reveal the simultaneous binding of S15 and 30S subunit on the mRNA. Otherwise, we show by filter binding assays that initiator tRNA remains bound to the 30S subunit even in the presence of S15. Our results indicate that S15 prevents the formation of a functional ternary 30S-mRNA-tRNA(fMet) complex, the ribosome being trapped in a preternary 30S-mRNA-tRNA(fMet) complex.},
note = {0027-8424
Journal Article},
keywords = {Bacterial Molecular Sequence Data Nucleic Acid Conformation Operator Regions (Genetics) *Peptide Chain Initiation RNA, Bacterial/genetics RNA, Base Sequence Escherichia coli/*genetics *Gene Expression Regulation, Messenger/genetics RNA, Met/metabolism Ribosomal Proteins/*genetics Ribosomes/*metabolism Structure-Activity Relationship Support, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Muller G, Gaspin C, Etienne A, Westhof E
Automatic display of RNA secondary structures Article de journal
Dans: Comput Appl Biosci, vol. 9, no. 5, p. 551-561, 1993, ISBN: 7507400, (0266-7061 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/genetics RNA, 5S/chemistry/genetics Ribonuclease P *Software, Algorithms Bacillus subtilis/chemistry/genetics Base Sequence *Computer Graphics Endoribonucleases/genetics Escherichia coli/chemistry/genetics Molecular Sequence Data Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Bacterial/genetics RNA, Catalytic/genetics RNA, Ribosomal, Unité ARN
@article{,
title = {Automatic display of RNA secondary structures},
author = {G Muller and C Gaspin and A Etienne and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7507400},
isbn = {7507400},
year = {1993},
date = {1993-01-01},
journal = {Comput Appl Biosci},
volume = {9},
number = {5},
pages = {551-561},
abstract = {A set of programs written in C language with the GL library and under UNIX has been developed for generating compact, pleasant and non-overlapping displays of secondary structures of ribonucleic acids. The first program, rnasearch, implements a new search procedure that dynamically rearranges overlapping portions of the two-dimensional drawing while preserving clear and readable displays of the two-dimensional structure. The algorithm is fast (the execution time for the command rnasearch is 38.6 s for the 16S rRNA of Escherichia coli with 1542 bases), accepts outputs from two-dimensional prediction programs and therefore allows for rapid comparison between the various two-dimensional folds generated. A second program, rnadisplay, allows the graphical display of the computed two-dimensional structures on a graphics workstation. Otherwise, it is possible to obtain a paper output of the two-dimensional structure by using the program print2D which builds a Postscript file. Moreover the two-dimensional drawing can be labelled for representing data coming from chemical modifications and/or enzymatic cleavages. Application to a few secondary structures such as RNaseP, 5S rRNA and 16S rRNA are given.},
note = {0266-7061
Journal Article},
keywords = {16S/chemistry/genetics RNA, 5S/chemistry/genetics Ribonuclease P *Software, Algorithms Bacillus subtilis/chemistry/genetics Base Sequence *Computer Graphics Endoribonucleases/genetics Escherichia coli/chemistry/genetics Molecular Sequence Data Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Bacterial/genetics RNA, Catalytic/genetics RNA, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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 Article de journal
Dans: J Mol Biol, vol. 227, no. 3, p. 621-634, 1992, ISBN: 1383551, (0022-2836).
Résumé | Liens | BibTeX | Étiquettes: 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}
}