Imagerie PI2

@article{,

title = {Structural analysis of new local features in SECIS RNA hairpins},

author = {D Fagegaltier and A Lescure and R Walczak and P Carbon and A Krol},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10908323},

isbn = {10908323},

year  = {2000},

date = {2000-01-01},

journal = {Nucleic Acids Res},

volume = {28},

number = {14},

pages = {2679-2689},

abstract = {Decoding of the UGA selenocysteine codon for selenoprotein translation requires the SECIS element, a stem-loop motif in the 3'-UTR of the mRNA carrying short or large apical loops. In previous structural studies, we derived a secondary structure model for SECIS RNAs with short apical loops. Work from others proposed that intra-apical loop base pairing can occur in those SECIS that possess large apical loops, yielding form 2 SECIS versus the form 1 with short loops. In this work, SECIS elements arising from eight different selenoprotein mRNAs were assayed by enzymatic and/or chemical probing showing that seven can adopt form 2. Further, database searches led to the discovery in drosophila and zebrafish of SECIS elements in the selenophosphate synthetase 2, type 1 deiodinase and SelW mRNAs. Alignment of SECIS sequences not only highlighted the predominance of form 2 but also made it possible to classify the SECIS elements according to the type of selenoprotein mRNA they belong to. Interestingly, the alignment revealed that an unpaired adenine, previously thought to be invariant, is replaced by a guanine in four SECIS elements. Tested in vivo, neither the A to G nor the A to U changes at this position greatly affected the activity while the most detrimental effect was provided by a C. The putative contribution of the various SECIS motifs to function and ligand binding is discussed.},

note = {1362-4962 

Journal Article},

keywords = {Animals  Base Sequence  COS Cells  DNA/chemistry/genetics  DNA, DNA  Support, Factual  Drosophila melanogaster/genetics  Glutathione Peroxidase/genetics/metabolism  Human  Mice  Molecular Sequence Data  Mutagenesis, LESCURE, Non-U.S. Gov't  Xenopus laevis, Nucleic Acid/*genetics  Selenocysteine/*genetics/metabolism  Sequence Alignment  Sequence Analysis, Recombinant/genetics/metabolism  Databases, Site-Directed  Nucleic Acid Conformation  Phosphotransferases/genetics  RNA/chemistry/*genetics  Rats  Regulatory Sequences, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {RNAs mediating cotranslational insertion of selenocysteine in eukaryotic selenoproteins},

author = {N Hubert and R Walczak and C Sturchler and E Myslinski and C Schuster and E Westhof and P Carbon and A Krol},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8955902},

isbn = {8955902},

year  = {1996},

date = {1996-01-01},

journal = {Biochimie},

volume = {78},

number = {7},

pages = {590-596},

abstract = {Selenocysteine, a selenium-containing analog of cysteine, is found in the prokaryotic and eukaryotic kingdoms in active sites of enzymes involved in oxidation-reduction reactions. Its biosynthesis and cotranslational insertion into selenoproteins is performed by an outstanding mechanism, implying the participation of several gene products. The tRNA(Sec) is one of these. In eukaryotes, its transcription mode by RNA polymerase III differs from that of classical tRNA genes, both at the level of the promoter elements and transcription factors involved. In addition, enhanced transcription is afforded by a newly characterized zinc finger activator. Not only transcription of the gene, but also the tRNA(Sec) itself is atypical since its 2D and 3D structures exhibit features which set it apart from classical tRNAs. Decoding of eukaryotic selenocysteine UGA codons requires a stem-loop structure in the 3'UTR of mRNAs, the selenocysteine insertion sequence (SECIS) element. Structure probing and sequence comparisons led us to propose a 2D structure model for the SECIS element, containing a novel RNA motif composed of four consecutive non-Watson-Crick base-pairs. A 3D model, rationalizing the accessibility data, was elaborated by computer modeling. It yields indicative or suggestive evidence for the role that could play some conserved residues and/or structural features in SECIS function. These might act as signals for interaction with SBP, the SECIS binding protein that we have characterized.},

note = {0300-9084 

Journal Article 

Review 

Review, Tutorial},

keywords = {Amino Acid-Specific/chemistry/metabolism  Rats  Schistosoma mansoni  Selenocysteine/chemistry/*metabolism  Support, Animals  Base Sequence  Cattle  Escherichia coli  Human  Mice  Models, Molecular  Molecular Sequence Data  Nucleic Acid Conformation  Proteins/chemistry/*metabolism  RNA/chemistry/*metabolism  RNA, Non-U.S. Gov't  Xenopus laevis, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Native bovine selenocysteine tRNA(Sec) secondary structure as probed by two plant single-strand-specific nucleases},

author = {J Gabryszuk and A Przykorska and M Monko and E Kuligowska and C Sturchler and A Krol and G Dirheimer and J W Szarkowski and G Keith},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7665090},

isbn = {7665090},

year  = {1995},

date = {1995-01-01},

journal = {Gene},

volume = {161},

number = {2},

pages = {259-263},

abstract = {Two single-strand-specific nucleases, discovered in plants, have been used to investigate the secondary and tertiary structures of the native bovine liver selenocysteine tRNA(Sec). To check the possible influence of nucleotide modifications on these structures, we compared the results obtained with the fully modified tRNA to the unmodified transcript prepared by in vitro T7 transcription of the Xenopus laevis tRNA(Sec) gene. We found that the structures in solution of the native tRNA(Sec) and the transcript are very similar despite some differences in accessibility to the enzymatic probes. Indeed, the modified anticodon-loop of native bovine tRNA(Sec), containing 5-methylcarboxymethyluridine (mcm5U34) and N6-isopentenyladenosine (i6A37), is less accessible to Rn nuclease than that of the transcript: the intensity of bands representing cuts at A36 and A38 is much lower as compared to those of the transcript, whereas no cuts were found at the level of i6A37 in the anticodon loop of the native molecule. Surprisingly, the variable arm of the native molecule has been found to be more susceptible to single-strand-specific nuclease action, suggesting a looser structure of the variable arm in native bovine tRNA(Sec) than in the transcript.},

note = {0378-1119 

Journal Article},

keywords = {Amino Acid-Specific/*chemistry/*genetics  Support, Animals  Anticodon/chemistry/genetics  Base Sequence  Cattle  Comparative Study  Endonucleases  Liver/chemistry  Molecular Sequence Data  Molecular Structure  *Nucleic Acid Conformation  Plants/enzymology  RNA, Non-U.S. Gov't  Xenopus laevis, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Eukaryotic selenocysteine inserting tRNA species support selenoprotein synthesis in Escherichia coli},

author = {C Baron and C Sturchler and X Q Wu and H J Gross and A Krol and A Bock},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8036149},

isbn = {8036149},

year  = {1994},

date = {1994-01-01},

journal = {Nucleic Acids Res},

volume = {22},

number = {12},

pages = {2228-2233},

abstract = {Although the tRNA species directing selenocysteine insertion in prokaryotes differ greatly in their primary structure from that of their eukaryotic homologues they share very similar three-dimensional structures. To analyse whether this conservation of the overall shape of the molecules reflects a conservation of their functional interactions it was tested whether the selenocysteine inserting tRNA species from Homo sapiens supports selenoprotein synthesis in E. coli. It was found that the expression of the human tRNA(Sec) gene in E.coli can complement a lesion in the tRNA(Sec) gene of this organism. Transcripts of the Homo sapiens and Xenopus laevis tRNA(Sec) genes synthesised in vitro were amino-acylated by the E.coli seryl-tRNA ligase although at a very low rate and the resulting seryl-tRNA(Sec) was bound to and converted into selenocysteyl-tRNA(Sec) by the selenocysteine synthase of this organism. Selenocysteyl-tRNA(Sec) from both eukaryotes was able to form a complex with translation factor SELB from E.coli. Although the mechanism of selenocysteine incorporation into seleno-proteins appears to be rather different in E.coli and in vertebrates, we observe here a surprising conservation of functions over an enormous evolutionary distance.},

note = {0305-1048 

Journal Article},

keywords = {Amino Acid-Specific/chemistry/*genetics  Selenocysteine/chemistry  Serine-tRNA Ligase/metabolism  Support, Animals  Bacterial Proteins/metabolism  Base Sequence  Cloning, Molecular  Escherichia coli/*genetics  Genetic Complementation Test  Human  Nucleic Acid Conformation  Peptide Elongation Factors/metabolism  Proteins/*biosynthesis/genetics  RNA, Non-U.S. Gov't  Xenopus laevis, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec)},

author = {C Sturchler and E Westhof and P Carbon and A Krol},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8464694},

isbn = {8464694},

year  = {1993},

date = {1993-01-01},

journal = {Nucleic Acids Res},

volume = {21},

number = {5},

pages = {1073-1079},

abstract = {Cotranslational insertion of selenocysteine into selenoenzymes is mediated by a specialized transfer RNA, the tRNA(Sec). We have carried out the determination of the solution structure of the eucaryotic tRNA(Sec). Based on the enzymatic and chemical probing approach, we show that the secondary structure bears a few unprecedented features like a 9 bp aminoacid-, a 4 bp thymine- and a 6 bp dihydrouridine-stems. Surprisingly, the eighth nucleotide, although being a uridine, is base-paired and cannot therefore correspond to the single-stranded invariant U8 found in all tRNAs. Rather, experimental evidence led us to propose that the role of the invariant U8 is actually played by the tenth nucleotide which is an A, numbered A8 to indicate this fact. The experimental data therefore demonstrate that the cloverleaf structure we derived experimentally resembles the hand-folded model proposed by Bock et al (ref. 3). Using the solution data and computer modelling, we derived a three-dimensional structure model which shows some unique aspects. Basically, A8, A14, U21 form a novel type of tertiary interaction in which A8 interacts with the Hoogsteen sites of A14 which itself forms a Watson-Crick pair with U21. No coherent model containing the canonical 15-48 interaction could be derived. Thus, the number of tertiary interactions appear to be limited, leading to an uncoupling of the variable stem from the rest of the molecule.},

note = {0305-1048 

Journal Article},

keywords = {Amino Acid-Specific/*chemistry  *Selenocysteine  Support, Animals  Base Sequence  Cloning, Molecular  Computer Simulation  DNA, Molecular  Molecular Sequence Data  *Nucleic Acid Conformation  RNA, Non-U.S. Gov't  Xenopus laevis, Single-Stranded  Models, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}