PUBLICATION
Structural analysis of new local features in SECIS RNA hairpins
- Authors
- Fagegaltier, D., Lescure, A., Walczak, R., Carbon, P., and Krol, A.
- ID
- ZDB-PUB-000825-7
- Date
- 2000
- Source
- Nucleic acids research 28(14): 2679-2689 (Journal)
- Registered Authors
- Krol, Alain, Lescure, Alain
- Keywords
- none
- MeSH Terms
-
- Animals
- Base Sequence
- COS Cells
- DNA/chemistry
- DNA/genetics
- DNA, Recombinant/genetics
- DNA, Recombinant/metabolism
- Databases, Factual
- Drosophila Proteins*
- Drosophila melanogaster/genetics
- Glutathione Peroxidase/genetics
- Glutathione Peroxidase/metabolism
- Humans
- Mice
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- Phosphotransferases/genetics
- RNA/chemistry
- RNA/genetics*
- Rats
- Regulatory Sequences, Nucleic Acid/genetics*
- Selenocysteine/genetics*
- Selenocysteine/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Xenopus laevis
- PubMed
- 10908323 Full text @ Nucleic Acids Res.
Citation
Fagegaltier, D., Lescure, A., Walczak, R., Carbon, P., and Krol, A. (2000) Structural analysis of new local features in SECIS RNA hairpins. Nucleic acids research. 28(14):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 invari-ant, 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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping