Lescoute A, Leontis N B, Massire C, Westhof E
Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments Article de journal
Dans: Nucleic Acids Res, vol. 33, no. 8, p. 2395-2409, 2005, ISBN: 15860776, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Pairing Models, Molecular Nucleic Acid Conformation RNA, Non-U.S. Gov't Research Support, Nucleic Acid, P.H.S. *Sequence Alignment Sequence Analysis, Ribosomal/*chemistry Research Support, RNA/*methods Sequence Homology, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments},
author = {A Lescoute and N B Leontis and C Massire and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15860776},
isbn = {15860776},
year = {2005},
date = {2005-01-01},
journal = {Nucleic Acids Res},
volume = {33},
number = {8},
pages = {2395-2409},
abstract = {The occurrences of two recurrent motifs in ribosomal RNA sequences, the Kink-turn and the C-loop, are examined in crystal structures and systematically compared with sequence alignments of rRNAs from the three kingdoms of life in order to identify the range of the structural and sequence variations. Isostericity Matrices are used to analyze structurally the sequence variations of the characteristic non-Watson-Crick base pairs for each motif. We show that Isostericity Matrices for non-Watson-Crick base pairs provide important tools for deriving the sequence signatures of recurrent motifs, for scoring and refining sequence alignments, and for determining whether motifs are conserved throughout evolution. The systematic use of Isostericity Matrices identifies the positions of the insertion or deletion of one or more nucleotides relative to the structurally characterized examples of motifs and, most importantly, specifies whether these changes result in new motifs. Thus, comparative analysis coupled with Isostericity Matrices allows one to produce and refine structural sequence alignments. The analysis, based on both sequence and structure, permits therefore the evaluation of the conservation of motifs across phylogeny and the derivation of rules of equivalence between structural motifs. The conservations observed in Isostericity Matrices form a predictive basis for identifying motifs in sequences.},
note = {1362-4962
Journal Article},
keywords = {Base Pairing Models, Molecular Nucleic Acid Conformation RNA, Non-U.S. Gov't Research Support, Nucleic Acid, P.H.S. *Sequence Alignment Sequence Analysis, Ribosomal/*chemistry Research Support, RNA/*methods Sequence Homology, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Castellano S, Lobanov A V, Chapple C, Novoselov S V, Albrecht M, Hua D, Lescure A, Lengauer T, Krol A, Gladyshev V N, Guigo R
Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 102, no. 45, p. 16188-16193, 2005, ISBN: 16260744, (0027-8424 (Print) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Extramural Research Support, KROL Adenosine Diphosphate Ribose/metabolism Animals Fish Proteins/chemistry/genetics/*physiology Genome Mice NIH 3T3 Cells Phylogeny Promoter Regions (Genetics) Proteome Research Support, LESCURE, N.I.H., Non-P.H.S. Selenoproteins/chemistry/genetics/*physiology Tetraodontiformes/*genetics, Non-U.S. Gov't Research Support, U.S. Gov't, Unité ARN
@article{,
title = {Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family},
author = {S Castellano and A V Lobanov and C Chapple and S V Novoselov and M Albrecht and D Hua and A Lescure and T Lengauer and A Krol and V N Gladyshev and R Guigo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16260744},
isbn = {16260744},
year = {2005},
date = {2005-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {102},
number = {45},
pages = {16188-16193},
abstract = {Selenoproteins are a diverse group of proteins that contain selenocysteine (Sec), the 21st amino acid. In the genetic code, UGA serves as a termination signal and a Sec codon. This dual role has precluded the automatic annotation of selenoproteins. Recent advances in the computational identification of selenoprotein genes have provided a first glimpse of the size, functions, and phylogenetic diversity of eukaryotic selenoproteomes. Here, we describe the identification of a selenoprotein family named SelJ. In contrast to known selenoproteins, SelJ appears to be restricted to actinopterygian fishes and sea urchin, with Cys homologues only found in cnidarians. SelJ shows significant similarity to the jellyfish J1-crystallins and with them constitutes a distinct subfamily within the large family of ADP-ribosylation enzymes. Consistent with its potential role as a structural crystallin, SelJ has preferential and homogeneous expression in the eye lens in early stages of zebrafish development. A structural role for SelJ would be in contrast to the majority of known selenoenzymes. The unusually highly restricted phylogenetic distribution of SelJ, its specialization, and the comparative analysis of eukaryotic selenoproteomes reveal the diversity and functional plasticity of selenoproteins and point to a mosaic evolution of the use of Sec in proteins.},
note = {0027-8424 (Print)
Journal Article},
keywords = {Extramural Research Support, KROL Adenosine Diphosphate Ribose/metabolism Animals Fish Proteins/chemistry/genetics/*physiology Genome Mice NIH 3T3 Cells Phylogeny Promoter Regions (Genetics) Proteome Research Support, LESCURE, N.I.H., Non-P.H.S. Selenoproteins/chemistry/genetics/*physiology Tetraodontiformes/*genetics, Non-U.S. Gov't Research Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}