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PlantRNA


NAR Molecular Biology Database Collection entry number 1578
Valérie Cognat*, Gaël Pawlak*, Anne-Marie Duchêne, Magali Daujat, Anaïs Gigant, Thalia Salinas, Morgane Michaud, Bernard Gutmann, Philippe Giegé, Anthony Gobert and Laurence Maréchal-Drouard
Institut de Biologie Moléculaire des Plantes, UPR 2357-CNRS, associated with the Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France

Database Description

The PlantRNA database compiles 4,375 tRNA gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. To the manually curated lists of tRNA genes that we recently extracted from the genomes of five angiosperms (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula, Brachypodium distachyon) and one green alga (Chlamydomonas reinhardtii) (1), we retrieved tRNA genes from the genomes of 6 other photosynthetic organisms, namely another green alga (Ostreococcus tauri), a glaucophyte (Cyanophora paradoxa), a brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). Whole genomes were scanned by tRNAscan-SE (2) and then manually annotated as described in (1). For each tRNA gene, the linear secondary structure is given as well as biological information. This includes 5'- and 3'- flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Due to the importance of the dual-targeting phenomenon for proteins involved in translation in plants (3), we also put strong effort in providing the subcellular localization of these enzymes. Finally, data on mitochondrial import (3) of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA binding proteins are also included. Transfer RNA gene sequences and optional information can be downloaded in xls or FASTA file formats. In addition, a SQL dump of the database is available upon request.

Acknowledgements

B.G. and M.M. were supported by the French Ministère de l’Education et de la Recherche. This work was supported by the Centre National de la Recherche Scientifique (CNRS), the University of Strasbourg, the French Agence Nationale de la Recherche (ANR) grants and by the French National Program "Investissement d'Avenir" (Labex MitoCross).

References

1. Michaud, M., Cognat, V., Duchêne, A.M. and Maréchal-Drouard, L. (2011) A global picture of tRNA genes in plant genomes. Plant J, 66, 80-93.

2. Schattner, P., Brooks, A.N. and Lowe, T.M. (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res, 33, w686-689.

3. Duchêne, A.M., Pujol, C. and Maréchal-Drouard, L. (2009) Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria. Curr Genet, 55, 1-18.



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