PlantRNA, a database for tRNAs of photosynthetic eukaryotes

Abstract

PlantRNA database (http://plantrna.ibmp.cnrs.fr/) compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. The set of annotated tRNA gene sequences has been manually curated for maximum quality and confidence. The novelty of this database resides in the inclusion of biological information relevant to the function of all the tRNAs entered in the library. 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. Finally, data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA-binding proteins are also included. The current annotation concerns complete genomes from 11 organisms: five flowering plants (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula and Brachypodium distachyon), a moss (Physcomitrella patens), two green algae (Chlamydomonas reinhardtii and Ostreococcus tauri), one glaucophyte (Cyanophora paradoxa), one brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). The database will be regularly updated and implemented with new plant genome annotations so as to provide extensive information on tRNA biology to the research community.

Figure 1.

Phylogenetic tree of photosynthetic organisms found in the PlantRNA database. The phylogenetic tree was constructed with the full-length 18S rRNA gene sequences using the neighbor-joining method. The presence of intron-containing tRNA genes, of genomes encoding a tRNA^Sec and the occurrence of tRNA mitochondrial import are reported. ^aMinus 5 = A, E, Mi, V, W; ^bminus 4 = Q, H, Mi, F; ^c8 = R, E, Q, Me, P, S, T, W, Y. The one-letter code for amino acids is used.

Figure 2.

PlantRNA database: overview of the web interface and basic functions.