Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures

Abstract

Mamit-tRNA (http://mamit-tRNA.u-strasbg.fr), a database for mammalian mitochondrial genomes, has been developed for deciphering structural features of mammalian mitochondrial tRNAs and as a helpful tool in the frame of human diseases linked to point mutations in mitochondrial tRNA genes. To accommodate the rapid growing availability of fully sequenced mammalian mitochondrial genomes, Mamit-tRNA has implemented a relational database, and all annotated tRNA genes have been curated and aligned manually. System administrative tools have been integrated to improve efficiency and to allow real-time update (from GenBank Database at NCBI) of available mammalian mitochondrial genomes. More than 3000 tRNA gene sequences from 150 organisms are classified into 22 families according to the amino acid specificity as defined by the anticodon triplets and organized according to phylogeny. Each sequence is displayed linearly with color codes indicating secondary structural domains and can be converted into a printable two-dimensional (2D) cloverleaf structure. Consensus and typical 2D structures can be extracted for any combination of primary sequences within a given tRNA specificity on the basis of phylogenetic relationships or on the basis of structural peculiarities. Mamit-tRNA further displays static individual 2D structures of human mitochondrial tRNA genes with location of polymorphisms and pathology-related point mutations. The site offers also a table allowing for an easy conversion of human mitochondrial genome nucleotide numbering into conventional tRNA numbering. The database is expected to facilitate exploration of structure/function relationships of mitochondrial tRNAs and to assist clinicians in the frame of pathology-related mutation assignments.

FIGURE 1.

Screen picture of linear sequence alignments of mitochondrial tRNAs on Mamit-tRNA.

FIGURE 2.

Example of sequence conservation within phylogenetic subgroups: the case of tRNA^Asp. (A) Outputs of database searches. Consensus sequences obtained for indicated subgroups. The number of considered sequences is indicated in parenthesis. Y stands for pyrimidine, R for purine. The color code for nucleotides is the following: green stands for 100% conservation, blue for >90% conservation, white for >50% conservation. The color code for base pairing is the following: green for 100% conservation of Watson–Crick (WC) pairs, blue for high frequency of WC pairs and <50% G–T pairs, white for high frequency of WC and G–T pairs but <50% mismatches. Specific nucleotide positions of interest (discussed in the text) are pointed by arrows. (B) Overview of the phylogenetic links of the considered examples.