Introduction
Mamit-tRNA is a compilation of mammalian mitochondrial tRNA genes. It contains presently 3064 tRNA gene sequences from 150 fully sequenced genomes available on GenBank database (NCBI). This is the follow-up of our previous investigation on a smaller set of mammals which allowed to highlight peculiar and specific structural characteristics of mammalian mitochondrial tRNAs (Helm M. et al. RNA. 6, 1356-79 (2000)).
Mamit-tRNA, to be updated regularly, is expected to serve as basis towards the deciphering of structural features of mammalian mitochondrial tRNAs and a helpful tool in the frame of human diseases linked to point mutations in mitochondrial tRNA genes.


Sequence comparisons

Sequences are classified into 22 families according to the amino acid specificity of the different tRNAs as defined by the anticodon triplets. Each sequence is displayed linearly with color codes indicating secondary structural domains, and can be converted into printable 2D cloverleaf structures.
Multiple sequences can be selected by organism, order or superorder in any combination for compilation. The outcome appears dynamically on cloverleaf shaped secondary structures either as 'typical' or 'consensus' sequences with supplementary statistical data for each position within the tRNA. Due to large variations in size, D- and T- loops escape the analysis. However, tRNA sequences can be selected according to the size of their D- and/or T- loop and/or variable region.


Mutations in human tRNA genes

Numerous point mutations have been reported for human (Hs) mitochondrial tRNA genes, either as polymorphisms or related to pathologies. Positions of these mutations are displayed in the corresponding cloverleaf secondary structures and are color coded according to their potential role in pathologies (McFarland R. et al. Trends Genet 20, 591-6 (2004)).

Further, we offer a table allowing for an easy conversion of nucleotide numbering in the human mitochondrial genome (Anderson, S. et al. Nature 290, 457-65 (1981)) to conventional tRNA numbering.


Please use one of the following formats to cite Mamit-tRNA:
Mamit-tRNA: Compilation of mammalian mitochondrial tRNA genes http://mamit-tRNA.u-strasbg.fr 2007
or
Joern Pütz, Bruno Dupuis, Marie Sissler and Catherine Florentz, (2007), RNA, 13, pp 1184-90.
Reprint (PDF) Version of this Article (4735K).

Last update : 24/10/2007

 

 

Mito3D.jpg

 

 

 

 

 

 

 

 

Structure of a mitochondrion. The electron micrograph
shows the extensive infolding of the inner membrane;
the folds are called cristae. Borrowed from Lehninger,
D. L. Nelson & M. M. Cox
: Principles of Biochemistry,
3rd edition 2000