Comparative sequence analysis of the non-protein-coding mitochondrial DNA of inbred rat strains

Abstract

The proper function of mammalian mitochondria necessitates a coordinated expression of both nuclear and mitochondrial genes, most likely due to the co-evolution of nuclear and mitochondrial genomes. The non-protein coding regions of mitochondrial DNA (mtDNA) including the D-loop, tRNA and rRNA genes form a major component of this regulated expression unit. Here we present comparative analyses of the non-protein-coding regions from 27 Rattus norvegicus mtDNA sequences. There were two variable positions in 12S rRNA, 20 in 16S rRNA, eight within the tRNA genes and 13 in the D-loop. Only one of the three neutrality tests used demonstrated statistically significant evidence for selection in 16S rRNA and tRNA-Cys. Based on our analyses of conserved sequences, we propose that some of the variable nucleotide positions identified in 16S rRNA and tRNA-Cys, and the D-loop might be important for mitochondrial function and its regulation.

Figure 1. Location of variable position 2170 in the predicted secondary structure of the mammalian mitochondrial 16S rRNA.

In the enlarged L1 binding domain, position 2170 is encircled and highlighted by a red arrow. L1-BD denotes the L1 binding domain. I, II, III, IV, V and VI represent the rRNA domains, while black arrows represent the predicted tertiary interactions. Blue color represents regions predicted from comparative sequence analysis, orange colour represents predictions by Mfold software, while green colour in domain III represents alternative secondary structure predicted using Alifold software. The figure has been modified from reference .

Figure 2. Inferred secondary structures for (A) tRNA-Cys, (B) tRNA-Tyr, (C) tRNA-Asp, (D) tRNA-Thr and (E) tRNA-Pro.

Variable sites are highlighted in grey. The anticodon loop appears at the bottom of each model.