Cytochrome oxidase subunit III fromArbacia lixula: Detection of functional constraints by comparison with homologous sequences

Abstract

In this paper we report the comparison of the sequences of the cytochrome oxidase subunit III from three different sea urchin species. Both nucleotide and amino acid sequences have been analyzed. The nucleotide sequence analysis reveals that the sea urchin sequences obey some rules already found in mammals. The base substitution analysis carried out on the sequences of the three species pairs, shows that the evolutionary dynamics of the first and the second codon positions are so slow that do not allow a quantitative measurement of their genetic distances, thus demonstrating that also in these species the COIII gene is strongly conserved during evolution. Changes occurring at the third codon positions indicate that the three species evolved from a common ancestor under different directional mutational pressure. The multi-alignment of the sea urchin proteins indicates the existence of the amino acid sequence motif N R T that represents a possible glycosylation site. Another glycosylation site has been detected in the mammalian cytochrome oxidase subunit III, in a position slightly different. Such an analysis revealed, for the first time, a new functional aspect of this sequence.

Phylogeny of Cephalopods Inferred from Mitochondrial DNA Sequences

“…With the transversions only, the bootstrap values of some families (closest species) like sepiids and oegopsids are reduced; the transitions discriminate close taxa, and the transversions discriminate distant taxa (Beckenbach et al, 1993), bearing in mind that transitions lead primarily to saturation. The transitions are more abundant than the transversions in some vertebrate species but this is not the rule in invertebrates (Ho et al, 1995;de Giorgi et al, 1993). In our case, the more distant taxa (octopods-decapods) show a transversion rate higher than the transition rate.…”