Graphical abstract

Mitochondria are the centre of energy metabolism in eukaryotic cells and its genes are thus key to the evolution of molecular mechanisms that metabolize cellular energy. Intertidal zone is one of the most stressful environments with extreme shifts in temperature, salinity, pH and oxygen concentrations. Marine molluscs, particularly chitons belong to the ecologically dominant organisms in this extreme environment, symbolizing an ideal model to understand mitochondrial stress adaptation. Here, we used concatenated mitochondrial genetic components separately from seven chitons of the intertidal zone to reconstruct phylogenetic relationships among these species. We performed selection analyses considering sites and branches of individual proteincoding genes to identify potentially adaptive residues and localize them in the protein structures of mt subunits. Our results exhibited significant amino acid changes in sites under diversifying selection of all the protein-coding genes, indicative of the adaptive evolution of mitochondrial genome in chitons. Furthermore, we obtained sites in the transmembrane helices lining the proton translocation channel as well as in surrounding loop regions, providing implication towards functional modification of the OXPHOS proteins essential for survival in dynamic environment of the intertidal zone.

The importance of the widely spread leucine-rich repeat (LRR) motif has been studied considering TLRs, the LRR-containing protein involved in animal immune response. The protein connects intracellular signalling with a chain of molecular interaction through the presence of LRRs in the ectodomain and TIR in the endodomain. Domain analyses with human TLR1-9 reported ectodomain with tandem repeats, transmembrane domain and TIR domain. The repeat number varied across members of TLRs and remains characteristic to a particular member. Analysis of gene structure revealed absence of codon interruption with TLR3 and TLR4 as exceptions. Extensive study with TLR4 from metazoans confirmed the presence of 23 LRRs in tandem. Distinct clade formation using coding and amino acid sequence of individual repeats illustrated independent evolution. Although ectodomain and endodomain exhibited differential selection pressure, however, within the ectodomain, the individual repeats displayed positive, negative and neutral selection pressure depending on their structural and functional significance.

The intertidal zone is one of the most stressful environments, with extreme shifts in temperature, salinity, pH and oxygen concentration. Marine molluscs, particularly chitons that belong to the category of ecologically significant organisms, survive in this extreme environment, and are ideal systems for studying stress adaptation. Mitochondria are known to be critical for energy homeostasis, and changes in environmental factors result in their dysfunction and consequent injury to the organism. Intertidal organisms are exception in this respect because they are capable of maintaining mitochondrial integrity. Here, we used mitochondrial genetic components from seven chitons of the intertidal zone to infer phylogenetic relationships. Selection analyses on individual protein-coding genes (PCGs) were performed to identify and map potentially adaptive residues in the modelled structures of the mitochondrial respiratory chain complexes. The results showed significant amino acid changes in sites under diversifying selection for all the PCGs, indicating that the mitochondrial genome in chitons is undergoing adaptive evolution. Such sites were observed in the proton pump as well as in the translocation channel of the transmembrane helices and the surrounding loop regions, thus implying functional modification of the mitochondrial proteins essential for survival in the dynamic environment of the intertidal zone.

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