Molecular assessment of proteins encoded by the mitochondrial genome of Clarias batrachus and Clarias gariepinus

Abstract

The population of catfish, Clarias batrachus has substantially diminished in various countries and studies show that another related species Clarias gariepinus is replacing it. The better adaptability and survivability of C. gariepinus over C. batrachus could be attributed to the metabolic differences between these two species, which is primarily regulated by mitochondrial activities. To understand the reasons behind this phenomenon, we performed in silico analyses to decipher the differences between the proteins encoded by the mitochondrial genome of these two related species. Our analysis revealed that out of thirteen, twelve proteins encoded by the mitochondrial genome of these two species have substantial variations between them. We characterised these variations by analysing their effect on secondary structure, intrinsic disorder predisposition, and functional impact on protein and stability parameters. Our data show that most of the parameters are changing between these two closely related species. Altogether, we demonstrate the molecular insights into the mitochondrial genome-encoded proteins of these two species and predict their effect on protein function and stability that might be helping C. gariepinus to gain survivability better than the C. batrachus.

Keywords: Clarias batrachus; Clarias gariepinus; Mitochondrial genome; Protein stability; Variations.

Fig. 1

The sequence alignment of the NADH Dehydrogenase subunits encoded by mitochondrial genome of C. batrachus and C. gariepinus reported from China. (A–F) The amino acid substitutions are highlighted in the schematics of individual proteins.

Fig. 2

The sequence alignment of the Cytochrome C Oxidase subunits, ATP Synthase F0 subunits and Cytochrome b encoded by mitochondrial genome of C. batrachus and C. gariepinus reported from China. (A–F) The amino acid substitutions are highlighted in the schematics of individual proteins.

Fig. 3

Effect of amino acid substitutions on the secondary structure of proteins encoded by mitochondrial genome of C. batrachus and C. gariepinus. Panel (i) represents sequence of C. batrachus and panel (ii) represents sequence of C. gariepinus. (A–F) represents the individual proteins and asterisk show the locations of the variation in the secondary structure of C. gariepinus protein.

Fig. 4

Comparisons of the intrinsic disorder predisposition of the C. batrachus and C. gariepinus. A disorder threshold is indicated at score = 0.5, residues/regions with the disorder scores >0.5 are considered as disordered. (A–D) Each panel represents the disorder parameters of individual proteins including NADH dehydrogenase subunit 1, 2, 6 and ATP Synthase F0 subunit 8.

figs1

Effect of amino acid substitutions on the secondary structure of proteins encoded by mitochondrial genome of C. batrachus and C. gariepinus. Panel (i) represents sequence of C. batrachus and panel (ii) represents sequence of C. gariepinus. (A-F) represents the individual proteins and asterisk show the locations of the variation in the secondary structure of C. gariepinus protein.

figs2

Comparisons of the intrinsic disorder predisposition of the C. batrachus and C. gariepinus. A disorder threshold is indicated at score = 0.5, residues/regions with the disorder scores >0.5 are considered as disordered. (A-H) Each panel represents the disorder parameters of individual protein (mentioned in each panel)