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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.

SUBMITTER: Chand GB

PROVIDER: S-EPMC8024883 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes "walks" to search for suitable environments during summer. It has evolved accessory air-breathing organs for respiring air and corresponding mechanisms to survive in such challenging environments. Thereby, it serves as a great model for understanding adaptations to terrestrial life. RESULTS:Comparative genomics with channel catfish (Ictalurus punctatus) revealed specific adaptations of C. batrachus in DNA repair, enzyme activator activity, and small GTPase regulator activity. Comparative analysis with 11 non-air-breathing fish species suggested adaptive evolution in gene expression and nitrogenous waste metabolic processes. Further, myoglobin, olfactory receptor related to class A G protein-coupled receptor 1, and sulfotransferase 6b1 genes were found to be expanded in the air-breathing walking catfish genome, with 15, 15, and 12 copies, respectively, compared to non-air-breathing fishes that possess only 1-2 copies of these genes. Additionally, we sequenced and compared the transcriptomes of the gill and the air-breathing organ to characterize the mechanism of aerial respiration involved in elastic fiber formation, oxygen binding and transport, angiogenesis, ion homeostasis and acid-base balance. The hemoglobin genes were expressed dramatically higher in the air-breathing organ than in the gill of walking catfish. CONCLUSIONS:This study provides an important genomic resource for understanding the adaptive mechanisms of walking catfish to terrestrial environments. It is possible that the coupling of enhanced abilities for oxygen storage and oxygen transport through genomic expansion of myoglobin genes and transcriptomic up-regulation of hemoglobin and angiogenesis-related genes are important components of the molecular basis for adaptation of this aquatic species to terrestrial life.

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

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