Comparative Transcriptome Analysis Reveals Tissue-Specific Expression and Conservation of Mitochondrial Metal and Cofactor Genes in Buffalo.

Mitochondrial function relies heavily on metal ions and metabolic cofactors that support oxidative phosphorylation and essential enzymatic processes. However, the tissue-specific regulation of these pathways remains poorly understood in large ruminants. This study performed a comprehensive transcriptomic analysis of nuclear-encoded mitochondrial genes involved in metal ion and cofactor metabolism across four physiologically distinct tissues kidney, heart, brain, and ovary in female buffalo. Reanalysis of high-quality RNA-seq data identified 94 genes categorized into 13 functional classes, including those associated with iron–sulfur (Fe-S) cluster assembly, heme biosynthesis, coenzyme A and coenzyme Q metabolism, molybdenum cofactor synthesis, NAD metabolism, carnitine synthesis and transport, copper metabolism, tetrahydrobiopterin synthesis, Fe-S-containing and heme-containing proteins, and other metal-associated mitochondrial processes, revealing pronounced tissue-specific expression patterns. High-energy-demand tissues such as the heart and brain exhibited elevated expression of genes linked to iron handling, coenzyme Q biosynthesis, and oxidative metabolism, consistent with their sustained bioenergetic requirements. In contrast, the kidney showed selective enrichment of genes involved in molybdenum cofactor synthesis and NAD metabolism, reflecting its specialized roles in detoxification and metabolic homeostasis. The ovary displayed comparatively moderate mitochondrial metal and cofactor gene expression, aligned with its reproductive and steroidogenic functions. Functional enrichment analyses further confirmed that mitochondrial metal- and cofactor-dependent pathways are finely tuned according to organ-specific metabolic demands. Cross-species comparison with human transcriptomic data demonstrated strong conservation of tissue-level expression profiles, highlighting the evolutionary stability of mitochondrial metallome regulation. Collectively, these findings provide new insights into organ-specific mitochondrial adaptations in buffalo and establish a molecular framework for understanding metal-dependent mitochondrial function with potential translational relevance to metabolic health and disease.