Sadeesh E M, Lahamge Madhuri S, Malik Anuj, Ampadi A N
Laboratory of Mitochondrial Biology of Farm Animals, Animal Biochemistry Division, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India.
University of Bonn, Institute of Animal Sciences, Katzenburgweg 7 - 9, 53115, Bonn, Germany.
Mol Biotechnol. 2025 Jun;67(6):2411-2427. doi: 10.1007/s12033-024-01206-6. Epub 2024 Jun 15.
Buffalo physiology intricately balances energy, profoundly influencing health, productivity, and reproduction. This study explores nuclear-mitochondrial crosstalk, revealing OXPHOS Complex I gene expression variations in buffalo tissues through high-throughput RNA sequencing. Unveiling tissue-specific disparities, the research elucidates the genomic landscape of crucial energy production genes, with broader implications for veterinary and agricultural progress. Post-slaughter, tissues from post-pubertal female buffaloes underwent meticulous processing and RNA extraction using the TRIzol method. RNA-Seq library preparation and IlluminaHiSeq 2500 sequencing were performed on QC-passed samples. Data underwent stringent filtration, mapping to the Bubalus bubalis genome using HISAT2. DESeq2 facilitated differential expression gene (DEG) analysis focusing on 57 Mitocarta 3-derived genes associated with OXPHOS complex I. Nuclear-encoded mitochondrial protein transcripts of OXPHOS complex 1 exhibited tissue-specific variations, with 51 genes expressing significantly across tissues. DEG analysis emphasized tissue-specific expression patterns, highlighting a balanced OXPHOS complex I subunit expression in the kidney vs. brain. Gene Ontology (GO) enrichment showcased mitochondria-centric terms, revealing distinct proton motive force-driven mitochondrial ATP synthesis regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses emphasized Thermogenesis and OXPHOS pathways, enriching our understanding of tissue-specific energy metabolism. Noteworthy up-regulation of NDUFB10 in the heart and kidney aligned with heightened metabolic activity. Brain-specific up-regulation of NDUFAF6 indicated a focus on mitochondrial function, while variations in NDUFA11 and ACAD9 underscored pivotal roles in the heart and kidney. GO and KEGG analyses highlighted tissue-specific mitochondrial ATP synthesis and NADH dehydrogenase processes, providing molecular insights into organ-specific metabolic demands and regulatory mechanisms. Our study unveils conserved and tissue-specific nuances in nuclear-encoded mitochondrial OXPHOS complex I genes, laying a foundation for understanding diverse energy demands and potential health implications.
水牛的生理机能精细地平衡着能量，对健康、生产力和繁殖有着深远影响。本研究探索核-线粒体间的相互作用，通过高通量RNA测序揭示水牛组织中氧化磷酸化复合体I基因的表达变化。该研究揭示了组织特异性差异，阐明了关键能量产生基因的基因组格局，对兽医和农业发展具有更广泛的意义。屠宰后，对青春期后雌性水牛的组织进行了细致处理，并使用TRIzol法提取RNA。对质量控制合格的样本进行了RNA-Seq文库制备和IlluminaHiSeq 2500测序。数据经过严格筛选，使用HISAT2映射到水牛基因组。DESeq2有助于对57个与氧化磷酸化复合体I相关的Mitocarta 3衍生基因进行差异表达基因（DEG）分析。氧化磷酸化复合体1的核编码线粒体蛋白转录本表现出组织特异性变化，有51个基因在各组织中显著表达。DEG分析强调了组织特异性表达模式，突出了肾脏与大脑中氧化磷酸化复合体I亚基表达的平衡。基因本体（GO）富集展示了以线粒体为中心的术语，揭示了由质子动力驱动的独特线粒体ATP合成调控。京都基因与基因组百科全书（KEGG）通路分析强调了产热和氧化磷酸化通路，加深了我们对组织特异性能量代谢的理解。值得注意的是，心脏和肾脏中NDUFB10的上调与代谢活性增强一致。大脑中NDUFAF6的特异性上调表明对线粒体功能的关注，而NDUFA11和ACAD9的变化突出了它们在心脏和肾脏中的关键作用。GO和KEGG分析突出了组织特异性线粒体ATP合成和NADH脱氢酶过程，为了解器官特异性代谢需求和调控机制提供了分子见解。我们的研究揭示了核编码线粒体氧化磷酸化复合体I基因中保守和组织特异性的细微差别，为理解不同的能量需求和潜在的健康影响奠定了基础。
