Adrián A. Estrada-Graf, Juan‐Carlos Sigala, Mishael Sánchez-Pérez, Marcia Morales
Despite the widespread use of stress conditions to induce lipid accumulation in microalgae, the systems-level mechanisms coupling photosynthetic energy imbalance, carbon redistribution, and lipid biosynthesis remain poorly resolved. This lack of integrative understanding limits the rational optimization of strategies to enhance lipid productivity in algal systems. Here, we address this gap by integrating transcriptomic profiling, BlastKOALA annotation, and weighted gene co-expression network analysis to identify coordinated transcriptional programs associated with high lipid accumulation in Scenedesmus obtusiusculus AT-UAM. In this strain, lipid content can reach up to 60% under nitrogen depletion combined with controlled acidification, yet the mechanisms linking these conditions to lipid accumulation remain unclear. Results revealed a concerted reorganization of photosynthesis, central carbon metabolism, and the electron transport chain. Glycolysis, the tricarboxylic acid cycle, and the oxidative pentose phosphate pathway were upregulated, supporting increased supply of carbon precursors and reducing equivalents for lipid synthesis. Notably, photosynthesis-related genes were induced after acidification despite reduced chlorophyll content. Weighted gene co-expression network analysis identified a lipid-associated module enriched in redox and energy metabolism genes rather than canonical lipid biosynthetic genes, indicating that lipid accumulation is indirectly associated with the management of excess reducing power. Accordingly, a malate–oxaloacetate–pyruvate cycle is proposed as a redox-balancing framework linking photosynthetic electron flow to acetyl-CoA generation and lipid biosynthesis, supporting photoprotection under combined nitrogen limitation and acidification stress. This integrative framework provides a systems-level basis for targeted metabolic engineering strategies.