Decoding nitrogen depletion–induced lipid accumulation in Aurantiochytrium sp. YHPM1 through integrated proteomic and transcriptomic analyses

Docosahexaenoic acid (DHA) is a high-value omega-3 polyunsaturated fatty acid (PUFA) with critical roles in human health and nutrition, and Aurantiochytrium species have emerged as promising microbial cell factories for sustainable and scalable DHA biosynthesis, achieving yields of up to 43% of total fatty acids. To elucidate the regulatory mechanisms underlying lipid overproduction in this organism, we performed an integrated proteomic and transcriptomic analysis of the high-yield mutant Aurantiochytrium sp. YHPM1 under a two-stage nitrogen depletion strategy, at 48 and 108 h, the strain exhibited a biphasic metabolic response. Initially, β-oxidation and amino-acid catabolism were suppressed. This was followed by enhanced fatty-acid (FA) and triacylglycerol (TAG) biosynthesis. Moreover, key lipid biosynthetic enzymes, including DGAT, DLAT, and GPAT were markedly upregulated at both transcriptomic and proteomic levels, while β-oxidation enzymes, such as ACADM and FOX2 were suppressed. Notably, 8% of transcripts exhibited discordant transcript–protein expression, most prominently at 48 h, suggesting extensive post-transcriptional regulation. Overall, these findings demonstrate a phased metabolic reprogramming strategy in YHPM1 and advance our understanding of post-transcriptional mechanisms governing DHA accumulation, thereby facilitating the industrial-scale production of DHA using Aurantiochytrium.