Gluth Austin, Czajka Jeffrey J, Li Xiaolu, Bloodsworth Kent J, Eder Josie G, Kyle Jennifer E, Chu Rosalie K, Yang Bin, Qian Wei-Jun, Bohutskyi Pavlo, Zhang Tong
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
Department of Biological Systems Engineering, Washington State University, Richland, WA, USA.
Biotechnol Biofuels Bioprod. 2025 Jul 21;18(1):80. doi: 10.1186/s13068-025-02657-y.
Oleaginous yeast are prodigious producers of oleochemicals, offering alternative and secure sources for applications in foodstuff, skincare, biofuels, and bioplastics. Nitrogen starvation is the primary strategy used to induce oil accumulation in oleaginous yeast as part of a global stress response. While research has demonstrated that post-translational modifications (PTMs), including phosphorylation and protein cysteine thiol oxidation (redox PTMs), are involved in signaling pathways that regulate stress responses in metazoa and algae, their role in oleaginous yeast remain understudied and unexplored.
Towards linking the yeast oleaginous phenotype to protein function, we integrated lipidomics, redox proteomics, and phosphoproteomics to investigate Rhodotorula toruloides under nitrogen-rich and starved conditions over time. Our lipidomics results unearthed interactions involving sphingolipids and cardiolipins with ER stress and mitophagy. Our redox and phosphoproteomics data highlighted the roles of the AMPK, TOR, and calcium signaling pathways in regulation of lipogenesis, autophagy, and oxidative stress response. As a first, we also demonstrated that lipogenic enzymes including fatty acid synthase are modified as a consequence of shifts in cellular redox states due to nutrient availability.
We conclude that lipid accumulation is largely a consequence of carbon rerouting and autophagy governed by changes to PTMs, and not increases in the abundance of enzymes involved in central carbon metabolism and fatty acid biosynthesis. Our systems-level approach sets the stage for acquiring multidimensional data sets for protein structural modeling and predicting the functional relevance of PTMs using Artificial Intelligence/Machine Learning (AI/ML). Coupled to those bioinformatics approaches, the putative PTM switches that we delineate will enable advanced metabolic engineering strategies to decouple lipid accumulation from nitrogen limitation.
产油酵母是油脂化学品的巨大生产者，为食品、护肤品、生物燃料和生物塑料的应用提供了替代且可靠的来源。氮饥饿是用于诱导产油酵母中油脂积累的主要策略，这是全球应激反应的一部分。虽然研究表明翻译后修饰（PTMs），包括磷酸化和蛋白质半胱氨酸硫醇氧化（氧化还原PTMs），参与调节后生动物和藻类应激反应的信号通路，但它们在产油酵母中的作用仍未得到充分研究和探索。
为了将酵母的产油表型与蛋白质功能联系起来，我们整合了脂质组学、氧化还原蛋白质组学和磷酸蛋白质组学，以研究在富氮和饥饿条件下随着时间推移的红酵母。我们的脂质组学结果揭示了鞘脂和心磷脂与内质网应激和线粒体自噬之间的相互作用。我们的氧化还原和磷酸蛋白质组学数据突出了AMPK、TOR和钙信号通路在脂肪生成、自噬和氧化应激反应调节中的作用。作为首次尝试，我们还证明了包括脂肪酸合酶在内的脂肪生成酶会因营养物质可用性导致的细胞氧化还原状态变化而被修饰。
我们得出结论，脂质积累在很大程度上是由翻译后修饰变化所控制的碳重新分配和自噬的结果，而不是参与中心碳代谢和脂肪酸生物合成的酶丰度增加的结果。我们的系统水平方法为获取用于蛋白质结构建模的多维数据集以及使用人工智能/机器学习（AI/ML）预测翻译后修饰的功能相关性奠定了基础。与这些生物信息学方法相结合，我们描绘的假定翻译后修饰开关将使先进的代谢工程策略能够将脂质积累与氮限制脱钩。
