Data for: Substitute yeast extract while maintaining performance: showcase amorpha-4,11-diene production

The DaRUS repository contains the raw data corresponding to the figures of the manuscript "Substitute yeast extract while maintaining performance: showcase amorpha-4,11-diene production". Yeast extract (YE) is a complex nutritional source associated with high performance on microbial production processes. However, its inherent compositional variability challenges its scalability. While prior efforts have focused on growth-associated products, the dynamics of growth-uncoupled production, which leads to higher production rates and conversion yields, still need to be explored. This production scenario is common in large-scale applications. This study presents a systematic approach to replace YE for the production of the terpene amorpha-4,11-diene in Escherichia coli. Sequential processing was successfully applied to identify glutamic acid, alanine, leucine, valine, isoleucine, and glycine as the key amino acids (AAs) under slow growth conditions. Thoroughly applying biomass retention as part of sequential processing increased production capacity by 45% using these AAs instead of YE. Further studies, including flux balance analyses, targeted pyruvate as the common AA precursor. The optimized fed-batch process feeding pyruvate with 0.09 gPyr h-1 enhanced amorpha-4,11-diene production by 37 %, although adding only 1% carbon via pyruvate. Flux balance analysis revealed the criteria for optimum pyruvate feeding, e.g., to prevent succinate secretion and maintain the NADH/NAD+ balance. These findings illustrate the interplay between media composition and metabolic activity and provide a successful guideline for identifying lean, best-performing media for industrial applications.

DaRUS存储库包含与研究论文"Substitute yeast extract while maintaining performance: showcase amorpha-4,11-diene production"中各图表对应的原始实验数据。酵母提取物（Yeast Extract, YE）是一类复杂营养源，在微生物生产过程中常可助力实现优异的合成性能，但该原料本身的组分异质性对其规模化应用造成了阻碍。尽管此前的研究多聚焦于生长偶联型产物的合成，可实现更高生产速率与转化得率的生长非偶联生产过程的动态调控机制仍有待深入探究，而这类生产场景在大规模工业应用中十分常见。本研究开发了一套系统性方法，用于在大肠杆菌（Escherichia coli）中替换酵母提取物，以合成萜类（terpene）化合物紫穗槐-4,11-二烯（amorpha-4,11-diene）。研究人员通过序贯分析流程，成功筛选出在缓慢生长条件下的关键氨基酸（AAs）：谷氨酸、丙氨酸、亮氨酸、缬氨酸、异亮氨酸与甘氨酸。在序贯分析流程中引入完整的菌体保留策略后，使用上述氨基酸替代酵母提取物时，产物合成能力提升了45%。后续研究通过通量平衡分析（Flux Balance Analysis），确定丙酮酸为氨基酸合成的共同前体物质。优化后的补料分批发酵工艺以0.09 gPyr h⁻¹的速率补加丙酮酸，尽管丙酮酸仅贡献了1%的总碳源，却使紫穗槐-4,11-二烯的产量提升了37%。通量平衡分析揭示了丙酮酸最优补加的调控准则，例如避免琥珀酸分泌、维持NADH/NAD+辅酶平衡等。本研究结果阐明了培养基组成与细胞代谢活性之间的相互作用关系，同时为工业应用中筛选高效精简型培养基提供了可行的参考范式。