Systematic metabolic engineering of Yarrowia lipolytica for the enhanced production of erythritol

Metabolic engineering combined with fermentation optimization enables sustainable production of erythritol by Yarrowia lipolytica from peanut meal and glucose

Peanut meal (PM) is rich in proteins and fatty acids, which enables it to be a valuable substrate for microbial growth. This study aimed to investigate the effect of PM on the growth and erythritol production of Yarrowia lipolytica CA20 and to establish a procedure for low-cost erythritol production using PM. We found that PM could be used as the only medium component, except for glucose, to support cell growth and erythritol production during submerged fermentation. After optimization of medium compositions and growth conditions, erythritol of 125.25 ± 4.8 g/L was obtained after fermentation for 144 h in a 3.7-L bioreactor, with a yield of 0.69 ± 0.03 g/g. Transcriptome analysis showed that the enhanced erythritol production by CA20 was associated with an increased activity of the metabolism of carbohydrates, amino acids, and lipids. Condition optimization elevated the activity of glucose-6-phosphate dehydrogenase (ZWF1) and phosphogluconate dehydrogenase (GND1) involved in erythritol synthesis. Moreover, hyphal formation of Y. lipolytica was completely inhibited in medium with PM. Besides, A002891 and A001489 were identified to be the key genes associated with erythritol production. Finally, a robust strain, Yarrowia lipolytica CE1, was constructed by deletion of A002891 combined with overexpression of A001489 in CA20, which was able to produce erythritol of 168.78 ± 10 g/L within 108 h from PM and glucose, with a yield of 0.73 ± 0.05 g/g. Collectively, this study provides a valuable way for economical erythritol production and a high-value-added conversion of PM.

Synergistic effect of transporter and pathway engineering on the key performance indicators of erythritol synthesis by the yeast Yarrowia lipolytica

Erythritol, a food additive, is produced on an industrial scale using the yeast Yarrowia lipolytica. Nevertheless, the key performance indicators (KPIs) have been found to be unsatisfactory, resulting in elevated erythritol production cost. This study demonstrated that the KPIs (titer, productivity, and yield) of erythritol can be improved by the synergistic application of transporter and pathway engineering strategies in the producing strain. The engineered Y. lipolytica strain Ylxs48 exhibits a glucose consumption rate of 310 g/L of glucose within 46 h during batch culture in 3, 100, and 200 L bioreactors as compared to above 72 h for the parental strain Ylxs01. The erythritol yield achieved ranges from 0.69 to 0.74 g/g depending on the culture conditions as compared to 0.55-0.57 g/g for the parental strain Ylxs01. The productivity surpasses 4.60 g/(L·h), representing a 1.91-fold improvement over the parental strain Ylxs01 in 3, 100, or 200 L bioreactors. Under fed-batch conditions in a 200 L bioreactor, an erythritol titer of 355.81 g/L was achieved, marking the highest titer ever reported. This increased erythritol titer enabled crystallization at 4°C directly from the clear supernatant, eliminating the requirement for evaporation or concentration steps. A comprehensive techno-economic analysis of the entire process conclusively demonstrated that implementing the industrial process based on the engineered strain Ylxs48 led to a significant 23% reduction in production cost. This approach holds the potential to substantially reduce erythritol costs and provides novel insights for engineering other industrial strains.

IMPORTANCE

The expansion of the erythritol market attracted excessive capital injection, resulting in overcapacity, operational difficulties, and even bankruptcy of erythritol manufacturers. Technology upgrades in the industry are imminent. However, the production technology of existing enterprises is seriously homogenized, and there is a lack of competitive core-producing strains. In this study, the industrial erythritol-producing strain Y. lipolytica CGMCC7326 was genetically modified by integrating substrate transport and pathway modification, which improved the conversion of glucose and significantly improved KPIs, thereby reducing the erythritol production cost.

Metabolic engineering of the oleaginous yeast Yarrowia lipolytica for 2-phenylethanol overproduction

The rose fragrance molecule 2-phenylethanol (2-PE) has huge market demand in the cosmetics, food and pharmaceutical industries. However, current 2-PE synthesis methods do not meet the efficiency market requirement. In this study, CRISPR-Cas9-related metabolic engineering strategies were applied to Yarrowia lipolytica for the de novo biosynthesis of 2-PE. Initially, overexpressing exogenous feedback-resistant EcAROGfbr and EcPheAfbr increased 2-PE production to 276.3 mg/L. Subsequently, the ylARO10 and ylPAR4 from endogenous genes were enhanced with the multi-copies to increase the titer to 605 mg/L. Knockout of ylTYR1 and enhancement of shikimate pathway by removing the precursor metabolic bottleneck and overexpressing the genes ylTKT, ylARO1, and ylPHA2 resulted in a significant increase of the 2-PE titer to 2.4 g/L at 84 h, with the yield of 0.06 g/gglu, which is the highest yield for de novo synthesis in yeast. This study provides a valuable precedent for the efficient biosynthesis of shikimate pathway derivatives.

Multidimensional combinatorial screening for high-level production of erythritol in Yarrowia lipolytica

Yarrowia lipolytica was successfully engineered to synthesize erythritol from crude glycerol, a cheap by-product of biodiesel production, but the yield remained low. Here, a biosensor-guided adaptive evolution screening platform was constructed to obtain mutant strains which could efficiently utilize crude glycerol to produce erythritol. Erythrose reductase D46A (M1) was identified as a key mutant through whole-genome sequencing of the strain G12, which exhibited higher catalytic activity (1.6-fold of the wild-type). M1 was further modified to obtain a combinatorial mutant with 4.1-fold enhancement of catalytic activity. Finally, the metabolic network was reconfigured to redirect carbon fluxes toward erythritol synthesis. The erythritol titer of the engineered strain G31 reached 220.5 g/L with a productivity of 1.8 g/L/h in a 5-L bioreactor. The study provides valuable guidance for biosensor-based ultra-high-throughput screening strategies in Y. lipolytica, as well as presenting a new paradigm for the sustainable valorization of crude glycerol.

Research progress on biosynthesis of erythritol and multi-dimensional optimization of production strategies

Erythritol, as a new type of natural sweetener, has been widely used in food, medical, cosmetics, pharmaceutical and other fields due to its unique physical and chemical properties and physiological functions. In recent years, with the continuous development of strategies such as synthetic biology, metabolic engineering, omics-based systems biology and high-throughput screening technology, people's understanding of the erythritol biosynthesis pathway has gradually deepened, and microbial cell factories with independent modification capabilities have been successfully constructed. In this review, the cheap feedstocks for erythritol synthesis are introduced in detail, the environmental factors affecting the synthesis of erythritol and its regulatory mechanism are described, and the tools and strategies of metabolic engineering involved in erythritol synthesis are summarized. In addition, the study of erythritol derivatives is helpful in expanding its application field. Finally, the challenges that hinder the effective production of erythritol are discussed, which lay a foundation for the green, efficient and sustainable production of erythritol in the future and breaking through the bottleneck of production.

Metabolic engineering of Yarrowia lipolytica for high-level production of squalene

Squalene is an important triterpene with a wide range of applications. Given the growing market demand for squalene, the development of microbial cell factories capable of squalene production is considered a sustainable method. This study aimed to investigate the squalene production potential of Yarrowia lipolytica. First, HMG-CoA reductase from Saccharomyces cerevisiae and squalene synthase from Y. lipolytica was co-overexpressed in Y. lipolytica. Second, by enhancing the supply of NADPH in the squalene synthesis pathway, the production of squalene in Y. lipolytica was effectively increased. Furthermore, by constructing an isoprenol utilization pathway and overexpressing YlDGA1, the strain YLSQ9, capable of producing 868.1 mg/L squalene, was obtained. Finally, by optimizing the fermentation conditions, the highest squalene concentration of 1628.2 mg/L (81.0 mg/g DCW) in Y. lipolytica to date was achieved. This study demonstrated the potential for achieving high squalene production using Y. lipolytica.