Cyclodextrins facilitate the efficient secretion of an anti-tumor triterpenoid ganoderic acid HLDOA by Saccharomyces cerevisiae

Machine Learning-Guided Selection of Cyclodextrins for Enhanced Biosynthesis and Capture of Volatile Terpenes

Nootkatone and limonene are valuable volatile organic compounds (VOCs), but their biosynthetic production is hindered by volatility. This study employed machine learning to guide cyclodextrin (CD) selection for encapsulating these VOCs, with a focus on nootkatone capture during fermentation to prevent losses and potentially replace dodecane as an organic solvent extractant. A LightGBM model accurately predicted complexation free energies (ΔG) between CDs and guest molecules (R2 = 0.80 on a 10% test set, with a mean absolute error of 1.31 kJ/mol and a root-mean-squared error of 1.90 kJ/mol). Experimental ranking of 7 CD types validated the model's ΔG predictions and encapsulation performance rankings. Nootkatone showed high encapsulation efficiencies ranging from 21.29% (α-CD) to 88.41% (Me-β-CD), capturing 22.61-116.71 mg/g CD. Notably, Hp-γ-CD, which is the least studied or used CD in research, performed well with nootkatone (63.64%, 84.01 mg/g CD) despite model discrepancies. For limonene, encapsulation efficiencies spanned from 0.62% (Hp-γ-CD) to 55.45% (β-CD), with 0.61-84.28 mg/g CD encapsulated. Constructed engineered Saccharomyces cerevisiae strains produced nootkatone (up to 97.30 mg/L captured by 10 mM Me-β-CD) from de novo fermentation using glucose as a carbon source. This approach demonstrated the potential of CDs to replace dodecane as an organic solvent for terpene extraction during fermentation. The study highlights machine learning's potential for guiding CD selection to enhance volatile terpene biosynthesis, capture, and utilization during fermentation, offering a more environmentally friendly alternative to traditional organic solvent-based extraction methods.

Exploration of In Situ Extraction for Enhanced Triterpenoid Production by Saccharomyces cerevisiae

Plant-derived triterpenoids are in high demand due to their valuable applications in cosmetic, nutraceutical, and pharmaceutical industries. To meet this demand, microbial production of triterpenoids is being developed for large-scale production. However, a prominent limitation of microbial synthesis is the intracellular accumulation, requiring cell disruption during downstream processing. Destroying the whole-cell catalyst drives up production costs and limits productivity and product yield per cell. Here, in situ product extraction of triterpenoids into a second organic phase was researched to address this limitation. An organic solvent screening identified water-immiscible isopropyl myristate as a suitable in situ extractant, enabling extraction of up to 90% of total triterpenoids from engineered Saccharomyces cerevisiae. Combining isopropyl myristate and β-cyclodextrins improved extraction efficiency. In a first configuration, repeated batch fermentation with sequential product extraction and cell recycling resulted in 1.8 times higher production than a reference fermentation without in situ product extraction. In the second configuration, yeast cells were in contact with the second organic phase throughout a fed-batch fermentation to continuously extract triterpenoids. This resulted in 90% product extraction and an extended production phase. Further improvement of triterpenoid production was not achieved due to microbial host limitations uncovered through omics analyses.

Not all cytochrome b5s are created equal: How a specific CytB5 boosts forskolin biosynthesis in Saccharomyces cerevisiae

Cytochrome B5s, or CytB5s, are small heme-binding proteins, ubiquitous across all kingdoms of life that serve mainly as electron donors to enzymes engaged in oxidative reactions. They often function as redox partners of the cytochrome P450s (CYPs), a superfamily of enzymes participating in multiple biochemical processes. In plants, CYPs catalyze key reactions in the biosynthesis of plant specialized metabolites with their activity dependent on electron donation often from cytochrome P450 oxidoreductases (CPRs or PORs). In eukaryotic microsomal CYPs, CytB5s frequently participate in the electron transfer process although their exact role remains understudied, especially in plant systems. In this study, we assess the role of CytB5s in the heterologous biotechnological production of plant specialized metabolites in yeast. For this, we used as a case-study the biosynthesis of forskolin - a bioactive diterpenoid produced exclusively from the plant Coleus forskohlii. The complete biosynthetic pathway for forskolin is known and includes three CYP enzymes. We reconstructed the entire forskolin pathway in the yeast Saccharomyces cerevisiae, and upon co-expression of the three CytB5s - identified in C. forskohlii transcriptomes - alleviation of a CYP-related bottleneck step was noticed only when a specific CytB5, CfCytB5A, was used. Co-expression of CfCytB5A in yeast, in combination with forskolin pathway engineering, resulted in forskolin production at titers of 1.81 g/L in a bioreactor. Our findings demonstrate that CytB5s not only play an important role in plant specialized metabolism but also, they can interact with precision with specific CYPs, indicating that the properties of CytB5s are far from understood. Moreover, our work highlights how CytB5s may act as indispensable components in the sustainable microbial production of plant metabolites, when their biosynthetic pathways involve CYP enzymes.

Efficient Secretory Production of δ-Tocotrienol by Combining Pathway Modularization and Transportation Engineering

The vitamin E component δ-tocotrienol has shown impressive activities in radioprotection, neuroprotection, and cholesterol reduction. Its production is limited by the low content in plants and difficulty in separation from other tocotrienols. Fermentative production using a microbial cell factory that exclusively produces and secretes δ-tocotrienol is a promising alternative approach. Assembly of the δ-tocotrienol synthetic pathway in Saccharomyces cerevisiae followed by comprehensive pathway engineering led to the production of 73.45 mg/L δ-tocotrienol. Subsequent addition of 2-hydroxypropyl-β-cyclodextrin (CD) and overexpression of the transcription factor PDR1 significantly elevated δ-tocotrienol titer to 241.7 mg/L (63.65 mg/g dry cell weight) in shake flasks, with 30.4% secreted. By properly adding CD and the in situ extractant olive oil, 181.12 mg/L of δ-tocotrienol was collected as an extracellular product, accounting for 85.6% of the total δ-tocotrienol production. This process provides not only a promising δ-tocotrienol cell factory but also insights into yeast engineering toward secretory production of other terpenoids.

The Aspartic Protease Yps3p and Cell Wall Glucanase Scw10p Are Novel Determinants That Enhance the Secretion of the Antitumor Triterpenoid GA-HLDOA in Saccharomyces cerevisiae

Efficient bioproduction of triterpenoids is gaining increasing interest because of their significant biological applications; however, the secretion and bioproduction of triterpenoids are hindered by untapped genetic determinants. In our previous study, we observed that different engineered Saccharomyces cerevisiae strains exhibit different abilities for secreting the antitumor triterpenoid ganoderic acid 3-hydroxy-lanosta-8,24-dien-26-oic acid (GA-HLDOA). In the present study, we performed comparative proteomics analyses of the engineered strains and identified two genes, encoding an aspartic protease, YPS3, and a cell wall glucanase, SCW10, as the most effective determinants that enhance the secretion of GA-HLDOA. Compared with this control strain, strain BJ5464-r demonstrated an overexpression of YPS3 and SCW10 resulting in 3.9-fold and 4.7-fold higher secretion of GA-HLDOA, respectively, and these increases were accompanied by an increase in cell permeability. Moreover, compared with the YPS3-overexpressing strain, the SCW10-overexpressing strain had a thinner outer mannan layer. Our findings offer valuable insights into designing microbial cell factories for the efficient secretion of triterpenoids.

Recent advances in construction and regulation of yeast cell factories

The past decade has witnessed the rapid progress in development of synthetic biology, and advances in construction of yeast cell factories open vast opportunities for green and sustainable production of chemicals. Focusing on the progress in yeast engineering for production of plant natural products in the last 5 years, this review introduces different yeast chassis used for cell factory construction, including Saccharomyces cerevisiae, Yarrowia lipolytica and Komagataella phaffii, together with the emerging genome editing tools. The metabolic regulation strategies developed for yeast engineering are highlighted, such as subcellular pathway localization dynamic regulation, and transporter engineering. C1-based chemical bioproduction by engineered yeast is also covered. Finally, the existing challenges and future prospects in creating efficient yeast cell factories are summarized.

The Role of Cyclodextrins in the Design and Development of Triterpene-Based Therapeutic Agents

Triterpenic compounds stand as a widely investigated class of natural compounds due to their remarkable therapeutic potential. However, their use is currently being hampered by their low solubility and, subsequently, bioavailability. In order to overcome this drawback and increase the therapeutic use of triterpenes, cyclodextrins have been introduced as water solubility enhancers; cyclodextrins are starch derivatives that possess hydrophobic internal cavities that can incorporate lipophilic molecules and exterior surfaces that can be subjected to various derivatizations in order to improve their biological behavior. This review aims to summarize the most recent achievements in terms of triterpene:cyclodextrin inclusion complexes and bioconjugates, emphasizing their practical applications including the development of new isolation and bioproduction protocols, the elucidation of their underlying mechanism of action, the optimization of triterpenes’ therapeutic effects and the development of new topical formulations.