Systematic Engineering to Enhance 8-Hydroxygeraniol Production in Yeast

Multiplexed engineering of cytochrome P450 enzymes for promoting terpenoid synthesis in Saccharomyces cerevisiae cell factories: A review

Terpenoids, also known as isoprenoids, represent the largest and most structurally diverse family of natural products, and their biosynthesis is closely related to cytochrome P450 enzymes (P450s). Given the limitations of direct extraction from natural resources, such as low productivity and environmental concerns, heterologous expression of P450s in microbial cell factories has emerged as a promising, efficient, and sustainable strategy for terpenoid production. The yeast expression system is a preferred selection for terpenoid synthesis because of its inner membrane system, which is required for eukaryotic P450 expression, and the inherent mevalonate pathway providing precursors for terpenoid synthesis. In this review, we discuss the advanced strategies used to enhance the local enzyme concentration and catalytic properties of P450s in Saccharomyces cerevisiae, with a focus on recent developments in metabolic and protein engineering. Expression enhancement and subcellular compartmentalization are specifically employed to increase the local enzyme concentration, whereas cofactor, redox partner, and enzyme engineering are utilized to improve the catalytic efficiency and substrate specificity of P450s. Subsequently, we discuss the application of P450s for the pathway engineering of terpenoid synthesis and whole-cell biotransformation, which are profitable for the industrial application of P450s in S. cerevisiae chassis. Finally, we explore the potential of using computational and artificial intelligence technologies to rationally design and construct high-performance cell factories, which offer promising pathways for future terpenoid biosynthesis.

Efficient nepetalactone production in Saccharomyces cerevisiae via metabolic engineering and bioprocess optimization

Nepetalactone, a natural insect repellent comparable to N,N-diethyl-meta-toluamide (DEET), is challenging to produce through plant extraction or chemical synthesis. This study achieved the de novo synthesis of nepetalactone in Saccharomyces cerevisiae without expensive precursors or inducers. Initially, the metabolic pathway for nepetalactone synthesis was successfully established in Saccharomyces cerevisiae. A metabolic pathway was established using strategies such as iridoid synthase (ISY) source screening, enzyme fusion, and cofactor regeneration to optimize nepetalactone production. Bioprocess optimization through chromosomal integration and two-phase fermentation prevented its conversion to dihydronepetalactone, resulting in a high-yield strain, NTE21, with a titer of 2.5 g/L. A record titer of 4.5 g/L was achieved in 5.0 L fed-batch fermentation via continuous batch feeding. This study documents the potential of microbial platforms for the sustainable, cost-effective, and scalable production of nepetalactone, paving the way for its commercial application as a natural insect repellent.

Orchestrating multiple subcellular organelles of Saccharomyces cerevisiae for efficient production of squalene

Squalene widely used in medicines, food, and cosmetics. Subcellular organelle engineering is an effective way to develop squalene-hyperproducing yeasts. Here, we demonstrated that synergistically modifying multiple organelles in Saccharomyces cerevisiae, including mitochondria, endoplasmic reticulum (ER), lipid droplets (LDs), and cell wall (CW), effectively increased squalene production. Based on the previously developed dual cytoplasmic-mitochondrial engineering strain SquMC13, squalene production capacity was further enhanced by improving the ER function for protein expression, expanding the LDs size for squalene storage, and increasing CW integrity to maintain high cell viability. Combinatorial modification of these organelles enhanced squalene productivity to 3.4-times that of SquMC13. NADPH generation was optimized, resulting in a further 3.9 % increase in squalene production. An efficient strain for squalene production was developed, the squalene production titer of which reached 55.8 g/L with 0.5 g/L/h productivity and specific cell production of 0.5 g/g dry cell weight, paving the way for industrial squalene production.

De novo biosynthesis of mogroside V by multiplexed engineered yeasts

High sugar intake has become a global health concern due to its association with various diseases. Mogroside V (MG-V), a zero-calorie sweetener with multiple medical properties, is emerging as a promising sugar substitute. However, its application is hindered by low natural abundance and the inefficiency of conventional plant extraction methods. In this study, two glycosyltransferases were introduced into an engineered mogrol-producing Saccharomyces cerevisiae strain to enable the first de novo MG-V biosynthesis. Then, MG-V titer increased by 2.3 × 104-fold through a series of efficient metabolic engineering strategies, including the enhancement of precursors, inhibition of the competitive pathway, and prevention of MG-V degradation. The challenges of enzyme spatial separation and high protein folding stress were addressed through lipid droplet (LD) compartmentalization and endoplasmic reticulum expansion, respectively. The ty1 transposon was employed to increase the copies of LD-targeted fusion protein AtCPR2-CYP87D18, which possessed higher CYP450 catalytic efficiency, resulting in an MG-V titer of 10.25 mg/L in shake flasks and 28.62 mg/L in a 5-L bioreactor. Overall, this study realized de novo MG-V synthesis in S. cerevisiae for the first time and provided a valuable reference for constructing microbial factories for triterpenoid saponin synthesis.

Extending the G1 phase improves the production of lipophilic compounds in yeast by boosting enzyme expression and increasing cell size

Cell phase engineering can significantly impact protein synthesis and cell size, potentially enhancing the production of lipophilic products. This study investigated the impact of G1 phase extension on resource allocation, metabolic functions, and the unfolded protein response (UPR) in yeast, along with the potential for enhancing the production of lipophilic compounds. In brief, the regulation of the G1 phase was achieved by deleting CLN3 (G1 cyclin) in various yeast strains. This modification resulted in a 83% increase in cell volume, a 76.9% increase in dry cell weight, a 82% increase in total protein content, a 41% increase in carotenoid production, and a 159% increase in fatty alcohol production. Transcriptomic analysis revealed significant upregulation of multiple metabolic pathways involved in acetyl-CoA (acetyl coenzyme A) synthesis, ensuring an ample supply of precursors for the synthesis of lipophilic products. Furthermore, we observed improved protein synthesis, attributed to UPR activation during the prolonged G1 phase. These findings not only enhanced our understanding and application of yeast's capacity to synthesize lipophilic compounds in applied biotechnology but also offered unique insights into cellular behavior during the modified G1 phase, particularly regarding the UPR response, for basic research. This study demonstrates the potential of G1 phase intervention to increase the yield of hydrophobic compounds in yeast, providing a promising direction for further research.

Systematic metabolic engineering enables highly efficient production of vitamin A in Saccharomyces cerevisiae

Vitamin A is a micronutrient critical for versatile biological functions and has been widely used in the food, cosmetics, pharmaceutical, and nutraceutical industries. Synthetic biology and metabolic engineering enable microbes, especially the model organism Saccharomyces cerevisiae (generally recognised as safe) to possess great potential for the production of vitamin A. Herein, we first generated a vitamin A-producing strain by mining β-carotene 15,15'-mono(di)oxygenase from different sources and identified two isoenzymes Mbblh and Ssbco with comparable catalytic properties but different catalytic mechanisms. Combinational expression of isoenzymes increased the flux from β-carotene to vitamin A metabolism. To modulate the vitamin A components, retinol dehydrogenase 12 from Homo sapiens was introduced to achieve more than 90 % retinol purity using shake flask fermentation. Overexpressing POS5Δ17 enhanced the reduced nicotinamide adenine dinucleotide phosphate pool, and the titer of vitamin A was elevated by almost 46 %. Multi-copy integration of the key rate-limiting step gene Mbblh further improved the synthesis of vitamin A. Consequently, the titer of vitamin A in the strain harbouring the Ura3 marker was increased to 588 mg/L at the shake-flask level. Eventually, the highest reported titer of 5.21 g/L vitamin A in S. cerevisiae was achieved in a 1-L bioreactor. This study unlocked the potential of S. cerevisiae for synthesising vitamin A in a sustainable and economical way, laying the foundation for the commercial-scale production of bio-based vitamin A.

Metabolic engineering of Pichia pastoris for overproduction of cis-trans nepetalactol

Monoterpene indole alkaloids (MIAs) are a group of plant-derived natural products with high-value medicinal properties. However, their availability for clinical application is limited due to challenges in plant extraction. Microbial production has emerged as a promising strategy to meet the clinical demands for MIAs. The biosynthetic pathway of cis-trans nepetalactol, which serves as the universal iridoid scaffold for all MIAs, has been successfully identified and reconstituted. However, bottlenecks and challenges remain to construct a high-yielding platform strain for cis-trans nepetalactol production, which is vital for subsequent MIAs biosynthesis. In the present study, we focused on engineering of Pichia pastoris cell factories to enhance the production of geraniol, 8-hydroxygeraniol, and cis-trans nepetalactol. By targeting the biosynthetic pathway from acetyl-CoA to geraniol in both peroxisomes and cytoplasm, we achieved comparable geraniol titers in both compartments. Through protein engineering, we found that either G8H or CPR truncation increased the production of 8-hydroxygeraniol, with a 47.8-fold and 14.0-fold increase in the peroxisomal and cytosolic pathway strain, respectively. Furthermore, through a combination of dynamical control of ERG20, precursor and cofactor supply engineering, diploid engineering, and dual subcellular compartmentalization engineering, we achieved the highest ever reported production of cis-trans nepetalactol, with a titer of 4429.4 mg/L using fed-batch fermentation in a 5-L bioreactor. We anticipate our systematic metabolic engineering strategies to facilitate the development of P. pastoris cell factories for sustainable production of MIAs and other plant natural products.

Systems Metabolic Engineering for Efficient Violaxanthin Production in Yeast

Violaxanthin is a plant-derived orange xanthophyll with remarkable antioxidant activity that has wide applications in various industries, such as food, agriculture, and cosmetics. In addition, it is the key precursor of important substances such as abscisic acid and fucoxanthin. Saccharomyces cerevisiae, as a GRAS (generally regarded as safe) chassis, provides a good platform for producing violaxanthin production with a yield of 7.3 mg/g DCW, which is far away from commercialization. Herein, an integrated strategy involving zeaxanthin epoxidase (ZEP) source screening, cytosol redox state engineering, and nicotinamide adenine dinucleotide phosphate (NADPH) regeneration was implemented to enhance violaxanthin production in S. cerevisiae. 58aa-truncated ZEP from Vitis vinifera exhibited optimal efficiency in an efficient zeaxanthin-producing strain. The titer of violaxanthin gradually increased by 17.9-fold (up to 119.2 mg/L, 15.19 mg/g DCW) via cytosol redox state engineering and NADPH supplementation. Furthermore, balancing redox homeostasis considerably improved the zeaxanthin concentration by 139.3% (up to 143.9 mg/L, 22.06 mg/g DCW). Thus, the highest reported titers of violaxanthin and zeaxanthin in S. cerevisiae were eventually achieved. This study not only builds an efficient platform for violaxanthin biosynthesis but also serves as a useful reference for the microbial production of xanthophylls.

Genome-Wide Mining of CULLIN E3 Ubiquitin Ligase Genes from Uncaria rhynchophylla

CULLIN (CUL) protein is a subtype of E3 ubiquitin ligase that is involved in a variety of biological processes and responses to stress in plants. In Uncaria rhynchophylla, the CUL gene family has not been identified and its role in plant development, stress response and secondary metabolite synthesis has not been studied. In this study, 12 UrCUL gene members all contained the typical N-terminal domain and C-terminal domain identified from the U. rhynchophylla genome and were classified into four subfamilies based on the phylogenetic relationship with CULs in Arabidopsis thaliana. They were unevenly distributed on eight chromosomes but had a similar structural composition in the same subfamily, indicating that they were relatively conserved and potentially had similar gene functions. An interspecific and intraspecific collinearity analysis showed that fragment duplication played an important role in the evolution of the CUL gene family. The analysis of the cis-acting elements suggests that the UrCULs may play an important role in various biological processes, including the abscisic acid (ABA) response. To investigate this hypothesis, we treated the roots of U. rhynchophylla tissue-cultured seedlings with ABA. The expression pattern analysis showed that all the UrCUL genes were widely expressed in roots with various expression patterns. The co-expression association analysis of the UrCULs and key enzyme genes in the terpenoid indole alkaloid (TIA) synthesis pathway revealed the complex expression patterns of 12 UrCUL genes and some key TIA enzyme genes, especially UrCUL1, UrCUL1-likeA, UrCUL2-likeA and UrCUL2-likeB, which might be involved in the biosynthesis of TIAs. The results showed that the UrCULs were involved in the response to ABA hormones, providing important information for elucidating the function of UrCULs in U. rhynchophylla. The mining of UrCULs in the whole genome of U. rhynchophylla provided new information for understanding the CUL gene and its function in plant secondary metabolites, growth and development.

Genome-wide identification of GATA transcription factor family and the effect of different light quality on the accumulation of terpenoid indole alkaloids in Uncaria rhynchophylla

Uncaria rhynchophylla is an evergreen vine plant, belonging to the Rubiaceae family, that is rich in terpenoid indole alkaloids (TIAs) that have therapeutic effects on hypertension and Alzheimer's disease. GATA transcription factors (TF) are a class of transcription regulators that participate in the light response regulation, chlorophyll synthesis, and metabolism, with the capability to bind to GATA cis-acting elements in the promoter region of target genes. Currently the charactertics of GATA TFs in U. rhynchophylla and how different light qualities affect the expression of GATA and key enzyme genes, thereby affecting the changes in U. rhynchophylla alkaloids have not been investigated. In this study, 25 UrGATA genes belonging to four subgroups were identified based on genome-wide analysis. Intraspecific collinearity analysis revealed that only segmental duplications were identified among the UrGATA gene family. Collinearity analysis of GATA genes between U. rhynchophylla and four representative plant species, Arabidopsis thaliana, Oryza sativa, Coffea Canephora, and Catharanthus roseus was also performed. U. rhynchophylla seedlings grown in either red lights or under reduced light intensity had altered TIAs content after 21 days. Gene expression analysis reveal a complex pattern of expression from the 25 UrGATA genes as well as a number of key TIA enzyme genes. UrGATA7 and UrGATA8 were found to have similar expression profiles to key enzyme TIA genes in response to altered light treatments, implying that they may be involved in the regulation TIA content. In this research, we comprehensively analyzed the UrGATA TFs, and offered insight into the involvement of UrGATA TFs from U. rhynchophylla in TIAs biosynthesis.

The construction and optimization of engineered yeast chassis for efficient biosynthesis of 8-hydroxygeraniol

Microbial production of monoterpenoid indole alkaloids (MIAs) provides a sustainable and eco-friendly means to obtain compounds with high pharmaceutical values. However, efficient biosynthesis of MIAs in heterologous microorganisms is hindered due to low supply of key precursors such as geraniol and its derivative 8-hydroxygeraniol catalyzed by geraniol 8-hydroxylase (G8H). In this study, we developed a facile evolution platform to screen strains with improved yield of geraniol by using the SCRaMbLE system embedded in the Sc2.0 synthetic yeast and confirmed the causal role of relevant genomic targets. Through genome mining, we identified several G8H enzymes that perform much better than the commonly used CrG8H for 8-hydroxygeraniol production in vivo. We further showed that the N-terminus of these G8H enzymes plays an important role in cellular activity by swapping experiments. Finally, the combination of the engineered chassis, optimized biosynthesis pathway, and utilization of G8H led to the final strain with more than 30-fold improvement in producing 8-hydroxygeraniol compared with the starting strain. Overall, this study will provide insights into the construction and optimization of yeast cells for efficient biosynthesis of 8-hydroxygeraniol and its derivatives.