Efficient Production of Chlorogenic Acid in Escherichia coli Via Modular Pathway and Cofactor Engineering

Enhanced chlorogenic acid production from glucose via systematic metabolic engineering of Saccharomyces cerevisiae

Chlorogenic acid (CGA) is a valuable phenolic acid with various pharmaceutical functions. In our previous study, de novo synthesis of CGA in Saccharomyces cerevisiae was achieved. However, its yield required improvement before large scale production. In this study, systematic metabolic engineering strategy was used to reconstruct chassis cell S. cerevisiae YC0707 to enhance its CGA yield from glucose. To balance the supply of phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P), ZWF1 (encoding glucose-6-phosphate dehydrogenase) and GND1 (encoding 6-phosphogluconate dehydrogenase) were overexpressed by strong promoter P TEF1 swapping, thereby strengthening the pentose phosphate pathway. The mutant of phosphofructokinase (PFK2 S718D ) was further introduced to weaken the glycolytic pathway. Then, the p-coumaric acid synthesis capacity was enhanced by employing tyrosine ammonia lyase from Rhodotorula glutinis (RgTAL), ΔHAM1, and ΔYJL028W. Fusion expression of AtC4H (cinnamate-4-hydroxylase) and At4CL1 (4-coumarate CoA ligase 1), together with CsHQT (hydroxycinnamoyl CoA quinate transferase) and AtC3'H (p-coumaroyl shikimate 3-hydroxylase), improved biosynthetic flux to CGA. Subsequently, the microenvironment of P450 enzymes was improved by overexpressing INO2 (a transcription factor for lipid biosynthesis) and removal of heme oxygenase gene HMX1. Furthermore, screening potential transporters to facilitate CGA accumulation. Finally, we optimized the fermentation conditions. Using these strategies, CGA titers increased from 234.8 mg/L to 837.2 mg/L in shake flasks and reached 1.62 g/L in a 5-L bioreactor, representing the highest report in S. cerevisiae and providing new insights for CGA production.

Efficient production of hydroxysalidroside in Escherichia coli via enhanced glycosylation and semi-rational design of UGT85A1

Hydroxysalidroside is an important natural phenylethanoid glycoside with broad application prospects in the food and pharmaceutical fields. However, its low concentration in plants and complex extraction hinder its production. Despite being a promising way to synthesize hydroxysalidroside in Escherichia coli, glycosylation remains the limiting factor for its production. A de novo biosynthetic pathway for hydroxysalidroside was successfully constructed in E. coli via the screening of glycosyltransferase, overexpressing phosphoglucomutase (pgm) and UDP-glucose pyrophosphorylase (galU) to ensure a sufficient supply of UDP-glucose (UDPG). Additionally, a semi-rational design of UGT85A1 was conducted to expand the acceptor-binding pocket to eliminate steric hindrance interfering with the binding of hydroxytyrosol. The endogenous genes ushA and otsA were knocked out to further reduce the consumption of UDPG. Finally, a titer of 5837.2 mg/L was achieved in a 5 L fermenter by optimizing the feeding times of carbon sources. This laid the foundation for the subsequent biosynthesis of phenylethanoid glycosides.

Efficient Synthesis of Vitamin B5 in Escherichia coli by Engineering Ketopantoate Hydroxymethyltransferase and Cofactor Supply

d-pantothenic acid (d-PA), also known as vitamin B5, is an essential precursor of coenzyme A and plays a crucial role in maintaining the physiological functions of organisms. Ketopantoate hydroxymethyltransferase (PanB), encoded by panB gene, serves as a key rate-limiting enzyme in d-PA synthesis. Additionally, the catalytic function of PanB requires the cofactor 5,10-methylenetetrahydrofolate (5,10-CH2-THF). This study aimed to increase d-PA production by engineering ketopantoate hydroxymethyltransferase and cofactor supply. The key transcription factor bhsA that restricts d-PA production was screened and identified through transcription factor engineering applications. Subsequently, PanB was coexpressed with PanC to regulate expression. Furthermore, the highly catalytic mutant PanBMV123I/K124W was generated through Km/Kcat algorithm prediction and enzyme engineering, leading to a 2.5-fold increase in d-PA production. The de novo synthesis pathway of 5,10-CH2-THF was enhanced, whereas its degradation pathway was suppressed to improve cofactor supply. Then, the extracellular transport of d-PA was enhanced by introducing the d-PA transporter PanT from Streptococcus intermedius. The plasmid-free strain DPA23 produced 78.48 g/L of d-PA in a 5-L bioreactor, with a productivity of 2.69 g/L/h after 24 h and a glucose yield of 0.54 g/g. These strategies provided a reference for constructing microbial cell factories for d-PA and its derivatives.

De Novo Biosynthesis of Chlorogenic Acid in Yarrowia lipolytica through Cis-Acting Element Optimization and NADPH Regeneration Engineering

Chlorogenic acid (CGA) is a natural hydroxycinnamic acid ester with significant applications in food preservation and nutritional health. However, extraction of CGA from plants is challenging, resulting in low purity that fails to meet increasing market demands. Furthermore, the broad substrate specificity of hydroxycinnamoyl-CoA:quinic acid transferase catalysis generating a plethora of byproducts, lack of NADPH regeneration, and the presence of degrading proteins impede microbial synthesis of CGA. This study achieved de novo synthesis of CGA in Yarrowia lipolytica by introducing hydroxylation and condensation modules based on screening synthetic pathway genes and optimizing parallel promoters. Additionally, an NADPH regeneration system was incorporated to enhance the efficiency of hydroxylation, thereby increasing the titer of CGA to 333.16 mg/L. From transcriptome data, 528 significantly upregulated genes were identified, and deletion of YALI0_B21824g significantly slowed the rate of CGA degradation, which increased the titer of CGA to 351.33 mg/L in shake flasks. Applying fed-batch fermentation in a 5 L bioreactor further increased CGA production to 4837.32 mg/L (64 mg/g DCW). This study established de novo synthesis of CGA in Y. lipolytica, providing a foundation for microbial production of coumaric acid and its derivatives.

Copper Sulfate Elicitation Effect on Biomass Production, Phenolic Compounds Accumulation, and Antioxidant Activity of Morus nigra L. Stem Node Culture

Phenolic compounds are strong antioxidant and antibacterial agents with great pharmacological, medicinal, nutritional, and industrial value. The potential of Morus nigra in stem node culture was investigated for the production of phenolic compounds and their elicitation with CuSO4. Individual phenolic compounds in the samples were identified and quantified by using HPLC-PDA and HPLC-MS methods, while the content of total phenolic compounds, the content of total flavonoids, and the antioxidant activity of methanolic extracts were evaluated spectrophotometrically. The highest fresh and dry weights were obtained in plantlets treated with 0.5 mM CuSO4 for 42 days. The highest total phenolic content, total flavonoid content, and antioxidant activity of the extracts were determined in stem node cultures treated with 3 mM CuSO4 for 42 days. Under the latter conditions, the predominant representatives of the caffeoylquinic acids, p-coumaric acid derivatives, kaempferol derivatives, and quercetin derivatives also achieved the highest content. The most abundant phenolic compound in all samples was the chlorogenic acid. The nodal culture of M. nigra elicited with CuSO4 could potentially be used for the industrial production of phenolic compounds, especially caffeoylquinic acids. Moreover, considering the biochemical response to CuSO4 treatment and the ability to tolerate and accumulate copper, the potential application of M. nigra in phytoremediation is also highlighted.

The Effect of Combined Elicitation with Light and Temperature on the Chlorogenic Acid Content, Total Phenolic Content and Antioxidant Activity of Berula erecta in Tissue Culture

Chlorogenic acid is one of the most prominent bioactive phenolic acids with great pharmacological, cosmetic and nutritional value. The potential of Berula erecta in tissue culture was investigated for the production of chlorogenic acid and its elicitation combined with light of different wavelengths and low temperature. The content of chlorogenic acid in the samples was determined by HPLC-UV, while the content of total phenolic compounds and the antioxidant activity of their ethanol extracts were evaluated spectrophotometrically. The highest fresh and dry biomasses were obtained in plants grown at 23 °C. This is the first study in which chlorogenic acid has been identified and quantified in Berula erecta. The highest chlorogenic acid content was 4.049 mg/g DW. It was determined in a culture grown for 28 days after the beginning of the experiment at 12 °C and under blue light. The latter also contained the highest content of total phenolic compounds, and its extracts showed the highest antioxidant activity. Berula erecta could, potentially, be suitable for the in vitro production of chlorogenic acid, although many other studies should be conducted before implementation on an industrial scale.

Self-controlled in silico gene knockdown strategies to enhance the sustainable production of heterologous terpenoid by Saccharomyces cerevisiae

Microbial bioengineering is a growing field for producing plant natural products (PNPs) in recent decades, using heterologous metabolic pathways in host cells. Once heterologous metabolic pathways have been introduced into host cells, traditional metabolic engineering techniques are employed to enhance the productivity and yield of PNP biosynthetic routes, as well as to manage competing pathways. The advent of computational biology has marked the beginning of a novel epoch in strain design through in silico methods. These methods utilize genome-scale metabolic models (GEMs) and flux optimization algorithms to facilitate rational design across the entire cellular metabolic network. However, the implementation of in silico strategies can often result in an uneven distribution of metabolic fluxes due to the rigid knocking out of endogenous genes, which can impede cell growth and ultimately impact the accumulation of target products. In this study, we creatively utilized synthetic biology to refine in silico strain design for efficient PNPs production. OptKnock simulation was performed on the GEM of Saccharomyces cerevisiae OA07, an engineered strain for oleanolic acid (OA) bioproduction that has been reported previously. The simulation predicted that the single deletion of fol1, fol2, fol3, abz1, and abz2, or a combined knockout of hfd1, ald2 and ald3 could improve its OA production. Consequently, strains EK1∼EK7 were constructed and cultivated. EK3 (OA07△fol3), EK5 (OA07△abz1), and EK6 (OA07△abz2) had significantly higher OA titers in a batch cultivation compared to the original strain OA07. However, these increases were less pronounced in the fed-batch mode, indicating that gene deletion did not support sustainable OA production. To address this, we designed a negative feedback circuit regulated by malonyl-CoA, a growth-associated intermediate whose synthesis served as a bypass to OA synthesis, at fol3, abz1, abz2, and at acetyl-CoA carboxylase-encoding gene acc1, to dynamically and autonomously regulate the expression of these genes in OA07. The constructed strains R_3A, R_5A and R_6A had significantly higher OA titers than the initial strain and the responding gene-knockout mutants in either batch or fed-batch culture modes. Among them, strain R_3A stand out with the highest OA titer reported to date. Its OA titer doubled that of the initial strain in the flask-level fed-batch cultivation, and achieved at 1.23 ± 0.04 g L-1 in 96 h in the fermenter-level fed-batch mode. This indicated that the integration of optimization algorithm and synthetic biology approaches was efficiently rational for PNP-producing strain design.

High-Level Biosynthesis of Chlorogenic Acid from Mixed Carbon Sources of Xylose and Glucose through a Rationally Refactored Pathway Network

Chlorogenic acid (CGA) has incredible potential for various pharmaceutical, nutraceutical, and agricultural applications. However, the traditional extraction approach from plants is time-consuming, further limiting its production. Herein, we design and construct the de novo biosynthesis pathway of CGA using modular coculture engineering in Escherichia coli, which is composed of MG09 and BD07 strains. To accomplish this, the phenylalanine-deficient MG09 strain was engineered to utilize xylose preferentially and to overproduce precursor caffeic acid, while the tyrosine-deficient BD07 strain was constructed to consume glucose exclusively to enhance another precursor quinic acid availability for the biosynthesis of CGA. Further pathway modularization and balancing in the context of syntrophic cocultures resulted in additional production improvement. The coculture strategy avoids metabolic flux competition in the biosynthesis of two CGA precursors, caffeic acid and quinic acid, and allows for production improvement by balancing module proportions. Finally, the optimized coculture based on the aforementioned efforts produced 131.31 ± 7.89 mg/L CGA. Overall, the modular coculture engineering strategy in this study provides a reference for constructing microbial cell factories that can efficiently biomanufacture complex natural products.