Microbial synthesis of the plant natural product precursor p-coumaric acid with Corynebacterium glutamicum

Combined metabolic and enzymatic engineering for de novo biosynthesis of δ-tocotrienol in Yarrowia lipolytica

δ-Tocotrienol, an isomer of vitamin E with anti-inflammatory, neuroprotective and anti-coronary arteriosclerosis properties, is widely used in health care, medicine and other fields. Microbial synthesis of δ-tocotrienol offers significant advantages over plant extraction and chemical synthesis methods, including increased efficiency, cost-effectiveness and environmental sustainability. However, limited precursor availability and low catalytic efficiency of key enzymes remain major bottlenecks in the biosynthesis of δ-tocotrienol. In this study, we assembled the complete δ-tocotrienol biosynthetic pathway in Yarrowia lipolytica and enhanced the precursor supply, resulting in a titre of 102.8 mg/L. The catalytic efficiency of the rate-limiting steps in the pathway was then enhanced through various strategies, including fusion expression of key enzymes homogentisate phytyltransferaseand and tocopherol cyclase, semi-rational design of SyHPT and multi-copy integration of pathway genes. The final a δ-tocotrienol titre in a 5 L bioreactor was 466.8 mg/L following fed-batchfermentation. This study represents the first successful de novo biosynthesis of δ-tocotrienol in Y. lipolytica, providing valuable insights into the synthesis of vitamin E-related compounds.

Engineering the pH optimum of tyrosine ammonia lyase from Rhodobacter sphaeroides via computationally guided rational strategy

Tyrosine Ammonia Lyase (TAL) is a key enzyme used for the commercial production of p-coumaric acid. The currently known TAL enzymes encoded by diverse microbial species showed optimal activity at alkaline pH 9.0-10.5. However, efficient TAL variants that function at neutral pH are required to meet biorefinery demands. In this study, a computationally guided rational strategy was used to perform site-directed mutagenesis by decreasing negative charges on the surface residues and enhancing the positive charges near the active site of the TAL enzyme from the bacterium Rhodobacter sphaeroides. In total, 21 residues, including six near the active site and 15 on the enzyme's surface, were selected and subjected to site-directed mutagenesis. The mutants P68H, P9D, and P484E, demonstrated a pH optimal shift from 9.0 to 8.0 and increased activity by 0.8-, 4.8-, and 4.0-fold, respectively. These single optimal mutants were combined in different combinations (P9D/P68H, P9D/P484E, and P68H/P484E), and double mutants were designed. The double mutant P9D/P484E showed a shift in the pH from 9.0 to 7.0, with a 6-fold increase in the enzyme's activity at neutral pH. The double mutant (P9D/P484E) of the TAL enzyme from R. sphaeroides demonstrates potential for application in the industrial-scale production of p-coumaric acid.

Anthropogenic PFAS or Natural Products? Natural Products Cause Overestimation of C2-C5 Perfluoroalkyl Carboxylic Acid Levels

The increasing environmental concentrations of C2-C5 perfluoroalkyl carboxylic acids (PFCAs) have raised concerns about their global threat. However, analytical interference has been reported to cause overestimation of PFCA concentrations. Recently, we discovered that a human metabolite, γ-carboxyethyl hydroxychroman, caused overestimation of the perfluoropentanoic acid (PFPeA) concentration by 454 times due to its similar retention time and ion pair mass with those of PFPeA in low-resolution mass spectrometry. Using this interference mechanism, we developed a semitargeted screening method to identify all possible interferents of C2-C5 PFCAs in surface water, groundwater, wastewater, soil, fish, and human serum samples. Nine interferents were discovered, resulting in a 2.18-454 times overestimate of the concentration. Through the screening of 289 serum samples, most interferents were recognized as carboxylic acid natural products, possibly originating from human metabolism. Adjustment of the mobile phase to acidic or use of a pentafluorophenyl column can eliminate interferences. Retrospective screening against both 41 studies from 16 countries with significant concentrations of C2-C5 PFCAs and a public data repository revealed the global prevalence of analytical interferents. Our findings highlighted the necessity to re-evaluate the concentrations of C2-C5 PFCAs and subsequently their migration, transformation, and bioconcentration properties to accurately understand their environmental significance.

Expanding the application of tyrosine: engineering microbes for the production of tyrosine and its derivatives

Aromatic compounds are widely used in the fields of medicine, chemical industry, and food, with a considerable market size. Tyrosine, an aromatic amino acid, boasts not only a wide range of applications but also serves as a valuable precursor for synthesizing a diverse array of high-value aromatic compounds. Amid growing concerns over environmental and resource challenges, the adoption of green, clean, and sustainable biotechnology for producing aromatic compounds is gaining increasing recognition as a viable alternative to traditional chemical synthesis and plant extraction methods. This article provides an overview of the current status of tyrosine biomanufacturing and explores the methods for generating derivatives, including resveratrol, levodopa, p-coumaric acid, caffeic acid, zosteric acid, tyrosol, hydroxytyrosol, tanshinol, naringenin, eriodictyol, and salidroside, using tyrosine as a primary raw material. Furthermore, this review examines the current challenges and outlines future directions for microbial fermentation for the production of tyrosine and its derivatives.

p-Hydroxycinnamic Acids: Advancements in Synthetic Biology, Emerging Regulatory Targets in Gut Microbiota Interactions, and Implications for Animal Health

p-hydroxycinnamic acids (p-HCAs), a class of natural phenolic acid compounds extracted from plant resources and widely distributed, feature a C6-C3 phenylpropanoid structure. Their antioxidant, anti-inflammatory, and antibacterial activities have shown great potential for applications in food and animal feed. The interactions between p-HCAs and the gut microbiota, as well as their subsequent effects on animal health, have increasingly attracted the attention of researchers. In the context of a greener and safer future, the progress and innovation in biosynthetic technology have occupied a central position in ensuring the safety of food and feed. This review emphasizes the complex mechanisms underlying the interactions between p-HCAs and the gut microbiota, providing a solid explanation for the remarkable bioactivities of p-HCAs and their subsequent impact on animal health. Furthermore, it explores the advancements in the synthetic biology of p-HCAs. This review could aid in a basis for better understanding the underlying interactions between p-HCAs and gut microbiota and animal health.

Production of aromatic amino acids and their derivatives by Escherichia coli and Corynebacterium glutamicum

Demand for aromatic amino acids (AAAs), such as L-phenylalanine, L-tyrosine, and L-tryptophan, has been increasing as they are used in animal feed and as precursors in the synthesis of industrial and pharmaceutical compounds. These AAAs are biosynthesized through the shikimate pathway in microorganisms and plants, and the reactions in the AAA biosynthesis pathways are strictly regulated at the levels of both gene expression and enzyme activity. Various attempts have been made to produce AAAs and their derivatives using microbial cells and to optimize production. In this review, we summarize the metabolic pathways involved in the biosynthesis of AAAs and their regulation and review recent research on AAA production using industrial bacteria, such as Escherichia coli and Corynebacterium glutamicum. Studies on fermentative production of AAA derivatives, including L-3,4-dihydroxyphenylalanine, tyrosol, and 3-hydroxytyrosol, are also discussed.

Concatenating Microbial, Enzymatic, and Organometallic Catalysis for Integrated Conversion of Renewable Carbon Sources

The chemical industry can now seize the opportunity to improve the sustainability of its processes by replacing fossil carbon sources with renewable alternatives such as CO2, biomass, and plastics, thereby thinking ahead and having a look into the future. For their conversion to intermediate and final products, different types of catalysts-microbial, enzymatic, and organometallic-can be applied. The first part of this review shows how these catalysts can work separately in parallel, each route with unique requirements and advantages. While the different types of catalysts are often seen as competitive approaches, an increasing number of examples highlight, how combinations and concatenations of catalysts of the complete spectrum can open new roads to new products. Therefore, the second part focuses on the different catalysts either in one-step, one-pot transformations or in reaction cascades. In the former, the reaction conditions must be conflated but purification steps are minimized. In the latter, each catalyst can work under optimal conditions and the "hand-over points" should be chosen according to defined criteria like minimal energy usage during separation procedures. The examples are discussed in the context of the contributions of catalysis to the envisaged (bio)economy.

Metabolic engineering of Corynebacterium glutamicum: Unlocking its potential as a key cell factory platform for organic acid production

Corynebacterium glutamicum, a well-studied industrial model microorganism, has garnered widespread attention due to its ability for producing amino acids with a long history. In recent years, research efforts have been increasingly focused on exploring its potential for producing various organic acids beyond amino acids. Organic acids, which are characterized by their acidic functional groups, have diverse applications across industries such as food, agriculture, pharmaceuticals, and biobased materials. Leveraging advancements in metabolic engineering and synthetic biology, the metabolic pathways of C. glutamicum have been broadened to facilitate the production of numerous high-value organic acids. This review summarizes the recent progress in metabolic engineering for the production of both amino acids and other organic acids by C. glutamicum. Notably, these acids include, amino acids (lysine, isoleucine, and phenylalanine), TCA cycle-derived organic acids (succinic acid, α-ketoglutaric acid), aromatic organic acids (protocatechuate, 4-amino-3-hydroxybenzoic acid, anthranilate, and para-coumaric acid), and other organic acids (itaconic acid and cis, cis-muconic acid).

Drying of Saffron Petals as a Critical Step for the Stabilization of This Floral Residue Prior to Extraction of Bioactive Compounds

Saffron petals represent floral biomass generally wasted due to rapid deterioration. Previous characterization studies have revealed the presence of bioactive compounds in petals, such as flavonols and anthocyanins. Petal stabilization is a challenge for the efficient isolation of these compounds. This research evaluated three different drying techniques before the solid-liquid extraction of bioactive compounds: oven-drying (40 and 60 °C), lyophilization, and vacuum evaporation (25 and 50 °C). The characterization of the extracts allowed the annotation of 22 metabolites with a quantitative predominance of anthocyanins and derivatives of kaempferol and quercetin. Oven-drying at 60 °C was the most suitable approach for extracting minor compounds, such as crocins and safranal, at concentrations below 1 mg/g dry weight. Vacuum evaporation (50 °C) and lyophilization were the most recommended strategies for efficiently isolating flavonoids. Therefore, drying saffron petals is crucial to ensure the efficient extraction of bioactive compounds.

Rational and Semirational Approaches for Engineering Salicylate Production in Escherichia coli

Salicylate plays a pivotal role as a pharmaceutical intermediate in drugs, such as aspirin and lamivudine. The low catalytic efficiency of key enzymes and the inherent toxicity of salicylates to cells pose significant challenges to large-scale microbial production. In this study, we introduced the salicylate synthase Irp9 into an l-phenylalanine-producing Escherichia coli, constructing the shortest salicylate biosynthetic pathway. Subsequent protein engineering increased the catalytic efficiency of Irp9 by 33.5%. Furthermore, by integrating adaptive evolution with transcriptome analysis, we elucidated the crucial mechanism of efflux proteins in salicylate tolerance. The elucidation of this mechanism guided us in the targeted modification of these transport proteins, achieving a reported maximum level of 3.72 g/L of salicylate in a shake flask. This study highlights the importance of efflux proteins for enhancing the productivity of microbial cell factories in salicylate production, which also holds potential for application in the green synthesis of other phenolic acids.

Phytochemical Characterization and Antioxidant Activity Evaluation for Some Plant Extracts in Conjunction with Pharmacological Mechanism Prediction: Insights into Potential Therapeutic Applications in Dyslipidemia and Obesity

Lipid metabolism dysregulation can lead to dyslipidemia and obesity, which are major causes of cardiovascular disease and associated mortality worldwide. The purpose of the study was to obtain and characterize six plant extracts (ACE-Allii cepae extractum; RSE-Rosmarini extractum; CHE-Cichorii extractum; CE-Cynarae extractum; AGE-Apii graveolentis extractum; CGE-Crataegi extractum) as promising adjuvant therapies for the prevention and treatment of dyslipidemia and its related metabolic diseases. Phytochemical screening revealed that RSE was the richest extract in total polyphenols (39.62 ± 13.16 g tannic acid/100 g dry extract) and phenolcarboxylic acids (22.05 ± 1.31 g chlorogenic acid/100 g dry extract). Moreover, the spectrophotometric chemical profile highlighted a significant concentration of flavones for CGE (5.32 ± 0.26 g rutoside/100 g dry extract), in contrast to the other extracts. UHPLC-MS quantification detected considerable amounts of phenolic constituents, especially chlorogenic acid in CGE (187.435 ± 1.96 mg/g extract) and rosmarinic acid in RSE (317.100 ± 2.70 mg/g extract). Rosemary and hawthorn extracts showed significantly stronger free radical scavenging activity compared to the other plant extracts (p < 0.05). Pearson correlation analysis and the heatmap correlation matrix indicated significant correlations between phytochemical contents and in vitro antioxidant activities. Computational studies were performed to investigate the potential anti-obesity mechanism of the studied extracts using target prediction, homology modeling, molecular docking, and molecular dynamics approaches. Our study revealed that rosmarinic acid (RA) and chlorogenic acid (CGA) can form stable complexes with the active site of carbonic anhydrase 5A by either interacting with the zinc-bound catalytic water molecule or by directly binding Zn2+. Further studies are warranted to experimentally validate the predicted CA5A inhibitory activities of RA and CGA and to investigate the hypolipidemic and antioxidant activities of the proposed plant extracts in animal models of dyslipidemia and obesity.

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.