Coupling the Isopentenol Utilization Pathway and Prenyltransferase for the Biosynthesis of Licoflavanone in Recombinant Escherichia coli

Catalytic mechanism and engineering of aromatic prenyltransferase: A review

The prenylation of aromatic compounds significantly enhances their metabolic stability and bioactivity. Prenyltransferases, as essential biocatalysts, facilitate the regioselective transfer of prenyl groups from donors to aromatic substrates. This review systematically summarizes recent progress in the rational engineering of prenyltransferases through protein-based strategies, critically evaluates current challenges, and outlines future research priorities. Firstly, we delineate the biosynthetic pathways of prenylated phenolic compounds, emphasizing the pivotal roles of prenyltransferases, and classify these enzymes according to the structural diversity of their aromatic acceptor molecules. Secondly, the current state of prenyltransferase biosynthesis by comparing their heterologous expression levels across diverse microbial hosts is discussed, highlighting key factors influencing catalytic efficiency. Furthermore, we dissect the molecular mechanisms governing prenyltransferase activity and propose innovative engineering approaches integrating artificial intelligence and deep learning to develop high-performance biocatalysts for industrial applications. Finally, we address unresolved challenges in this field, including suboptimal catalytic activity, narrow substrate specificity, and limitations in multi-enzyme cascade systems and immobilization techniques. This review offers strategic insights to guide the engineering and scalable application of prenyltransferases in synthetic biology and pharmaceutical innovation.

De novo production of prenylnaringenin compounds by a metabolically engineered Escherichia coli

Prenylnaringenin (PN) compounds, namely 8-prenylnaringenin (8-PN), 3'-prenylnaringenin (3'-PN), and 6-prenylnaringenin (6-PN), are reported to have several interesting bioactivities. This study aimed to validate a biosynthetic pathway for de novo production of PN in Escherichia coli. A previously optimized E. coli chassis capable of efficiently de novo producing naringenin was used to evaluate eleven prenyltransferases (PTs) for the production of PN compounds. As PT reaction requires dimethylallyl pyrophosphate (DMAPP) as extended substrate that has limited availability inside the cells, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 12a (Cas12a) (CRISPR-Cas12a) was used to construct ten boosted DMAPP-E. coli strains. All the PTs, in combination with the naringenin biosynthetic pathway, were tested in these strains. Experiments in 96-well deep well plates identified twelve strains capable of producing PN. E. coli M-PAR-121 with the integration of the 1-deoxy-D-xylulose-5-phosphate synthase (DXS) gene from E. coli (EcDXS) into the lacZ locus of the genome (E. coli M-PAR-121:EcDXS) expressing the soluble aromatic PT from Streptomyces roseochromogenes (CloQ) and the naringenin biosynthetic pathway was selected as the best producer strain. After optimizing the production media in shake flasks, 160.57µM of 3'-PN, 4.4µM of 6-PN, and 2.66µM of 8-PN were obtained. The production was then evaluated at the bioreactor scale and 397.57µM of 3'-PN (135.33mg/L) and 25.61µM of 6-PN (8.72mg/L) were obtained. To the best of our knowledge, this work represents the first report of de novo production of PN compounds using E. coli as a chassis.

Biotransformation of Kaempferol to Icaritin in Engineered Saccharomyces cerevisiae

Flavonoids are bioactive natural products known for their pharmaceutical properties and health-promoting applications. Microbial transformation offers a promising and sustainable approach for the biosynthesis of flavonoids. However, challenges such as the lack of well-established synthesis pathways and inefficient heterologous expression of key enzymes limit the flavonoid production such as icaritin. Here, a Saccharomyces cerevisiae strain was engineered to produce icaritin from kaempferol through a metabolic engineering strategy. Enzyme screening strategies identified the functional prenyltransferases, enabling the construction of a bioconversion pathway. The engineered isopentenol and mevalonate pathway boosted the supply of dimethylallyl pyrophosphate, producing 10.4 mg/L 8-prenylkaempferol. Redesigning the N-terminal of prenyltransferase resulted in a 7.5-fold increase in the titer of 8-prenylkaempferol. Cofactor engineering strategies of S-adenosyl-l-methionine recycling resulted in a substantial 139.8% increase in icaritin production. Additionally, the rational design of rate-limiting enzymes significantly improved catalytic performance, enhancing overall icaritin production. Ultimately, engineered S. cerevisiae transformed kaempferol to icaritin successfully through engineered enzymatic modifications with a titer of 14.4 mg/L. This study offers valuable insights into the enzyme design and sustainable natural products production.

Chromatic symphony of fleshy fruits: functions, biosynthesis and metabolic engineering of bioactive compounds

Fleshy fruits are popular among consumers due to their significant nutritional value, which includes essential bioactive compounds such as pigments, vitamins, and minerals. Notably, plant-derived pigments are generally considered safe and reliable, helping to protect humans against various inflammatory diseases. Although the phytochemical diversity and their biological activities have been extensively reviewed and summarized, the status of bioactive nutrients in fleshy fruits, particularly with a focusing on different colors, has received less attention. Therefore, this review introduces five common types of fleshy fruits based on coloration and summarizes their major bioactive compounds. It also provides the latest advancements on the function, biosynthesis, and metabolic engineering of plant-derived pigments. In this review, we emphasize that promoting the consumption of a diverse array of colorful fruits can contribute to a balanced diet; however, optimal intake levels still require further clinical validation. This review may serve as a useful guide for decisions that enhance the understanding of natural pigments and accelerate their application in agriculture and medicine.

Heterologous Biosynthesis of Prenylflavonoids in Escherichia coli Based on Fungus Screening of Prenyltransferases

Flavonoids are natural products with high biological activity and potential applications. Prenylation increases the lipophilicity of flavonoids, endowing them with specific functions, selectivity, and pharmacological properties. However, traditional methods of plant extraction and chemical synthesis are insufficient to meet the demand for prenylflavonoids. Heterologous biosynthesis of prenylflavonoids in microorganisms provides an alternative approach. Compared with plant prenyltransferases, microbial prenyltransferases showed broad substrate specificity, which is more conducive to the biosynthesis of diverse prenylflavonoids. In this study, we cloned 31 dimethylallyltryptophan synthase prenyltransferases from five fungal species and tested candidate substrates. The products of Ad03 and Ao01 were identified, resulting in two unnatural prenylflavonoids and four natural prenylflavonoids. We constructed the isopentenol utilization pathway in Escherichia coli to develop the efficient dimethylallyl diphosphate synthesis pathway for 6-prenylsilybin (6-PS) synthesis. By optimizing the whole cell catalysis and two-phase reaction system, the 6-PS production titer reached 176 mg/L and the yield of silybin was 88%. Our study provides an efficient method for prenylflavonoids production.