Engineering Saccharomyces cerevisiae to produce plant benzylisoquinoline alkaloids

Advancements in Microbial Cell Engineering for Benzylisoquinoline Alkaloid Production

Benzylisoquinoline alkaloids (BIAs) are a class of natural compounds found in plants of the Ranunculaceae family, known for their diverse pharmacological activities. However, the extraction yields of BIAs from plants are limited, and the cost of chemical synthesis is prohibitively high. Recent advancements in systems metabolic engineering and genomics have made it feasible to use microbes as bioreactors for BIAs production. This review explores recent progress in enhancing the production and yields of BIAs in two microbial systems: Escherichia coli and Saccharomyces cerevisiae. It covers various BIAs, including (S)-reticuline, morphinane, protoberberine, and aporphine alkaloids. The review provides strategies and technologies for BIAs synthesis, analyzes current challenges in BIAs research, and offers recommendations for future research directions.

Identification of the cytochrome P450s responsible for the biosynthesis of two types of aporphine alkaloids and their de novo biosynthesis in yeast

Aporphine alkaloids have diverse pharmacological activities; however, our understanding of their biosynthesis is relatively limited. Previous studies have classified aporphine alkaloids into two categories based on the configuration and number of substituents of the D-ring and have proposed preliminary biosynthetic pathways for each category. In this study, we identified two specific cytochrome P450 enzymes (CYP80G6 and CYP80Q5) with distinct activities toward (S)-configured and (R)-configured substrates from the herbaceous perennial vine Stephania tetrandra, shedding light on the biosynthetic mechanisms and stereochemical features of these two aporphine alkaloid categories. Additionally, we characterized two CYP719C enzymes (CYP719C3 and CYP719C4) that catalyzed the formation of the methylenedioxy bridge, an essential pharmacophoric group, on the A- and D-rings, respectively, of aporphine alkaloids. Leveraging the functional characterization of these crucial cytochrome P450 enzymes, we reconstructed the biosynthetic pathways for the two types of aporphine alkaloids in budding yeast (Saccharomyces cerevisiae) for the de novo production of compounds such as (R)-glaziovine, (S)-glaziovine, and magnoflorine. This study provides key insight into the biosynthesis of aporphine alkaloids and lays a foundation for producing these valuable compounds through synthetic biology.

Cutting-edge plant natural product pathway elucidation

Plant natural products (PNPs) play important roles in plant physiology and have been applied across diverse fields of human society. Understanding their biosynthetic pathways informs plant evolution and meanwhile enables sustainable production through metabolic engineering. However, the discovery of PNP biosynthetic pathways remains challenging due to the diversity of enzymes involved and limitations in traditional gene mining approaches. In this review, we will summarize state-of-the-art strategies and recent examples for predicting and characterizing PNP biosynthetic pathways, respectively, with multiomics-guided tools and heterologous host systems and share our perspectives on the systematic pipelines integrating these various bioinformatic and biochemical approaches.

De novo biosynthesis of berberine and halogenated benzylisoquinoline alkaloids in Saccharomyces cerevisiae

Berberine is an extensively used pharmaceutical benzylisoquinoline alkaloid (BIA) derived from plants. Microbial manufacturing has emerged as a promising approach to source valuable BIAs. Here, we demonstrated the complete biosynthesis of berberine in Saccharomyces cerevisiae by engineering 19 genes including 12 heterologous genes from plants and bacteria. Overexpressing bottleneck enzymes, fermentation scale-up, and heating treatment after fermentation increased berberine titer by 643-fold to 1.08 mg L-1. This pathway also showed high efficiency to incorporate halogenated tyrosine for the synthesis of unnatural BIA derivatives that have higher therapeutical potentials. We firstly demonstrate the in vivo biosynthesis of 11-fluoro-tetrahydrocolumbamine via nine enzymatic reactions. The efficiency and promiscuity of our pathway also allow for the simultaneous incorporation of two fluorine-substituted tyrosine derivatives to 8, 3'-di-fluoro-coclaurine. This work highlights the potential of yeast as a versatile microbial biosynthetic platform to strengthen current pharmaceutical supply chain and to advance drug development.

Exploring the Agrobacterium-mediated transformation with CRISPR/Cas9 in cucumber (Cucumis sativus L.)

BACKGROUNDS

The narrow genetic basis of cucumber makes breeding of this species difficult. CRISPR/Cas9 system is  characteristic of  simple design, low cost and  high efficiency, which has opened a new path for cucumber functional genetics and the development of cucumber mocular breeding. However, the immature genetic transformation system is the main limiting factor for applying this technology in cucumber.

METHODS AND RESULTS

In this study, a Histochemical β-glucuronidase (GUS) assay was used to analyze the effect of various parameters, including slight scratch of explants, pre-culture time, acetosyringone (AS) concentration, infection time in Agrobacterium solution, and co-culture period on the transformation efficiency. The results showed that the explants slightly scratched after cutting, pre-cultured for 1 day, Agrobacterium bacterial solution containing AS, and 20 min length of infection could significantly increase the GUS staining rate of explants. On this basis, two sequences with high specificity (sgRNA-1 and sgRNA-2) targeted different loci of gene CsGCN5 were designed. The corresponding vectors Cas9-sgRNA-1 and Cas9-sgRNA-2 were constructed and transformed using the above-optimized cucumber genetic transformation system, and three and two PCR positive lines were obtained from 210 and 207 explants, respectively. No sequence mutation at target loci of CsGCN5 was detected in the Cas9-sgRNA-1 transformed three PCR positive lines. However, one mutant line with targeted homozygous change was recognized from the Cas9-sgRNA-2 transformed two PCR positive lines.

CONCLUSION

In this study, 2.4‰ of total explants had directed mutation in the CsGCN5 gene. The results in the present study would be beneficial to further optimize and improve the efficiency of the genetic transformation of cucumber.

Biosynthesis of tetrahydropapaverine and semisynthesis of papaverine in yeast

Tetrahydropapaverine (THP) and papaverine are plant natural products with clinically significant roles. THP is a precursor in the production of the drugs atracurium and cisatracurium, and papaverine is used as an antispasmodic during vascular surgery. In recent years, metabolic engineering advances have enabled the production of natural products through heterologous expression of pathway enzymes in yeast. Heterologous biosynthesis of THP and papaverine could play a role in ensuring a stable supply of these clinically significant products. Biosynthesis of THP and papaverine has not been achieved to date, in part because multiple pathway enzymes have not been elucidated. Here, we describe the development of an engineered yeast strain for de novo biosynthesis of THP. The production of THP is achieved through heterologous expression of two enzyme variants with activity on nonnative substrates. Through protein engineering, we developed a variant of N-methylcoclaurine hydroxylase with activity on coclaurine, enabling de novo norreticuline biosynthesis. Similarly, we developed a variant of scoulerine 9-O-methyltransferase capable of O-methylating 1-benzylisoquinoline alkaloids at the 3' position, enabling de novo THP biosynthesis. Flux through the heterologous pathway was improved by knocking out yeast multidrug resistance transporters and optimization of media conditions. Overall, strain engineering increased the concentration of biosynthesized THP 600-fold to 121 µg/L. Finally, we demonstrate a strategy for papaverine semisynthesis using hydrogen peroxide as an oxidizing agent. Through optimizing pH, temperature, reaction time, and oxidizing agent concentration, we demonstrated the ability to produce semisynthesized papaverine through oxidation of biosynthesized THP.

Plant-microbe hybrid synthesis provides new insights for the efficient use of Macleaya cordata

Sanguinarine and chelerytrine have antibacterial and anti-inflammatory effects and is the main active ingredients of growth promoters in animals. Currently, Sanguinarine and chelerytrine were extracted from the capsules of the medicinal plant Macleaya cordata. However, the biomass of M. cordata nonmedicinal parts (leaves) accounted for a large proportion and contained a rich presentation of protopine and allocryptopine which are the precursor compounds of sanguinarine and chelerytrine. The aim of this study was to develop a new method for producing sanguinarine and chelerytrine through yeast transformation of protopine and allocryptopine in M. cordata leaves. First, we isolated different genes from Papaver somniferum (PsP6H, PsCPR, PsDBOX), Eschscholtzia californica (EcP6H), Cucumis sativus (CuCPR), Arabidopsis thaliana (AtCPR) and M. cordata (Mc11229, Mc11218, Mc6408, Mc6407, Mc19967, Mc13802). Additionally, some of the gene sequences were codon optimized. Then, we transformed these genes into yeast cells to compare the catalytic efficiency. Second, we used the most efficient strains to biotransform the leaves of M. cordata. Finally, we obtained 85.415 ± 11.887 ng mL^-1 sanguinarine and 4.288 ± 1.395 ng mL^-1 chelerytrine, which was more than 2-3 times the content in leaves of M. cordata. Overall, we using the nonmedicinal parts of M. cordata and successfully obtained sanguinarine and chelerytrine by the plant-microbial hybrid synthesis method.

Biotechnological production of specialty aromatic and aromatic-derivative compounds

Aromatic compounds are an important class of chemicals with different industrial applications. They are usually produced by chemical synthesis from petroleum-derived feedstocks, such as toluene, xylene and benzene. However, we are now facing threats from the excessive use of fossil fuels causing environmental problems such as global warming. Furthermore, fossil resources are not infinite, and will ultimately be depleted. To cope with these problems, the sustainable production of aromatic chemicals from renewable non-food biomass is urgent. With this in mind, the search for alternative methodologies to produce aromatic compounds using low-cost and environmentally friendly processes is becoming more and more important. Microorganisms are able to produce aromatic and aromatic-derivative compounds from sugar-based carbon sources. Metabolic engineering strategies as well as bioprocess optimization enable the development of microbial cell factories capable of efficiently producing aromatic compounds. This review presents current breakthroughs in microbial production of specialty aromatic and aromatic-derivative products, providing an overview on the general strategies and methodologies applied to build microbial cell factories for the production of these compounds. We present and describe some of the current challenges and gaps that must be overcome in order to render the biotechnological production of specialty aromatic and aromatic-derivative attractive and economically feasible at industrial scale.