Structural insights revealed by crystal structures of CYP76AH1 and CYP76AH1 in complex with its natural substrate

New insights of advanced biotechnological engineering strategies for tanshinone biosynthesis in Salvia miltiorrhiza

Salvia miltiorrhiza Bunge, a well-known traditional Chinese herbal medicine, has been served as not only medicine for human ailments, but also health care products. As one of major bioactive ingredients, tanshinones are widely used to treat cardiovascular and cerebrovascular diseases, and also possess different pharmacological activities including anti-tumor, anti-inflammatory, anti-fibrotic and others. However, the content of tanshinones is relatively low in S. miltiorrhiza plants. Recently, multiple biotechnological strategies have been applied to improve tanshinone production. In this review, advances in bioactivities, biosynthesis pathway and regulation, transcriptional regulatory network, epigenetic modification and synthetic biology are summarized, and future perspectives are discussed, which will help develop high-quality S. miltiorrhiza resources.

Functional characterization of Camptotheca acuminata 7-deoxyloganetic acid synthases and 7-deoxyloganetic acid glucosyltransferases involved in camptothecin biosynthesis

Camptothecin (CAM), a well-known plant-derived antitumor compound, is a structurally complex pentacyclic pyrroloquinoline monoterpene indole alkaloid (MIA) found in various plant species. As a specific MIA, CAM had been thought to share a common upstream biosynthetic pathway with other MIAs such as the antitumor vinblastine and vincristine from Catharanthus roseus. Nevertheless the key enzymes responsible for the consecutive three-step oxidation of the -CH3 of nepetalactol to form the -COOH of 7-deoxyloganetic acid and the subsequent glycosylation of 7-deoxyloganetic acid to yield 7-deoxyloganic acid have yet to be functionally characterized. Here we established an in vivo tandem catalysis assay for the enzymatic catalytic activity characterization of 7-deoxyloganetic acid synthase (7DLS) and 7-deoxyloganetic acid glucosyltransferase (7DLGT), two crucial catalytic enzymes in MIAs biosynthesis, thereby avoiding the difficulty in the detection of the unstable biosynthetic intermediates. The enzyme activity assay platform was conducted through the co-expression of functionally characterized Cr7DLS and Cr7DLGT in Saccharomyces cerevisiae WAT11, substrate feeding, and enzymatic product verification. Two cytochrome P450 enzymes (CYPs) from Camptotheca acuminata, the prestigious resource for CAM, CaCYP76A75 and CaCYP76A76, were identified and functionally characterized to be responsible for the consecutive three-step oxidation of nepetalactol to yield 7-deoxyloganetic acid through reciprocal replacement of Cr7DLS in the in vivo tandem enzyme activity assay platform. Two uridine 5'-diphosphate glycosyltransferases (UGTs), CaUGT709C10 and CaUGT709C11, were functionally characterized to be capable of glycosylating 7-deoxyloganetic acid to yield 7-deoxyloganic acid. This study provides two CYPs as 7DLSs and two UGTs as 7DLGTs, offering potential applications in MIAs biosynthesis.

Genome-based discovery of pachysiphine synthases in Tabernaemontana elegans

Plant-specialized metabolism represents an inexhaustible source of active molecules, some of which have been used in human health for decades. Among these, monoterpene indole alkaloids (MIAs) include a wide range of valuable compounds with anticancer, antihypertensive, or neuroactive properties. This is particularly the case for the pachysiphine derivatives which show interesting antitumor and anti-Alzheimer activities but accumulate at very low levels in several Tabernaemontana species. Unfortunately, genome data in Tabernaemontanaceae are lacking and knowledge on the biogenesis of pachysiphine-related MIAs in planta remains scarce, limiting the prospects for the biotechnological supply of many pachysiphine-derived biopharmaceuticals. Here, we report a raw version of the toad tree (Tabernaemontana elegans) genome sequence. These new genomic resources led to the identification and characterization of a couple of genes encoding cytochrome P450 with pachysiphine synthase activity. Our phylogenomic and docking analyses highlight the different evolutionary processes that have been recruited to epoxidize the pachysiphine precursor tabersonine at a specific position and in a dedicated orientation, thus enriching our understanding of the diversification and speciation of the MIA metabolism in plants. These gene discoveries also allowed us to engineer the synthesis of MIAs in yeast through the combinatorial association of metabolic enzymes resulting in the tailor-made synthesis of non-natural MIAs. Overall, this work represents a step forward for the future supply of pachysiphine-derived drugs by microbial cell factories.

Cytochrome P450 Enzyme Design by Constraining the Catalytic Pocket in a Diffusion Model

Although cytochrome P450 enzymes are the most versatile biocatalysts in nature, there is insufficient comprehension of the molecular mechanism underlying their functional innovation process. Here, by combining ancestral sequence reconstruction, reverse mutation assay, and progressive forward accumulation, we identified 5 founder residues in the catalytic pocket of flavone 6-hydroxylase (F6H) and proposed a "3-point fixation" model to elucidate the functional innovation mechanisms of P450s in nature. According to this design principle of catalytic pocket, we further developed a de novo diffusion model (P450Diffusion) to generate artificial P450s. Ultimately, among the 17 non-natural P450s we generated, 10 designs exhibited significant F6H activity and 6 exhibited a 1.3- to 3.5-fold increase in catalytic capacity compared to the natural CYP706X1. This work not only explores the design principle of catalytic pockets of P450s, but also provides an insight into the artificial design of P450 enzymes with desired functions.

Oxidation of Naringenin, Apigenin, and Genistein by Human Family 1 Cytochrome P450 Enzymes and Comparison of Interaction of Apigenin with Human P450 1B1.1 and Scutellaria P450 82D.1

Naringenin, an initial synthesized flavanone in various plant species, is further utilized for production of many biologically active flavonoids, e.g., apigenin, eriodictyol, and genistein, by various plant enzymes including cytochrome P450s (P450s or CYPs). We examined how these flavonoids are oxidized by human P450 family 1 and 2A enzymes. Naringenin was principally oxidized at the 3'-position to form eriodictyol by CYP1 enzymes more efficiently than by CYP2A enzymes, and the resulting eriodictyol was further oxidized to two penta-hydroxylated products. In contrast to plant P450 enzymes, these human P450s did not mediate the desaturation of naringenin and eriodictyol to give apigenin and luteolin, respectively. Apigenin was oxidized at the C3' and C6 positions to form luteolin and scutellarein by these P450s. CYP1B1.1 and 1B1.3 had high activities in apigenin 6-hydroxylation with a homotropic cooperative manner, as has been observed previously in chrysin 6-hydroxylation (Nagayoshi et al., Chem. Res. Toxicol. 2019, 32, 1268-1280). Molecular docking analysis suggested that CYP1B1 had two apigenin binding sites and showed similarities in substrate recognition sites to plant CYP82D.1, one of the enzymes in catalyzing apigenin and chrysin 6-hydroxylations in Scutellaria baicalensis. The present results suggest that human CYP1 enzymes and CYP2A13 in some reactions have important roles in the oxidation of naringenin, eriodictyol, apigenin, and genistein and that human CYP1B1 and Scutellaria CYP82D.1 have similarities in their SRS regions, catalyzing 6-hydroxylation of both apigenin and chrysin.

Comparison of herbicide specificity of CYP81A cytochrome P450s from rice and a multiple-herbicide resistant weed, Echinochloa phyllopogon

BACKGROUND

CYP81A cytochrome P450s (CYP81As) play a key role in herbicide detoxification in Poaceae plants. Crop CYP81As confer natural tolerance to multiple herbicides, whereas CYP81As in weeds disrupt herbicide action. Identifying differences in CYP81A herbicide specificity between crops and weeds could provide valuable information for controlling weeds. In this study, we quantitatively compared herbicide specificity between CYP81A6 from rice (Oryza sativa) and CYP81A12 and CYP81A21 from a weed, Echinochloa phyllopogon, using transgenic Escherichia coli and Arabidopsis.

RESULTS

All three CYP81As metabolized the five tested herbicides and formed similar metabolites, with the highest relative activities of 400 to 580% toward bentazone compared to their activity on bensulfuron-methyl (defined as 100%). However, they showed differing activity toward propyrisulfuron. The relative activities of Echinochloa phyllopogon CYP81A12 (12.2%) and CYP81A21 (34.4%) toward propyrisulfuron were lower than that of rice CYP81A6 (98.5%). Additionally, rice CYP81A6 produced O-demethylated propyrisulfuron and hydroxylated products, whereas Echinochloa phyllopogon CYP81As produced only hydroxylated products. Arabidopsis expressing CYP81A12 and CYP81A21 exhibited lower levels of resistance against propyrisulfuron compared to that in Arabidopsis expressing CYP81A6. Homology modeling and in silico docking revealed that bensulfuron-methyl docked well into the active centers of all three CYP81As, whereas propyrisulfuron docked into rice CYP81A6 but not into Echinochloa phyllopogon CYP81As.

CONCLUSION

The differing herbicide specificity displayed by rice CYP81A6 and Echinochloa phyllopogon CYP81A12 and CYP81A21 will help design inhibitors (synergists) of weed CYP81As, as well as develop novel herbicide ingredients that are selectively metabolized by crop CYP81As, to overcome the problem of herbicide resistance. © 2022 Society of Chemical Industry.