Research advances in cytochrome P450-catalysed pharmaceutical terpenoid biosynthesis in plants

Metabolic engineering for compartmentalized biosynthesis of the valuable compounds in Saccharomyces cerevisiae

Saccharomyces cerevisiae is commonly used as a microbial cell factory to produce high-value compounds or bulk chemicals due to its genetic operability and suitable intracellular physiological environment. The current biosynthesis pathway for targeted products is primarily rewired in the cytosolic compartment. However, the related precursors, enzymes, and cofactors are frequently distributed in various subcellular compartments, which may limit targeted compounds biosynthesis. To overcome above mentioned limitations, the biosynthesis pathways are localized in different subcellular organelles for product biosynthesis. Subcellular compartmentalization in the production of targeted compounds offers several advantages, mainly relieving competition for precursors from side pathways, improving biosynthesis efficiency in confined spaces, and alleviating the cytotoxicity of certain hydrophobic products. In recent years, subcellular compartmentalization in targeted compound biosynthesis has received extensive attention and has met satisfactory expectations. In this review, we summarize the recent advances in the compartmentalized biosynthesis of the valuable compounds in S. cerevisiae, including terpenoids, sterols, alkaloids, organic acids, and fatty alcohols, etc. Additionally, we describe the characteristics and suitability of different organelles for specific compounds, based on the optimization of pathway reconstruction, cofactor supplementation, and the synthesis of key precursors (metabolites). Finally, we discuss the current challenges and strategies in the field of compartmentalized biosynthesis through subcellular engineering, which will facilitate the production of the complex valuable compounds and offer potential solutions to improve product specificity and productivity in industrial processes.

RNA-seq analysis reveals narrow differential gene expression in MEP and MVA pathways responsible for phytochemical divergence in extreme genotypes of Thymus daenensis Celak

BACKGROUND

Here, we investigated the underlying transcriptional-level evidence behind phytochemical differences between two metabolically extreme genotypes of Thymus daenensis. The genotypes 'Zagheh-11' (thymol/carvacrol type, poor in essential oil [EO] [2.9%] but rich in triterpenic acids) and 'Malayer-21' (thymol type and rich in EO [3.8%]) were selected from an ongoing breeding program and then clonally propagated for further experimental use.

MATERIALS AND METHODS

GC-MS, GC-FID, and HPLC-PDA were utilized to monitor the fluctuation of secondary metabolites at four phenological stages (vegetative, bud burst, early, and full-flowering stages). The highest phytochemical divergence was observed at early flowering stage. Both genotypes were subjected to mRNA sequencing (approximately 100 million paired reads) at the aforementioned stage. The expression patterns of four key genes involved in the biosynthesis of terpenoids were also validated using qRT-PCR.

RESULTS

Carvacrol content in 'Zagheh-11' (26.13%) was approximately 23 times higher than 'Malayer-21' (1.12%). Reciprocally, about 10% higher thymol was found in 'Malayer-21' (62.15%). Moreover, the concentrations of three major triterpenic acids in 'Zagheh-11' were approximately as twice as those found in 'Malayer-21'. Transcriptome analysis revealed a total of 1840 unigenes that were differentially expressed, including terpene synthases, cytochrome P450, and terpenoid backbone genes. Several differentially expressed transcription factors (such as MYB, bZIP, HB-HD-ZIP, and WRKY families) were also identified. These results suggest that an active cytosolic mevalonate (MVA) pathway may be linked to higher levels of sesquiterpenes, triterpenic acids, and carvacrol in 'Zagheh-11'. The chloroplastic pathway of methyl erythritol phosphate (MEP) may have also contributed to a higher accumulation of thymol in Malayer-21. Indeed, 'Zagheh-11' showed higher expression of certain genes (HMGR, CYP71D180, β-amyrin 28-monooxygenase, and sesquiterpene synthases) in the MVA pathway, while some genes in the MEP pathway (including DXR, ispG, and γ-terpinene synthase) were distinctly expressed in Malayer-21. Future efforts in metabolic engineering of MVA/MEP pathways may benefit from these findings to produce increased levels of desired secondary metabolites at commercial scale.

Characterization of the Cytochrome P450 CYP716C52 in Celastrol Biosynthesis and Its Applications in Engineered Saccharomyces cerevisiae

Celastrol is a bioactive pentacyclic triterpenoid with promising therapeutic effects that is mainly distributed in Celastraceae plants. Although some enzymes involved in the celastrol biosynthesis pathway have been reported, many biosynthetic steps remain unknown. Herein, transcriptomics and metabolic profiles of multiple species in Celastraceae were integrated to screen for cytochrome P450s (CYPs) that are closely related to celastrol biosynthesis. The CYP716 enzyme, TwCYP716C52, was found to be able to oxidize the C-2 position of polpunonic acid, a precursor of celastrol, to form the wilforic acid C. RNAi-mediated repression of TwCYP716C52 in Tripterygium wilfordii suspension cells further confirmed its involvement in celastrol biosynthesis. The C-2 catalytic mechanisms of TwCYP716C52 were further explored by using molecular docking and site-directed mutagenesis experiments. Moreover, a modular optimization strategy was used to construct an engineered yeast to produce wilforic acid C at a titer of 5.8 mg·L-1. This study elucidates the celastrol biosynthetic pathway and provides important functional genes and sufficient precursors for further enzyme discovery.

The leaf idioblastome of the medicinal plant Catharanthus roseus is associated with stress resistance and alkaloid metabolism

Catharanthus roseus leaves produce a range of monoterpenoid indole alkaloids (MIAs) that include low levels of the anticancer drugs vinblastine and vincristine. The MIA pathway displays a complex architecture spanning different subcellular and cell type localizations, and is under complex regulation. As a result, the development of strategies to increase the levels of the anticancer MIAs has remained elusive. The pathway involves mesophyll specialized idioblasts where the late unsolved biosynthetic steps are thought to occur. Here, protoplasts of C. roseus leaf idioblasts were isolated by fluorescence-activated cell sorting, and their differential alkaloid and transcriptomic profiles were characterized. This involved the assembly of an improved C. roseus transcriptome from short- and long-read data, IDIO+. It was observed that C. roseus mesophyll idioblasts possess a distinctive transcriptomic profile associated with protection against biotic and abiotic stresses, and indicative that this cell type is a carbon sink, in contrast to surrounding mesophyll cells. Moreover, it is shown that idioblasts are a hotspot of alkaloid accumulation, suggesting that their transcriptome may hold the key to the in-depth understanding of the MIA pathway and the success of strategies leading to higher levels of the anticancer drugs.

Recent advances in triterpenoid pathway elucidation and engineering

Triterpenoids are among the most assorted class of specialized metabolites found in all the taxa of living organisms. Triterpenoids are the leading active ingredients sourced from plant species and are utilized in pharmaceutical and cosmetic industries. The triterpenoid precursor 2,3-oxidosqualene, which is biosynthesized via the mevalonate (MVA) pathway is structurally diversified by the oxidosqualene cyclases (OSCs) and other scaffold-decorating enzymes such as cytochrome P450 monooxygenases (P450s), UDP-glycosyltransferases (UGTs) and acyltransferases (ATs). A majority of the bioactive triterpenoids are harvested from the native hosts using the traditional methods of extraction and occasionally semi-synthesized. These methods of supply are time-consuming and do not often align with sustainability goals. Recent advancements in metabolic engineering and synthetic biology have shown prospects for the green routes of triterpenoid pathway reconstruction in heterologous hosts such as Escherichia coli, Saccharomyces cerevisiae and Nicotiana benthamiana, which appear to be quite promising and might lead to the development of alternative source of triterpenoids. The present review describes the biotechnological strategies used to elucidate complex biosynthetic pathways and to understand their regulation and also discusses how the advances in triterpenoid pathway engineering might aid in the scale-up of triterpenoid production in engineered hosts.

Unprecedented Benzoquinone Motifs Reveal Post-Oligomerizational Modification of Proanthocyanidins

Proanthocyanidins (PACs) are complex flavan-3-ol polymers with stunning chemical complexity due to oxygenation patterns, oxidative phenolic ring linkages, and intricate stereochemistry of their heterocycles and inter-flavan linkages. Being promising candidates for dental restorative biomaterials, trace analysis of dentin bioactive cinnamon PACs now yielded novel trimeric (1 and 2) and tetrameric (3) PACs with unprecedented o- and p-benzoquinone motifs (benzoquinonoid PACs). Challenges in structural characterization, especially their absolute configuration, prompted the development of a new synthetic-analytical approach involving comprehensive spectroscopy, including NMR with quantum mechanics-driven 1H iterative functionalized spin analysis (HifSA) plus experimental and computational electronic circular dichroism (ECD). Vital stereochemical information was garnered from synthesizing 4-(2,5-benzoquinone)flavan-3-ols and a truncated analogue of trimer 2 as ECD models. Discovery of the first natural benzoquinonoid PACs provides new evidence to the experimentally elusive PAC biosynthesis as their formation requires two oxidative post-oligomerizational modifications (POMs) that are distinct and occur downstream from both quinone-methide-driven oligomerization and A-type linkage formation. While Nature is known to achieve structural diversity of many major compound classes by POMs, this is the first indication of PACs also following this common theme.

Genome-wide presence/absence variation discovery and its application in Peach (Prunus persica)

Gene presence/absence variation (PAV) is an important contributor to the studies of genetic diversity, gene identification, and molecular marker development in plants. In the present study, 100 peach (Prunus persica) accessions were used for genome resequencing to identify PAVs. Alignmentwith a reference genome yielded a total of 2.52 Mb non-reference sequences and 923 novel genes were identified. The dispensable PAVs were enriched in resistance, perhaps reflecting their roles in plant adaptation to various environments. Furthermore, selection sweeps associated with peach domestication and improvement were identified based on PAV data. Only 4.3% and 13.4% of domestication and improvement sweeps, respectively, were identified simultaneously using single nucleotide polymorphism (SNP) data, suggesting flexible identification between the different methods. To further verify the applicability of PAV identification, a genome-wide association study was conducted using 21 agronomic traits. Some of the identified loci were consistent with those reported in previous studies, while some were mapped for the first time; the latter included petiole length, petiole gland shape, and petiole gland number. Through tissue-specific expression analysis and gene transformation experiments, a novel gene, evm.model.Contig322_A94.1, was identified and found to be involved in chilling requirements. We speculated that this novel gene might regulate the trait by participating in the ABA signaling pathway. The PAVs identified in P. persica provide valuable resources for mapping the entire gene set and identifying optional markers for molecular selection in future studies.

Genome and whole-genome resequencing of Cinnamomum camphora elucidate its dominance in subtropical urban landscapes

BACKGROUND

Lauraceae is well known for its significant phylogenetic position as well as important economic and ornamental value; however, most evergreen species in Lauraceae are restricted to tropical regions. In contrast, camphor tree (Cinnamomum camphora) is the most dominant evergreen broadleaved tree in subtropical urban landscapes.

RESULTS

Here, we present a high-quality reference genome of C. camphora and conduct comparative genomics between C. camphora and C. kanehirae. Our findings demonstrated the significance of key genes in circadian rhythms and phenylpropanoid metabolism in enhancing cold response, and terpene synthases (TPSs) improved defence response with tandem duplication and gene cluster formation in C. camphora. Additionally, the first comprehensive catalogue of C. camphora based on whole-genome resequencing of 75 accessions was constructed, which confirmed the crucial roles of the above pathways and revealed candidate genes under selection in more popular C. camphora, and indicated that enhancing environmental adaptation is the primary force driving C. camphora breeding and dominance.

CONCLUSIONS

These results decipher the dominance of C. camphora in subtropical urban landscapes and provide abundant genomic resources for enlarging the application scopes of evergreen broadleaved trees.

Genome-wide analysis of the P450 gene family in tea plant (Camellia sinensis) reveals functional diversity in abiotic stress

BACKGROUND

Cytochrome P450 (Cytochrome P450s) genes are involved in the catalysis of various reactions, including growth, development, and secondary metabolite biosynthetic pathways. However, little is known about the characteristics and functions of the P450 gene family in Camellia sinensis (C. sinensis).

RESULTS

To reveal the mechanisms of tea plant P450s coping with abiotic stresses, analyses of the tea plant P450 gene family were conducted using bioinformatics-based methods. In total, 273 putative P450 genes were identified from the genome database of C. sinensis. The results showed that P450s were well-balanced across the chromosomes I to XV of entire genome, with amino acid lengths of 268-612 aa, molecular weights of 30.95-68.5 kDa, and isoelectric points of 4.93-10.17. Phylogenetic analysis divided CsP450s into 34 subfamilies, of which CYP71 was the most abundant. The predicted subcellular localization results showed that P450 was distributed in a variety of organelles, with chloroplasts, plasma membrane,,and cytoplasm localized more frequently. The promoter region of CsP450s contained various cis-acting elements related to phytohormones and stress responses. In addition, ten conserved motifs (Motif1-Motif10) were identified in the CsP450 family proteins, with 27 genes lacking introns and only one exon. The results of genome large segment duplication showed that there were 37 pairs of genes with tandem duplication. Interaction network analysis showed that CsP450 could interact with multiple types of target genes, and there are protein interactions within the family. Tissue expression analysis showed that P450 was highly expressed in roots and stems. Moreover, qPCR analysis of the relative expression level of the gene under drought and cold stress correlated with the sequencing results.

CONCLUSIONS

This study lays the foundation for resolving the classification and functional study of P450 family genes and provides a reference for the molecular breeding of C. sinensis.

Proteomics-Guided Mining and Characterization of Epoxidase Involved in Camptothecin Biosynthesis from Camptotheca acuminata

The detailed metabolic map for camptothecin (CPT) biosynthesis in Camptotheca acuminata has been proposed according to our combined omics results. However, the CYP450-mediated epoxidation step in CPT biosynthesis remains unexplored. A proteomics-guided approach was used to identify and annotate the proteins enriched during the vigorous CPT metabolism period in mature C. acuminata and seedlings. Comparative analyses revealed that the CPT and flavonoid biosyntheses were vigorous in stems and all of the samples except the leaves, respectively. The CYP71BE genes were screened based on their enrichment patterns at the transcriptomic-proteomic level and biochemically characterized in Saccharomyces cerevisiae WAT11. Four CYP71BE proteins exhibited in vitro isoliquiritigenin epoxidase activity. Additionally, CYP71BE206 showed epoxidase activity toward strictosamide, the critical precursor for CPT biosynthesis, both in vitro and in Nicotiana benthamiana. In planta functional verification suggested that CYP71BE206 is involved in CPT biosynthesis. Their catalytic conditions were optimized, and the enzymatic parameters were determined. This study provides valuable insight into the CYP71BE-mediated epoxidation step for CPT biosynthesis and offers evidence to verify that the newly characterized epoxidase (CYP71BE206) is simultaneously responsible for the biosynthesis of CPT and the flavonoid in this plant. An evolution event probably happened on ancestral CYP71BE, resulting in the neofunctionalization of CYP71BE206.

Unveiling the spatial distribution and molecular mechanisms of terpenoid biosynthesis in Salvia miltiorrhiza and S. grandifolia using multi-omics and DESI-MSI

Salvia miltiorrhiza and S. grandifolia are rich in diterpenoids and have therapeutic effects on cardiovascular diseases. In this study, the spatial distribution of diterpenoids in both species was analyzed by a combination of metabolomics and mass spectrometry imaging techniques. The results indicated that diterpenoids in S. miltiorrhiza were mainly abietane-type norditerpenoid quinones with a furan or dihydrofuran D-ring and were mainly distributed in the periderm of the roots, e.g. cryptotanshinone and tanshinone IIA. The compounds in S. grandifolia were mainly phenolic abietane-type tricyclic diterpenoids with six- or seven-membered C-rings, and were widely distributed in the periderm, phloem, and xylem of the roots, e.g. 11-hydroxy-sugiol, 11,20-dihydroxy-sugiol, and 11,20-dihydroxy-ferruginol. In addition, the leaves of S. grandifolia were rich in tanshinone biosynthesis precursors, such as 11-hydroxy-sugiol, while those of S. miltiorrhiza were rich in phenolic acids. Genes in the upstream pathway of tanshinone biosynthesis were highly expressed in the root of S. grandifolia, and genes in the downstream pathway were highly expressed in the root of S. miltiorrhiza. Here, we describe the specific tissue distributions and mechanisms of diterpenoids in two Salvia species, which will facilitate further investigations of the biosynthesis of diterpenoids in plant synthetic biology.

Novel mechanisms for the synthesis of important secondary metabolites in Ginkgo biloba seed revealed by multi-omics data

Although the detailed biosynthetic mechanism is still unclear, the unique secondary metabolites of Ginkgo biloba, including ginkgolic acids (GAs) and terpene trilactones, have attracted increasing attention for their potent medicinal, physiological and biochemical properties. In particular, GAs have shown great potential in the fields of antibacterial and insecticidal activities, making it urgent to elucidate their biosynthetic mechanism. In this study, we systematically revealed the landscape of metabolic-transcriptional regulation across continuous growth stages of G. biloba seeds (GBS) based on multi-omics mining and experimental verification, and successfully identified all major types of GAs and terpene trilactones along with more than a thousand kinds of other metabolites. The phenological changes and the essential gene families associated with these unique metabolites were analyzed in detail, and several potential regulatory factors were successfully identified based on co-expression association analysis. In addition, we unexpectedly found the close relationship between large introns and the biosynthesis of these secondary metabolites. These genes with large introns related to the synthesis of secondary metabolites showed higher gene expression and expression stability in different tissues or growth stages. Our results may provide a new perspective for the study of the regulatory mechanism of these unique secondary metabolites in GBS.

Meliaceae genomes provide insights into wood development and limonoids biosynthesis

Meliaceae is a useful plant family owing to its high-quality timber and its many limonoids that have pharmacological and biological activities. Although some genomes of Meliaceae species have been reported, many questions regarding their unique family features, namely wood quality and natural products, have not been answered. In this study, we provide the whole-genome sequence of Melia azedarach comprising 237.16 Mb with a contig N50 of 8.07 Mb, and an improved genome sequence of Azadirachta indica comprising 223.66 Mb with a contig N50 of 8.91 Mb. Moreover, genome skimming data, transcriptomes and other published genomes were comprehensively analysed to determine the genes and proteins that produce superior wood and valuable limonoids. Phylogenetic analysis of chloroplast genomes, single-copy gene families and single-nucleotide polymorphisms revealed that Meliaceae should be classified into two subfamilies: Cedreloideae and Melioideae. Although the Meliaceae species did not undergo additional whole-genome duplication events, the secondary wall biosynthetic genes of the woody Cedreloideae species, Toona sinensis, expanded significantly compared to those of A. indica and M. azedarach, especially in downstream transcription factors and cellulose/hemicellulose biosynthesis-related genes. Moreover, expanded special oxidosqualene cyclase catalogues can help diversify Sapindales skeletons, and the clustered genes that regulate terpene chain elongation, cyclization and modification would support their roles in limonoid biosynthesis. The expanded clans of terpene synthase, O-methyltransferase and cytochrome P450, which are mainly derived from tandem duplication, are responsible for the different limonoid classes among the species. These results are beneficial for further investigations of wood development and limonoid biosynthesis.

Functional Study of PgGRAS68-01 Gene Involved in the Regulation of Ginsenoside Biosynthesis in Panax ginseng

Ginseng (Panax ginseng C. A. Meyer) is a perennial herb from the genus Panax in the family Araliaceae. It is famous in China and abroad. The biosynthesis of ginsenosides is controlled by structural genes and regulated by transcription factors. GRAS transcription factors are widely found in plants. They can be used as tools to modify plant metabolic pathways by interacting with promoters or regulatory elements of target genes to regulate the expression of target genes, thereby activating the synergistic interaction of multiple genes in metabolic pathways and effectively improving the accumulation of secondary metabolites. However, there are no reports on the involvement of the GRAS gene family in ginsenoside biosynthesis. In this study, the GRAS gene family was located on chromosome 24 pairs in ginseng. Tandem replication and fragment replication also played a key role in the expansion of the GRAS gene family. The PgGRAS68-01 gene closely related to ginsenoside biosynthesis was screened out, and the sequence and expression pattern of the gene were analyzed. The results showed that the expression of PgGRAS68-01 gene was spatio-temporal specific. The full-length sequence of PgGRAS68-01 gene was cloned, and the overexpression vector pBI121-PgGRAS68-01 was constructed. The ginseng seedlings were transformed by Agrobacterium rhifaciens-mediated method. The saponin content in the single root of positive hair root was detected, and the inhibitory role of PgGRAS68-01 in ginsenoside synthesis is reported.

Delineation of the CYP505E subfamily of fungal self-sufficient in-chain hydroxylating cytochrome P450 monooxygenases

Cytochrome P450 monooxygenases (CYP450s) are abundant in eukaryotes, specifically in plants and fungi where they play important roles in the synthesis and degradation of secondary metabolites. In eukaryotes, the best studied "self-sufficient" CYP450s, with a fused redox partner, belong to the CYP505 family. Members of the CYP505 family are generally considered sub-terminal fatty acid hydroxylases. CYP505E3 from Aspergillus terreus, however, gives remarkable in-chain hydroxylation at the ω-7 position of C10 to C16 alkanes and C12 and C14 fatty alcohols. Because CYP505E3 is a promising catalyst for the synthesis of δ-dodecalactone, we set out to delineate the unique ω-7 hydroxylase activity of CYP505E3. CYP505E3 and six additional CYP505Es as well as four closely related CYP505s from four different subfamilies were expressed in Pichia pastoris. Only the CYP505Es, sharing more than 70% amino acid identity, displayed significant ω-7 hydroxylase activity toward 1-dodecanol, dodecanoic acid, and tetradecanoic acid giving products that can readily be converted to δ-dodecalactone. Concentrations of δ-dodecalactone, directly extracted from dodecanoic acid biotransformations, were higher than previously obtained with E. coli. Searches of the UniProt and NCBI databases yielded a total of only 23 unique CYP505Es, all from the Aspergillaceae. Given that CYP505Es with this remarkable activity occur in only a few Aspergillus and Penicillium spp., we further explored the genetic environments in which they occur. These were found to be very distinct environments which include a specific ABC transporter but could not be linked to apparent secondary metabolite gene clusters. KEY POINTS: • Identified CYP505Es share > 70% amino acid identity. • CYP505Es hydroxylate 1-dodecanol, dodecanoic, and tetradecanoic acid at ω-7 position. • CYP505E genes occur in Aspergillus and Penicillium spp. near an ABC transporter.

Global regulatory factor AaLaeA upregulates the production of antitumor substances in the endophytic fungus Alternaria alstroemeria

The global regulatory factor LaeA has been shown to be involved in the biosynthesis of secondary metabolites in various fungi. In a previous work, we isolated an endophytic fungus from Artemisia annua, and its extract had a significant inhibitory effect on the A549 cancer cell line. Phylogenetic analysis further identified the strain as Alternaria alstroemeria. Overexpression of AalaeA gene resulted in significantly increased antitumor activity of this strain's extract. The 3-(4, 5- dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide assay results showed that the inhibition rate of the AalaeA^OE29 mutant extract on A549 cancer cells was significantly higher than that of the WT extract, as the IC₅₀ decreased from 195.0 to 107.4 μg/ml, and the total apoptosis rate was enhanced. Overexpression of the AalaeA gene significantly increased the contents of myricetin, geraniol, ergosterol, and 18 other antitumor compounds as determined by metabolomic analysis. Transcriptomic analysis revealed significant changes in 95 genes in the mutant strain, including polyketide synthases, nonribosomal peptide synthases, cytochrome P450s, glycosyltransferases, acetyl-CoA acetyltransferases, and others. These results suggested that AaLaeA mediated the antitumor activity of the metabolites in A. alstroemeria by regulating multiple metabolic pathways.

The chromosome-level holly (Ilex latifolia) genome reveals key enzymes in triterpenoid saponin biosynthesis and fruit color change

The Ilex L. (hollies) genus of Aquifoliaceae shows high species diversity in tropical and subtropical regions of Asia and South America. Throughout the range of the genus, Ilex species have been widely used in beverage and medicine production and as ornamentals. Here, we assembled a high-quality, chromosome-level genome of Ilex latifolia, which has extremely high economic value because of its useful secondary metabolite production and the high ornamental value of its decorative red berries. The 99.8% genome sequence was anchored to 20 pseudochromosomes, with a total length of 766.02 Mb and a scaffold N50 of 33.45 Mb. Based on the comparative genomic analysis of 14 angiosperm species, we recovered I. latifolia as the sister group to all other campanulids. Two whole-genome duplication (WGD) events were identified in hollies: one shared ancient WGD in the ancestor of all eudicots and a recent and independent WGD in hollies. We performed a genome-wide search to screen candidate genes involved in the biosynthesis of pentacyclic triterpenoid saponins in I. latifolia. Three subfamilies of CYP450 (CYP71A, CYP72A, and CYP716A) appear to have expanded. The transcriptomic analysis of I. latifolia leaves at five developmental stages revealed that two CYP716A genes and one CYP72A gene probably play important roles in this biosynthetic pathway. In addition, we totally identified 12 genes in the biosynthesis pathways of pelargonidin and cyanidin and observed their differential expression in green and red fruit pericarps, suggesting an association between pelargonidin and cyanidin biosynthesis and fruit pericarp color change. The accumulation of pelargonidin and cyanidin is expected to play an important role in the ornamental value of I. latifolia. Altogether, this study elucidated the molecular basis of the medicinal and ornamental value of I. latifolia, providing a data basis and promising clues for further applications.

Cold stress regulates accumulation of flavonoids and terpenoids in plants by phytohormone, transcription process, functional enzyme, and epigenetics

Plants make different defense mechanisms in response to different environmental stresses. One common way is to produce secondary metabolites. Temperature is the main environmental factor that regulates plant secondary metabolites, especially flavonoids and terpenoids. Stress caused by temperature decreasing to 4-10 °C is conducive to the accumulation of flavonoids and terpenoids. However, the accumulation mechanism under cold stress still lacks a systematic explanation. In this review, we summarize three aspects of cold stress promoting the accumulation of flavonoids and terpenoids in plants, that is, by affecting (1) the content of endogenous plant hormones, especially jasmonic acid and abscisic acid; (2) the expression level and activity of important transcription factors, such as bHLH and MYB families. This aspect also includes post-translational modification of transcription factors caused by cold stress; (3) key enzyme genes expression and activity in the biosynthesis pathway, in addition, the rate-limiting enzyme and glycosyltransferases genes are responsive to cold stress. The systematic understanding of cold stress regulates flavonoids, and terpenoids will contribute to the future research of genetic engineering breeding, metabolism regulation, glycosyltransferases mining, and plant synthetic biology.

Genome-wide identification, evolution analysis of cytochrome P450 monooxygenase multigene family and their expression patterns during the early somatic embryogenesis in Dimocarpus longan Lour

Cytochrome P450 (CYP), a multi-gene superfamily, is involved in a broad range of physiological processes, including hormone responses and secondary metabolism throughout the plant life cycle. Longan (Dimocarpus longan), a subtropical and tropical evergreen fruit tree, its embryonic development is closely related to the yield and quality of fruits. And a large number of secondary metabolites, such as flavonoids and carotenoids, are also produced during the longan somatic embryogenesis (SE). It is important, therefore, to study potential functions of CYPs in longan. However, the knowledge of longan CYPs is still very limited. Here, a total of 327 DlCYPs were identified using the genome-search method, which could be classified into nine clans. The expansion of the DlCYP family was mainly caused by tandem duplication (TD) events. Promoter cis-acting elements analysis elucidated that DlCYPs played important roles in hormonal responses. A total of 246 DlCYPs exhibited six different expression patterns during the early SE based on longan transcriptomic data. Eight DlCYPs underwent alternative splicing (AS) events, and they might produce one to six isoforms. And the AS transcript of DlCYP97C1 might act as an alternative to the full-length transcript in ICpEC and GE stages. Finally, protein-protein interaction (PPI) networks and miRNA target prediction elucidated that DlCYPs might be involved in the phenylpropanoid metabolic pathway and primarily regulated and targeted by miR413. In summary, our results provided valuable inventory for understanding the classification and biological functions of DlCYPs and provided insight into further functional verification of DlCYPs during the longan early SE.

Genome Sequencing of Amomum tsao-ko Provides Novel Insight Into Its Volatile Component Biosynthesis

As an important economic and medicinal crop, Amomum tsao-ko is rich in volatile oils and widely used in food additives, essential oils, and traditional Chinese medicine. However, the lack of the genome remains a limiting factor for understanding its medicinal properties at the molecular level. Here, based on 288.72 Gb of PacBio long reads and 105.45 Gb of Illumina paired-end short reads, we assembled a draft genome for A. tsao-ko (2.70 Gb in size, contig N50 of 2.45 Mb). Approximately 90.07% of the predicted genes were annotated in public databases. Based on comparative genomic analysis, genes involved in secondary metabolite biosynthesis, flavonoid metabolism, and terpenoid biosynthesis showed significant expansion. Notably, the DXS, GGPPS, and CYP450 genes, which participate in rate-limiting steps for terpenoid backbone biosynthesis and modification, may form the genetic basis for essential oil formation in A. tsao-ko. The assembled A. tsao-ko draft genome provides a valuable genetic resource for understanding the unique features of this plant and for further evolutionary and agronomic studies of Zingiberaceae species.

Jasmonic acid promotes glutathione assisted degradation of chlorothalonil during tomato growth

Glutathione (GSH) biosynthesis and regeneration play a significant role in the metabolism of chlorothalonil (CHT) in tomatoes. However, the specific regulatory mechanism of GSH in the degradation of CHT remains uncertain. To address this, we investigate the critical regulatory pathways in the degradation of residual CHT in tomatoes. The results revealed that the detoxification of CHT residue in tomatoes was inhibited by buthionine sulfoximine and oxidized glutathione pretreatment, which increased by 26% and 46.12% compared with control, respectively. Gene silencing of γECS, GS, and GR also compromised the CHT detoxification potential of plants, which could be alleviated by GSH application and decreased the CHT accumulation by 33%, 25%, and 21%, respectively. Notably, it was found that the jasmonic acid (JA) pathway participated in the degradation of CHT regulated by GSH. CHT residues reduced by 28% after application of JA. JA played a role downstream of the glutathione pathway by promoting the degradation of CHT residue in tomatoes via nitric oxide signaling and improving the gene expression of antioxidant and detoxification-related enzymes. This study unveiled a crucial regulatory mechanism of GSH via the JA pathway in CHT degradation in tomatoes and offered new insights for understanding residual pesticide degradation.

Advances and challenges in ginseng research from 2011 to 2020: the phytochemistry, quality control, metabolism, and biosynthesis

Covering: 2011 to the end of 2020Panax species (Araliaceae), particularly P. ginseng, P. quinquefolius, and P. notoginseng, have a long history of medicinal use because of their remarkable tonifying effects, and currently serve as crucial sources for various healthcare products, functional foods, and cosmetics, aside from their vast clinical preparations. The huge market demand on a global scale prompts the continuous prosperity in ginseng research concerning the discovery of new compounds, precise quality control, ADME (absorption/disposition/metabolism/excretion), and biosynthesis pathways. Benefitting from the ongoing rapid development of analytical technologies, e.g. multi-dimensional chromatography (MDC), personalized mass spectrometry (MS) scan strategies, and multi-omics, highly recognized progress has been made in driving ginseng analysis towards "systematicness, integrity, personalization, and intelligentization". Herein, we review the advances in the phytochemistry, quality control, metabolism, and biosynthesis pathway of ginseng over the past decade (2011-2020), with 410 citations. Emphasis is placed on the introduction of new compounds isolated (saponins and polysaccharides), and the emerging novel analytical technologies and analytical strategies that favor ginseng's authentic use and global consumption. Perspectives on the challenges and future trends in ginseng analysis are also presented.

Chromosome-level assembly of the Neolamarckia cadamba genome provides insights into the evolution of cadambine biosynthesis

Neolamarckia cadamba (Roxb.), a close relative of Coffea canephora and Ophiorrhiza pumila, is an important traditional medicine in Southeast Asia. Three major glycosidic monoterpenoid indole alkaloids (MIAs), cadambine and its derivatives 3β-isodihydrocadambine and 3β-dihydrocadambine, accumulate in the bark and leaves, and exhibit antimalarial, antiproliferative, antioxidant, anticancer and anti-inflammatory activities. Here, we report a chromosome-scale N. cadamba genome, with 744.5 Mb assembled into 22 pseudochromosomes with contig N50 and scaffold N50 of 824.14 Kb and 29.20 Mb, respectively. Comparative genomic analysis of N. cadamba with Co. canephora revealed that N. cadamba underwent a relatively recent whole-genome duplication (WGD) event after diverging from Co. canephora, which contributed to the evolution of the MIA biosynthetic pathway. We determined the key intermediates of the cadambine biosynthetic pathway and further showed that NcSTR1 catalyzed the synthesis of strictosidine in N. cadamba. A new component, epoxystrictosidine (C27H34N2O10, m/z 547.2285), was identified in the cadambine biosynthetic pathway. Combining genome-wide association study (GWAS), population analysis, multi-omics analysis and metabolic gene cluster prediction, this study will shed light on the evolution of MIA biosynthetic pathway genes. This N. cadamba reference sequence will accelerate the understanding of the evolutionary history of specific metabolic pathways and facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants.

Redox metabolism for improving whole-cell P450-catalysed terpenoid biosynthesis

The growing preference for producing cytochrome P450-mediated natural products in microbial systems stems from the challenging nature of the organic chemistry approaches. The P450 enzymes are redox-dependent proteins, through which they source electrons from reducing cofactors to drive their activities. Widely researched in biochemistry, most of the previous studies have extensively utilised expensive cell-free assays to reveal mechanistic insights into P450 functionalities in presence of commercial redox partners. However, in the context of microbial bioproduction, the synergic activity of P450- reductase proteins in microbial systems have not been largely investigated. This is mainly due to limited knowledge about their mutual interactions in the context of complex systems. Hence, manipulating the redox potential for natural product synthesis in microbial chassis has been limited. As the potential of redox state as crucial regulator of P450 biocatalysis has been greatly underestimated by the scientific community, in this review, we re-emphasize their pivotal role in modulating the in vivo P450 activity through affecting the product profile and yield. Particularly, we discuss the applications of widely used in vivo redox engineering methodologies for natural product synthesis to provide further suggestions for patterning on P450-based terpenoids production in microbial platforms.

Lepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuels

Terpenes constitute the largest class of natural products with over 55,000 compounds with versatile applications including drugs and biofuels. Introducing structural modifications to terpenes through metabolic engineering is an efficient and sustainable way to improve their properties. Here, we report the optimization of the lepidopteran mevalonate (LMVA) pathway towards the efficient production of isopentenyl pyrophosphate (IPP) analogs as terpene precursors. First, we linked the LMVA pathway to NudB, a promiscuous phosphatase, resulting in the production of the six-carbon analog of 3-methyl-3-buten-1-ol (isoprenol), 3-ethyl-3-buten-1-ol (C6-isoprenol). Using C6-isoprenol as the final product, we then engineered the LMVA pathway by redirecting its upstream portion from a thiolase-dependent pathway to a beta-oxidation pathway. The beta-oxidation LMVA pathway transforms valeric acid, a platform chemical that can be produced from biomass, into C6-isoprenol at a titer of 110.3 mg/L, improved from 5.5 mg/L by the thiolase LMVA pathway, which used propionic acid as a feedstock. Knockout of the E. coli endogenous thiolase genes further improved the C6-isoprenol titer to 390 mg/L, implying efficient production of homo isopentenyl pyrophosphate (HIPP). The beta-oxidation LMVA-NudB pathway also converts butanoic acid and hexanoic acid into isoprenol and isoprenol's seven-carbon analog, 3-propyl-3-buten-1-ol (C7-isoprenol), respectively, suggesting the beta-oxidation LMVA pathway produces IPP and C7-IPP from the corresponding fatty acids. Fuel property tests revealed the longer chain isoprenol analogs have lower water solubilities, similar or higher energy densities, and comparable research octane number (RON) boosting effects to isopentenols. This work not only optimizes the LMVA pathway, setting the basis for homoterpene biosynthesis to expand terpene chemical space, but provides an efficient pathway to produce isoprenol analogs as next-generation biofuels from sustainable feedstocks.

Transcriptomic Characterization of Nitrate-Enhanced Stevioside Glycoside Synthesis in Stevia (Stevia rebaudiana) Bertoni

Nitrogen forms (nitrate (NO₃⁻) or ammonium (NH₄⁺)) are vital to plant growth and metabolism. In stevia (Stevia rebaudiana), it is important to assess whether nitrogen forms can influence the synthesis of the high-value terpene metabolites-steviol glycosides (SGs), together with the underlying mechanisms. Field and pot experiments were performed where stevia plants were fertilized with either NO₃⁻ or NH₄⁺ nutrition to the same level of nitrogen. Physiological measurements suggested that nitrogen forms had no significant impact on biomass and the total nitrogen content of stevia leaves, but NO₃⁻-enhanced leaf SGs contents. Transcriptomic analysis identified 397 genes that were differentially expressed (DEGs) between NO₃⁻ and NH₄⁺ treatments. Assessment of the DEGs highlighted the responses in secondary metabolism, particularly in terpenoid metabolism, to nitrogen forms. Further examinations of the expression patterns of SGs synthesis-related genes and potential transcription factors suggested that GGPPS and CPS genes, as well as the WRKY and MYB transcription factors, could be driving N form-regulated SG synthesis. We concluded that NO₃⁻, rather than NH₄⁺, can promote leaf SG synthesis via the NO₃⁻-MYB/WRKY-GGPPS/CPS module. Our study suggests that insights into the molecular mechanism of how SG synthesis can be affected by nitrogen forms.

A novel method for ginkgolide biosynthesis elucidation based on MeJA induction and differential metabolomics

Ginkgolides from Ginkgo Biloba have significantly therapeutic effect to cardiovascular and cerebrovascular diseases. However, the biosynthetic pathway of ginkgolides has not been fully elucidated until now. As ginkgolides are synthesized in the ginkgo roots, the accumulation of ginkgolides intermediate metabolites varies greatly between roots and leaves. As Methyl jasmonate (MeJA) can effectively enhance the biosynthesis of ginkgolides, a novel method based on MeJA induction and differential metabolomics was used to screen the differentially intermediate metabolites among ginkgo leaves, roots and roots-MJ-3. Two differential intermediate metabolites (dehydroabietadienal and 1, 2, 3, 4, 4a, 9, 10, 10a-Octahydro-6-hydroxy-7-isopropyl-1, 4a-dimethyl-1-phenanthrenemethanol) were identified in ginkgo roots by UPLC-QTOF-MS. Then, a new ginkgolides biosynthetic pathway was proposed based on differential metabolomics. This study provides a novel method for the elucidation of nature product precursor and is helpful to promote the clarification of ginkgolides biosynthetic pathway.

Multiscale Simulations on the Catalytic Plasticity of CYP76AH1

The catalytic promiscuity and fidelity of cytochrome P450 enzymes are widespread in the skeletal modification of terpenoid natural products and have attracted much attention. CYP76AH1 is involved in key modification reactions in the biosynthetic pathway of tanshinone, a well-known medicinal norditerpenoid. In this work, classical molecular dynamic simulations, metadynamics, and DFT calculations were performed to investigate the protein conformational dynamics, ligand binding poses, and catalytic reaction mechanism in wide-type and mutant CYP76AH1. Our results not only reveal a plausible enzymatic mechanism for mutant CYP76AH1 leading to various products but also provide valuable guidance for rational protein engineering of the CYP76 family.

Transcriptomic analysis of saffron at different flowering stages using RNA sequencing uncovers cytochrome P450 genes involved in crocin biosynthesis

Saffron is a well-known Chinese traditional herb, and crocin biosynthesis is related to the yield and quality of saffron. This study aimed to screen differentially expressed genes (DEGs) in saffron at different flowering stages and identify cytochrome P450 (CYP) genes involved in crocin biosynthesis. Saffron samples at different flowering stages were used for RNA sequencing, and DEGs between the samples at three days before the flowering stage (- 3da) and two days after the flowering stage (+ 2da) were screened. Thereafter, significantly differentially expressed CYP genes were identified, and CYP gene expression at different flowering stages and in various tissues of saffron was determined using real-time quantitative polymerase chain reaction (RT-qPCR). After sequencing and analysis, 1508 DEGs between the samples at - 3da and + 2da were identified, including 487 upregulated and 1021 downregulated genes, which were enriched in 16 biological processes, 5 cellular components, 3 molecular functions, and 11 KEGG pathways, including protein processing in endoplasmic reticulum, pentose and glucuronate interconversions, starch and sucrose metabolism, estrogen signaling pathway, and mitogen-activated protein kinase signaling pathway. In addition, 12 significantly differentially expressed CYP genes were identified. The RT-qPCR results showed that CYP76C4, CYP72A15, CYP72A219, CYP97B2, CYP714C2, CYP71A1, CYP94C1, and CYP86A8 were all expressed in the pistils, and CYP72A219, CYP72A15, CYP97B2, CYP71A1, and CYP86A8 were highly expressed in the pistils. Our study established a transcriptome library of saffron and found that CYP72A219, CYP72A15, CYP97B2, CYP71A1, and CYP86A8 may be candidates involved crocin biosynthesis in saffron.

CYP82AR Subfamily Proteins Catalyze C-1' Hydroxylations of Deoxyshikonin in the Biosynthesis of Shikonin and Alkannin

Shikonin and S-enantiomer alkannin are important naphthoquinone derivatives present in many Boraginaceae species. We report that cytochrome P450 monooxygenases (CYPs) from a new CYP82AR subfamily catalyzed hydroxylations of deoxyshikonin at C-1' position of isoprenoid side chain. Two homologues were discovered from each species of the four Boraginaceae plants. One CYP preferred converting deoxyshikonin into shikonin, and the other stereoselectively hydroxylated deoxyshikonin into alkannin. The discovery might be a general feature of shikonin/alkannin-producing Boraginaceae plants.

Nutritional Aspects of Ecologically Relevant Phytochemicals in Ruminant Production

This review provides an update of ecologically relevant phytochemicals for ruminant production, focusing on their contribution to advancing nutrition. Phytochemicals embody a broad spectrum of chemical components that influence resource competence and biological advantage in determining plant species' distribution and density in different ecosystems. These natural compounds also often act as plant defensive chemicals against predatorial microbes, insects, and herbivores. They may modulate or exacerbate microbial transactions in the gastrointestinal tract and physiological responses in ruminant microbiomes. To harness their production-enhancing characteristics, phytochemicals have been actively researched as feed additives to manipulate ruminal fermentation and establish other phytochemoprophylactic (prevent animal diseases) and phytochemotherapeutic (treat animal diseases) roles. However, phytochemical-host interactions, the exact mechanism of action, and their effects require more profound elucidation to provide definitive recommendations for ruminant production. The majority of phytochemicals of nutritional and pharmacological interest are typically classified as flavonoids (9%), terpenoids (55%), and alkaloids (36%). Within flavonoids, polyphenolics (e.g., hydrolyzable and condensed tannins) have many benefits to ruminants, including reducing methane (CH4) emission, gastrointestinal nematode parasitism, and ruminal proteolysis. Within terpenoids, saponins and essential oils also mitigate CH4 emission, but triterpenoid saponins have rich biochemical structures with many clinical benefits in humans. The anti-methanogenic property in ruminants is variable because of the simultaneous targeting of several physiological pathways. This may explain saponin-containing forages' relative safety for long-term use and describe associated molecular interactions on all ruminant metabolism phases. Alkaloids are N-containing compounds with vast pharmacological properties currently used to treat humans, but their phytochemical usage as feed additives in ruminants has yet to be exploited as they may act as ghost compounds alongside other phytochemicals of known importance. We discussed strategic recommendations for phytochemicals to support sustainable ruminant production, such as replacements for antibiotics and anthelmintics. Topics that merit further examination are discussed and include the role of fresh forages vis-à-vis processed feeds in confined ruminant operations. Applications and benefits of phytochemicals to humankind are yet to be fully understood or utilized. Scientific explorations have provided promising results, pending thorough vetting before primetime use, such that academic and commercial interests in the technology are fully adopted.

The chromosome-based lavender genome provides new insights into Lamiaceae evolution and terpenoid biosynthesis

The aromatic shrub Lavandula angustifolia produces various volatile terpenoids that serve as resources for essential oils and function in plant-insect communication. To better understand the genetic basis of the terpenoid diversity in lavender, we present a high-quality reference genome for the Chinese lavender cultivar "Jingxun 2" using PacBio and Hi-C technologies to anchor the 894.50 Mb genome assembly into 27 pseudochromosomes. In addition to the γ triplication event, lavender underwent two rounds of whole-genome duplication (WGD) during the Eocene-Oligocene (29.6 MYA) and Miocene-Pliocene (6.9 MYA) transitions. As a result of tandem duplications and lineage-specific WGDs, gene families related to terpenoid biosynthesis in lavender are substantially expanded compared to those of five other species in Lamiaceae. Many terpenoid biosynthesis transcripts are abundant in glandular trichomes. We further integrated the contents of ecologically functional terpenoids and coexpressed terpenoid biosynthetic genes to construct terpenoid-gene networks. Typical gene clusters, including TPS-TPS, TPS-CYP450, and TPS-BAHD, linked with compounds that primarily function as attractants or repellents, were identified by their similar patterns of change during flower development or in response to methyl jasmonate. Comprehensive analysis of the genetic basis of the production of volatiles in lavender could serve as a foundation for future research into lavender evolution, phytochemistry, and ecology.

Two new seco-polycyclic polyprenylated acylphloroglucinol from Hypericum sampsonii

Two rare seco-polycyclic polyprenylated acylphloroglucinols (1 and 2) were isolated from Hypericum sampsonii. Compounds 1 and 2 showed moderate multidrug resistance (MDR) reversal activity to resistant cancer cells, HepG2/ADR and MCF-7/ADR.

Multi-tissue transcriptome analysis using hybrid-sequencing reveals potential genes and biological pathways associated with azadirachtin A biosynthesis in neem (azadirachta indica)

BACKGROUND

Azadirachtin A is a triterpenoid from neem tree exhibiting excellent activities against over 600 insect species in agriculture. The production of azadirachtin A depends on extraction from neem tissues, which is not an eco-friendly and sustainable process. The low yield and discontinuous supply of azadirachtin A impedes further applications. The biosynthetic pathway of azadirachtin A is still unknown and is the focus of our study.

RESULTS

We attempted to explore azadirachtin A biosynthetic pathway and identified the key genes involved by analyzing transcriptome data from five neem tissues through the hybrid-sequencing (Illumina HiSeq and Pacific Biosciences Single Molecule Real-Time (SMRT)) approach. Candidates were first screened by comparing the expression levels between the five tissues. After phylogenetic analysis, domain prediction, and molecular docking studies, 22 candidates encoding 2,3-oxidosqualene cyclase (OSC), alcohol dehydrogenase, cytochrome P450 (CYP450), acyltransferase, and esterase were proposed to be potential genes involved in azadirachtin A biosynthesis. Among them, two unigenes encoding homologs of MaOSC1 and MaCYP71CD2 were identified. A unigene encoding the complete homolog of MaCYP71BQ5 was reported. Accuracy of the assembly was verified by quantitative real-time PCR (qRT-PCR) and full-length PCR cloning.

CONCLUSIONS

By integrating and analyzing transcriptome data from hybrid-seq technology, 22 differentially expressed genes (DEGs) were finally selected as candidates involved in azadirachtin A pathway. The obtained reliable and accurate sequencing data provided important novel information for understanding neem genome. Our data shed new light on understanding the biosynthesis of other triterpenoids in neem trees and provides a reference for exploring other valuable natural product biosynthesis in plants.

Advances in biosynthesis, regulation, and metabolic engineering of plant specialized terpenoids

Plant specialized terpenoids are natural products that have no obvious role in growth and development, but play many important functional roles to improve the plant's overall fitness. Besides, plant specialized terpenoids have immense value to humans due to their applications in fragrance, flavor, cosmetic, and biofuel industries. Understanding the fundamental aspects involved in the biosynthesis and regulation of these high-value molecules in plants not only paves the path to enhance plant traits, but also facilitates homologous or heterologous engineering for overproduction of target molecules of importance. Recent developments in functional genomics and high-throughput analytical techniques have led to unraveling of several novel aspects involved in the biosynthesis and regulation of plant specialized terpenoids. The knowledge thus derived has been successfully utilized to produce target specialized terpenoids of plant origin in homologous or heterologous host systems by metabolic engineering and synthetic biology approaches. Here, we provide an overview and highlights on advances related to the biosynthetic steps, regulation, and metabolic engineering of plant specialized terpenoids.