Modules of co-regulated metabolites in turmeric (Curcuma longa) rhizome suggest the existence of biosynthetic modules in plant specialized metabolism

Functional characterization of key polyketide synthases by integrated metabolome and transcriptome analysis on curcuminoid biosynthesis in Curcuma wenyujin

Leaf and tuber extracts of Curcuma wenyujin contain a mixture of curcuminoids. However, the curcuminoid constituents and their molecular mechanisms are poorly understood, and the relevant curcumin synthases remain unclear. In this study, we comprehensively compared the metabolite profiles of the leaf and tuber tissues of C. wenyujin. A total of 11 curcuminoid metabolites were identified and exhibited differentially changed contents in the leaf and tuber tissues. An integrated analysis of metabolomic and transcriptomic data revealed the proposed biosynthesis pathway of curcuminoid. Two candidate type Ⅲ polyketide synthases (PKSs) were identified in the metabolically engineering yeasts, indicating that CwPKS1 and CwPKS2 maintained substrate and product specificities. Especially, CwPKS1 is the first type Ⅲ PKS identified to synthesize hydrogenated derivatives of curcuminoid, dihydrocurcumin and tetrehydrocurcumin. Interestingly, the substitution of the glycine at position 219 with aspartic acid (G219D mutant) resulted in the complete inactivation of CwPKS1. Our results provide the first comparative metabolome analysis of C. wenyujin and functionally identified type Ⅲ PKSs, giving valuable information for curcuminoids biosynthesis.

An Ancient Residue Metabolomics-Based Method to Distinguish Use of Closely Related Plant Species in Ancient Pipes

Residues from ancient artifacts can help identify which plant species were used for their psychoactive properties, providing important information regarding the deep-time co-evolutionary relationship between plants and humans. However, relying on the presence or absence of one or several biomarkers has limited the ability to confidently connect residues to particular plants. We describe a comprehensive metabolomics-based approach that can distinguish closely related species and provide greater confidence in species use determinations. An ~1430-year-old pipe from central Washington State not only contained nicotine, but also had strong evidence for the smoking of Nicotiana quadrivalvis and Rhus glabra, as opposed to several other species in this pre-contact pipe. Analysis of a post-contact pipe suggested use of different plants, including the introduced trade tobacco, Nicotiana rustica. Ancient residue metabolomics provides a new frontier in archaeo-chemistry, with greater precision to investigate the evolution of drug use and similar plant-human co-evolutionary dynamics.

An integrated strategy to identify genes responsible for sesquiterpene biosynthesis in turmeric

Metabolic module, gene expression pattern and PLS modeling were integrated to precisely identify the terpene synthase responsible for sesquiterpene formation. Functional characterization confirmed the feasibility and sensitivity of this strategy. Plant secondary metabolite biosynthetic pathway elucidation is crucial for the production of these compounds with metabolic engineering. In this study, an integrated strategy was employed to predict the gene function of sesquiterpene synthase (STS) genes using turmeric as a model. Parallel analysis of gene expression patterns and metabolite modules narrowed the candidates into an STS group in which the STSs showed a similar expression pattern. The projections to latent structures by means of partial least squares model was further employed to establish a clear relationship between the candidate STS genes and metabolites and to predict three STSs (ClTPS16, ClTPS15 and ClTPS14) involved in the biosynthesis of several sesquiterpene skeletons. Functional characterization revealed that zingiberene and β-sesquiphellandrene were the major products of ClTPS16, and β-eudesmol was produced by ClTPS15, both of which indicated the accuracy of the prediction. Functional characterization of a control STS, ClTPS1, produced a small amount of β-sesquiphellandrene, as predicted, which confirmed the sensitivity of metabolite module analysis. This integrated strategy provides a methodology for gene function predictions, which represents a substantial improvement in the elucidation of biosynthetic pathways in nonmodel plants.

Characterization of diarylheptanoids: An emerging class of bioactive natural products

Diarylheptanoids are a class of secondary plant metabolites with a wide variety of bioactivity. Research on their phytochemistry and phytoanalysis is rapidly growing and the number of identified structures bearing the aryl-C₇-aryl skeleton is at present approaching 500. Historically, the yellow pigment curcumin has been characterized as the first diarylheptanoid and the extensive research on naturally occurring analogues is still ongoing. In this review, studies dealing with the characterization of linear and cyclic derivatives are discussed from the phytoanalytical point of view. Isolation, fractionation and purification strategies from natural sources along with their chromatographic behavior and structural characteristics are discussed. The role of various techniques used for the extraction (such as Soxhlet extraction, sonication, maceration/percolation, microwave-assisted extraction, supercritical carbon dioxide extraction); isolation (liquid-liquid extraction, column chromatographic techniques, preparative thin-layer and high-performance liquid chromatography, centrifugal partition chromatography, counter-current chromatography); separation (thin-layer chromatography, high-performance liquid chromatography, gas chromatography, capillary electrophoresis) and structural characterization (UV/Vis spectroscopy, infrared spectroscopy, X-ray crystallography, mass spectrometry, nuclear magnetic resonance spectroscopy and circular dichroism spectroscopy) are critically reviewed.

Heterologous production of curcuminoids

SUMMARY

Curcuminoids, components of the rhizome of turmeric, show several beneficial biological activities, including anticarcinogenic, antioxidant, anti-inflammatory, and antitumor activities. Despite their numerous pharmaceutically important properties, the low natural abundance of curcuminoids represents a major drawback for their use as therapeutic agents. Therefore, they represent attractive targets for heterologous production and metabolic engineering. The understanding of biosynthesis of curcuminoids in turmeric made remarkable advances in the last decade, and as a result, several efforts to produce them in heterologous organisms have been reported. The artificial biosynthetic pathway (e.g., in Escherichia coli) can start with the supplementation of the amino acid tyrosine or phenylalanine or of carboxylic acids and lead to the production of several natural curcuminoids. Unnatural carboxylic acids can also be supplemented as precursors and lead to the production of unnatural compounds with possibly novel therapeutic properties. In this paper, we review the natural conversion of curcuminoids in turmeric and their production by E. coli using an artificial biosynthetic pathway. We also explore the potential of other enzymes discovered recently or already used in other similar biosynthetic pathways, such as flavonoids and stilbenoids, to increase curcuminoid yield and activity.

Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database

Biology is increasingly becoming a data-intensive science with the recent progress of the omics fields, e.g. genomics, transcriptomics, proteomics and metabolomics. The species-metabolite relationship database, KNApSAcK Core, has been widely utilized and cited in metabolomics research, and chronological analysis of that research work has helped to reveal recent trends in metabolomics research. To meet the needs of these trends, the KNApSAcK database has been extended by incorporating a secondary metabolic pathway database called Motorcycle DB. We examined the enzyme sequence diversity related to secondary metabolism by means of batch-learning self-organizing maps (BL-SOMs). Initially, we constructed a map by using a big data matrix consisting of the frequencies of all possible dipeptides in the protein sequence segments of plants and bacteria. The enzyme sequence diversity of the secondary metabolic pathways was examined by identifying clusters of segments associated with certain enzyme groups in the resulting map. The extent of diversity of 15 secondary metabolic enzyme groups is discussed. Data-intensive approaches such as BL-SOM applied to big data matrices are needed for systematizing protein sequences. Handling big data has become an inevitable part of biology.

Data Mining Methods for Omics and Knowledge of Crude Medicinal Plants toward Big Data Biology

Molecular biological data has rapidly increased with the recent progress of the Omics fields, e.g., genomics, transcriptomics, proteomics and metabolomics that necessitates the development of databases and methods for efficient storage, retrieval, integration and analysis of massive data. The present study reviews the usage of KNApSAcK Family DB in metabolomics and related area, discusses several statistical methods for handling multivariate data and shows their application on Indonesian blended herbal medicines (Jamu) as a case study. Exploration using Biplot reveals many plants are rarely utilized while some plants are highly utilized toward specific efficacy. Furthermore, the ingredients of Jamu formulas are modeled using Partial Least Squares Discriminant Analysis (PLS-DA) in order to predict their efficacy. The plants used in each Jamu medicine served as the predictors, whereas the efficacy of each Jamu provided the responses. This model produces 71.6% correct classification in predicting efficacy. Permutation test then is used to determine plants that serve as main ingredients in Jamu formula by evaluating the significance of the PLS-DA coefficients. Next, in order to explain the role of plants that serve as main ingredients in Jamu medicines, information of pharmacological activity of the plants is added to the predictor block. Then N-PLS-DA model, multiway version of PLS-DA, is utilized to handle the three-dimensional array of the predictor block. The resulting N-PLS-DA model reveals that the effects of some pharmacological activities are specific for certain efficacy and the other activities are diverse toward many efficacies. Mathematical modeling introduced in the present study can be utilized in global analysis of big data targeting to reveal the underlying biology.

Cytotoxic effect of commercial Humulus lupulus L. (hop) preparations - In comparison to its metabolomic fingerprint

Hops (Humulus lupulus L. Cannabaceae) is an economically important crop, that has drawn more attention in recent years due to its potential pharmaceutical applications. Bitter acids (prenylated polyketides) and prenylflavonoids are the primary phytochemical components that account for hops resins medicinal value. We have previously reported on utilizing untargeted NMR and MS metabolomics for analysis of 13 hops cultivars, revealing for differences in α- versus β-bitter acids composition in derived resins. In this study, effect of ratios of bitter α- to β-acids in hop resins to cytotoxicity of hop resins was investigated. In vitro cell culture assays revealed that β-acids were more effective than α-acids in growth inhibition of PC3 and HT29 cancer cell lines. Nevertheless, hop resins enriched in β-acids showed comparable growth inhibition patterns to α-enriched resins and suggesting that bioactivity may not be easily predicted by metabolomics and/or gross metabolic profiling in hops.

Molecular cloning and differential expressions of two cDNA encoding Type III polyketide synthase in different tissues of Curcuma longa L

Type III polyketide synthase family of enzymes play an important role in the biosynthesis of flavonoids and a variety of plant polyphenols by condensing multiple acetyl units derived from malonyl Co-A to thioester linked starter molecules covalently bound in the PKS active site. Turmeric (Curucma longa L.) through diverse metabolic pathways produces a large number of metabolites, of which curcuminoids had gained much attention due to its immense pharmaceutical value. Recent identification of multiple curcuminoid synthases from turmeric lead us to look for additional Type III PKS from this plant. The current study describes the occurrence of a multigene family of Type III PKS enzymes in C. longa by RT-PCR based genomic screening. We have also isolated two new Type III PKS, ClPKS9 and ClPKS10 using homology based RT-PCR and data mining. The comparative sequence and phylogenetic analysis revealed that the two PKSs belong to different groups with only 56% sequence similarity at their amino acid level. ClPKS9 shows all possible sequence requirements for a typical chalcone synthase whereas ClPKS10 shows promising variation at amino acid level and high similarity to reported curcuminoid synthases. ClPKS9 and ClPKS10 exhibited distinct tissue specific expression pattern in C. longa with the ClPKS9 transcript abundant in shoot and rhizome than leaves whereas ClPKS10 transcript was found to be high in leaf and very low in rhizome and root. Therefore it was concluded that ClPKS9 and ClPKS10 may have divergent function in planta, with possible role in typical chalcone forming reaction and curcuminoid scaffold biosynthetic pathway respectively.

Comparative functional genomic analysis of Solanum glandular trichome types

Glandular trichomes play important roles in protecting plants from biotic attack by producing defensive compounds. We investigated the metabolic profiles and transcriptomes to characterize the differences between different glandular trichome types in several domesticated and wild Solanum species: Solanum lycopersicum (glandular trichome types 1, 6, and 7), Solanum habrochaites (types 1, 4, and 6), Solanum pennellii (types 4 and 6), Solanum arcanum (type 6), and Solanum pimpinellifolium (type 6). Substantial chemical differences in and between Solanum species and glandular trichome types are likely determined by the regulation of metabolism at several levels. Comparison of S. habrochaites type 1 and 4 glandular trichomes revealed few differences in chemical content or transcript abundance, leading to the conclusion that these two glandular trichome types are the same and differ perhaps only in stalk length. The observation that all of the other species examined here contain either type 1 or 4 trichomes (not both) supports the conclusion that these two trichome types are the same. Most differences in metabolites between type 1 and 4 glands on the one hand and type 6 glands on the other hand are quantitative but not qualitative. Several glandular trichome types express genes associated with photosynthesis and carbon fixation, indicating that some carbon destined for specialized metabolism is likely fixed within the trichome secretory cells. Finally, Solanum type 7 glandular trichomes do not appear to be involved in the biosynthesis and storage of specialized metabolites and thus likely serve another unknown function, perhaps as the site of the synthesis of protease inhibitors.