Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus.

Mallotus japonicus is a valuable traditional medicinal plant in East Asia for applications as a gastrointestinal drug. However, the molecular components involved in the biosynthesis of bioactive metabolites have not yet been explored, primarily due to a lack of omics resources. In this study, we established metabolome and transcriptome resources for M. japonicus to capture the diverse metabolite constituents and active transcripts involved in its biosynthesis and regulation. A combination of untargeted metabolite profiling with data-dependent metabolite fragmentation and metabolite annotation through manual curation and feature-based molecular networking established an overall metabospace of M. japonicus represented by 2129 metabolite features. M. japonicus de novo transcriptome assembly showed 96.9% transcriptome completeness, representing 226,250 active transcripts across seven tissues. We identified specialized metabolites biosynthesis in a tissue-specific manner, with a strong correlation between transcripts expression and metabolite accumulations in M. japonicus. The correlation- and network-based integration of metabolome and transcriptome datasets identified candidate genes involved in the biosynthesis of key specialized metabolites of M. japonicus. We further used phylogenetic analysis to identify 13 C-glycosyltransferases and 11 methyltransferases coding candidate genes involved in the biosynthesis of medicinally important bergenin. This study provides comprehensive, high-quality multi-omics resources to further investigate biological properties of specialized metabolites biosynthesis in M. japonicus.

Role of Blood Stasis Syndrome of Kampo Medicine in the Early Pathogenic Stage of Atherosclerosis: A Retrospective Cross-Sectional Study.

In Kampo medicine, blood stasis (BS) syndrome is strongly associated with microangiopathy and can lead to atherosclerosis. Vascular endothelial dysfunction (VED), evaluated through flow-mediated dilation (FMD), plays an important role in the early stages of atherosclerosis. However, the association of BS syndrome with VED, as determined using FMD, has not been reported. This study investigated the association between BS syndrome and VED using FMD. Forty-one patients with normal glucose tolerance or impaired glucose tolerance (IGT) and without macrovascular complications were evaluated using FMD from May 2017 to August 2017. Based on the BS score, the patients were divided into the non-BS (n = 19) and BS syndrome (n = 22) groups. Physical and background characteristics, physiological function test results, and laboratory data were compared. Univariate analysis revealed that FMD and a history of dyslipidemia/IGT were significantly different between the two groups (p < 0.05). Multiple logistic regression analysis showed that BS syndrome was significantly associated with FMD (odds ratio: 6.26; p=0.03) after adjusting for the history of dyslipidemia/IGT. The receiver operating characteristic curve showed that the area under the curve for BS syndrome (0.74; p < 0.001) and history of IGT (p < 0.007) provided good diagnostic accuracy for FMD. The area under the curve for "BS syndrome + IGT" showed very good accuracy (0.80; p < 0.0001) and was higher than that for BS syndrome or IGT alone. In conclusion, the results of this study suggest that the BS score in Kampo medicine could be a useful tool for detecting the early pathogenic stages of atherosclerosis.

Multiomics-based characterization of specialized metabolites biosynthesis in Cornus Officinalis.

Cornus officinalis, an important traditional medicinal plant, is used as major constituents of tonics, analgesics, and diuretics. While several studies have focused on its characteristic bioactive compounds, little is known on their biosynthesis. In this study, we performed LC-QTOF-MS-based metabolome and RNA-seq-based transcriptome profiling for seven tissues of C. officinalis. Untargeted metabolome analysis assigned chemical identities to 1,215 metabolites and showed tissue-specific accumulation for specialized metabolites with medicinal properties. De novo transcriptome assembly established for C. officinalis showed 96% of transcriptome completeness. Co-expression analysis identified candidate genes involved in the biosynthesis of iridoids, triterpenoids, and gallotannins, the major group of bioactive metabolites identified in C. officinalis. Integrative omics analysis identified 45 cytochrome P450s genes correlated with iridoids accumulation in C. officinalis. Network-based integration of genes assigned to iridoids biosynthesis pathways with these candidate CYPs further identified seven promising CYPs associated with iridoids' metabolism. This study provides a valuable resource for further investigation of specialized metabolites' biosynthesis in C. officinalis.

The beneficial effect of traditional Japanese herbal (Kampo) medicine, Hochu-ekki-to (Bu-Zhong-Yi-Qi-Tang), for patients with chronic wounds refractory to conventional therapies: A prospective, randomized trial.

Hochu-ekki-to (HET) is a traditional Japanese herbal (Kampo) medicine for the treatment of severe weakness, loss of appetite, and indigestion in elderly patients and for the prevention of opportunistic infections. The impact of HET on patients with chronic wounds refractory to conventional therapies was investigated in a prospective, randomized trial, including 18 patients divided into medication (7.5 g oral HET per day, n = 9) and control (n = 9) groups. Wound healing during the 12-week study period was scored based on depth, exudate, size, inflammation/infection, granulation tissue, necrotic tissue, and pocket size. At 12 weeks, wound healing progressed in all nine patients in the medication group, whereas wound healing progressed in only three patients in the control group (significant difference, p < 0.01; relative risk: 3.00). In the medication group, the total score decreased significantly at 8 weeks and later. To the best of our knowledge, this study was the first to show that HET promoted the healing of chronic wounds resistant to conventional treatments. HET may be a choice as an adjunctive therapy for chronic wounds, particularly for patients with malnutrition. This trial was registered with the University Hospital Medical Information Network Clinical Trials Registry (UMIN000031620).

Identification of potential genes involved in triterpenoid saponins biosynthesis in Gleditsia sinensis by transcriptome and metabolome analyses.

Gleditsia sinensis is widely used as a medicinal plant in Asia, especially in China. Triterpenes, alkaloids, and sterols were isolated from Gleditsia species. Among them, triterpenoid saponins are very important metabolites owing to their various pharmacological activities. However, the triterpenoid saponin biosynthesis pathway has not been well characterized. In the present study, we performed de novo transcriptome assembly for 14.3 Gbps of clean reads sequenced from nine tissues of G. sinensis. The results showed that 81,511 unique transcripts (unitranscripts) (47,855 unigenes) were constructed, of which 31,717 unigenes were annotated with Gene Ontology and EC numbers by Blast2GO against the NCBI-nr protein database. We also analyzed the metabolite contents in the same nine tissues by LS-MS/MS, and saponins including gleditsioside I were found in fruit at higher levels. Many of the genes with tissue-specific expression in fruit are involved in the flavonoid biosynthesis pathway, and many of those have UDP-glucosyltransferase (UGT) activity. We constructed a saponin biosynthesis pathway and identified two key enzyme families in the triterpenoid saponin biosynthesis pathway, cytochrome P450 and UDP-glucosyltransferase, that are encoded by 37 unigenes and 77 unigenes, respectively. CYP72A, CYP716A, and CYP88D, which are known as key enzymes for saponin biosynthesis, were also identified among the P450s. Our results provide insight into the secondary metabolite biosynthesis and serve as important resources for future research and cultivation of G. sinensis.

Comparative transcriptome analyses of three medicinal Forsythia species and prediction of candidate genes involved in secondary metabolisms.

The three Forsythia species, F. suspensa, F. viridissima and F. koreana, have been used as herbal medicines in China, Japan and Korea for centuries and they are known to be rich sources of numerous pharmaceutical metabolites, forsythin, forsythoside A, arctigenin, rutin and other phenolic compounds. In this study, de novo transcriptome sequencing and assembly was performed on these species. Using leaf and flower tissues of F. suspensa, F. viridissima and F. koreana, 1.28-2.45-Gbp sequences of Illumina based pair-end reads were obtained and assembled into 81,913, 88,491 and 69,458 unigenes, respectively. Classification of the annotated unigenes in gene ontology terms and KEGG pathways was used to compare the transcriptome of three Forsythia species. The expression analysis of orthologous genes across all three species showed the expression in leaf tissues being highly correlated. The candidate genes presumably involved in the biosynthetic pathway of lignans and phenylethanoid glycosides were screened as co-expressed genes. They express highly in the leaves of F. viridissima and F. koreana. Furthermore, the three unigenes annotated as acyltransferase were predicted to be associated with the biosynthesis of acteoside and forsythoside A from the expression pattern and phylogenetic analysis. This study is the first report on comparative transcriptome analyses of medicinally important Forsythia genus and will serve as an important resource to facilitate further studies on biosynthesis and regulation of therapeutic compounds in Forsythia species.

De Novo Transcriptome Assembly and Characterization of Lithospermum officinale to Discover Putative Genes Involved in Specialized Metabolites Biosynthesis.

Lithospermum officinale is a valuable source of bioactive metabolites with medicinal and industrial values. However, little is known about genes involved in the biosynthesis of these metabolites, primarily due to the lack of genome or transcriptome resources. This study presents the first effort to establish and characterize de novo transcriptome assembly resource for L. officinale and expression analysis for three of its tissues, namely leaf, stem, and root. Using over 4Gbps of RNA-sequencing datasets, we obtained de novo transcriptome assembly of L. officinale, consisting of 77,047 unigenes with assembly N50 value as 1524 bps. Based on transcriptome annotation and functional classification, 52,766 unigenes were assigned with putative genes functions, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. KEGG pathway and gene ontology enrichment analysis using highly expressed unigenes across three tissues and targeted metabolome analysis showed active secondary metabolic processes enriched specifically in the root of L. officinale. Using co-expression analysis, we also identified 20 and 48 unigenes representing different enzymes of lithospermic/chlorogenic acid and shikonin biosynthesis pathways, respectively. We further identified 15 candidate unigenes annotated as cytochrome P450 with the highest expression in the root of L. officinale as novel genes with a role in key biochemical reactions toward shikonin biosynthesis. Thus, through this study, we not only generated a high-quality genomic resource for L. officinale but also propose candidate genes to be involved in shikonin biosynthesis pathways for further functional characterization.

De novo transcriptome assembly and characterization of nine tissues of Lonicera japonica to identify potential candidate genes involved in chlorogenic acid, luteolosides, and secoiridoid biosynthesis pathways.

Lonicera japonica is one of the most important medicinal plants with applications in traditional Chinese and Japanese medicine for thousands of years. Extensive studies on the constituents of L. japonica extracts have revealed an accumulation of pharmaceutically active metabolite classes, such as chlorogenic acid, luteolin and other flavonoids, and secoiridoids, which impart characteristic medicinal properties. Despite being a rich source of pharmaceutically active metabolites, little is known about the biosynthetic enzymes involved, and their expression profile across different tissues of L. japonica. In this study, we performed de novo transcriptome assembly for L. japonica, representing transcripts from nine different tissues. A total of 22 Gbps clean RNA-seq reads from nine tissues of L. japonica were used, resulting in 243,185 unigenes, with 99,938 unigenes annotated based on a homology search using blastx against the NCBI-nr protein database. Unsupervised principal component analysis and correlation studies using transcript expression data from all nine tissues of L. japonica showed relationships between tissues, explaining their association at different developmental stages. Homologs for all genes associated with chlorogenic acid, luteolin, and secoiridoid biosynthesis pathways were identified in the L. japonica transcriptome assembly. Expression of unigenes associated with chlorogenic acid was enriched in stems and leaf-2, unigenes from luteolin were enriched in stems and flowers, while unigenes from secoiridoid metabolic pathways were enriched in leaf-1 and shoot apex. Our results showed that different tissues of L. japonica are enriched with sets of unigenes associated with specific pharmaceutically important metabolic pathways and, therefore, possess unique medicinal properties. The present study will serve as a resource for future attempts for functional characterization of enzyme coding genes within key metabolic processes.

High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites.

KEY MESSAGE: Here, we report potential transcripts involved in the biosynthesis of therapeutic metabolites in Swertia japonica , the first report of transcriptome assembly, and characterization of the medicinal plant from Swertia genus. Swertia genus, representing over 170 plant species including herbs such as S. chirata, S. hookeri, S. longifolia, S. japonica, among others, have been used as the traditional medicine in China, India, Korea, and Japan for thousands of years. Due to the lack of genomic and transcriptomic resources, little is known about the molecular basis involved in the biosynthesis of characteristic key bioactive metabolites. Here, we performed deep-transcriptome sequencing for the aerial tissues and the roots of S. japonica, generating over 2 billion raw reads with an average length of 101 bps. Using a combined approach of three popular assemblers, de novo transcriptome assembly for S. japonica was obtained, yielding 81,729 unigenes having an average length of 884 bps and N50 value of 1452 bps, of which 46,963 unigenes were annotated based on the sequence similarity against NCBI-nr protein database. Annotation of transcriptome assembly resulted in the identification of putative genes encoding all enzymes from the key therapeutic metabolite biosynthesis pathways. Transcript abundance analysis, gene ontology enrichment analysis, and KEGG pathway enrichment analysis revealed metabolic processes being up-regulated in the aerial tissues with respect to the roots of S. japonica. We also identified 37 unigenes as potential candidates involved in the glycosylation of bioactive metabolites. Being the first report of transcriptome assembly and annotation for any of the Swertia species, this study will be a valuable resource for future investigations on the biosynthetic pathways of therapeutic metabolites and their regulations.

RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis.

The Panax genus has been a source of natural medicine, benefitting human health over the ages, among which the Panax japonicus represents an important species. Our understanding of several key pathways and enzymes involved in the biosynthesis of ginsenosides, a pharmacologically active class of metabolites and a major chemical constituents of the rhizome extracts from the Panax species, are limited. Limited genomic information, and lack of studies on comparative transcriptomics across the Panax species have restricted our understanding of the biosynthetic mechanisms of these and many other important classes of phytochemicals. Herein, we describe Illumina based RNA sequencing analysis to characterize the transcriptome and expression profiles of genes expressed in the five tissues of P. japonicus, and its comparison with other Panax species. RNA sequencing and de novo transcriptome assembly for P. japonicus resulted in a total of 135,235 unigenes with 78,794 (58.24%) unigenes being annotated using NCBI-nr database. Transcriptome profiling, and gene ontology enrichment analysis for five tissues of P. japonicus showed that although overall processes were evenly conserved across all tissues. However, each tissue was characterized by several unique unigenes with the leaves showing the most unique unigenes among the tissues studied. A comparative analysis of the P. japonicus transcriptome assembly with publically available transcripts from other Panax species, namely, P. ginseng, P. notoginseng, and P. quinquefolius also displayed high sequence similarity across all Panax species, with P. japonicus showing highest similarity with P. ginseng. Annotation of P. japonicus transcriptome resulted in the identification of putative genes encoding all enzymes from the triterpene backbone biosynthetic pathways, and identified 24 and 48 unigenes annotated as cytochrome P450 (CYP) and glycosyltransferases (GT), respectively. These CYPs and GTs annotated unigenes were conserved across all Panax species and co-expressed with other the transcripts involved in the triterpenoid backbone biosynthesis pathways. Unigenes identified in this study represent strong candidates for being involved in the triterpenoid saponins biosynthesis, and can serve as a basis for future validation studies.

Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling.

The genus Physalis in the Solanaceae family contains several species of benefit to humans. Examples include P. alkekengi (Chinese-lantern plant, hôzuki in Japanese) used for medicinal and for decorative purposes, and P. peruviana, also known as Cape gooseberry, which bears an edible, vitamin-rich fruit. Members of the Physalis genus are a valuable resource for phytochemicals needed for the development of medicines and functional foods. To fully utilize the potential of these phytochemicals we need to understand their biosynthesis, and for this we need genomic data, especially comprehensive transcriptome datasets for gene discovery. We report the de novo assembly of the transcriptome from leaves of P. alkekengi and P. peruviana using Illumina RNA-seq technologies. We identified 75,221 unigenes in P. alkekengi and 54,513 in P. peruviana. All unigenes were annotated with gene ontology (GO), Enzyme Commission (EC) numbers, and pathway information from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We classified unigenes encoding enzyme candidates putatively involved in the secondary metabolism and identified more than one unigenes for each step in terpenoid backbone- and steroid biosynthesis in P. alkekengi and P. peruviana. To measure the variability of the withanolides including physalins and provide insights into their chemical diversity in Physalis, we also analyzed the metabolite content in leaves of P. alkekengi and P. peruviana at five different developmental stages by liquid chromatography-mass spectrometry. We discuss that comprehensive transcriptome approaches within a family can yield a clue for gene discovery in Physalis and provide insights into their complex chemical diversity. The transcriptome information we submit here will serve as an important public resource for further studies of the specialized metabolism of Physalis species.

Transcriptomic landscape of Pueraria lobata demonstrates potential for phytochemical study.

Pueraria lobata (Willd.) Ohwi has a long and broad application in the treatment of disease. However, in the US and EU, it is treated as a notorious weed. The information to be gained from decoding the deep transcriptome profile would facilitate further research on P. lobata. In this study, more than 93 million fastq format reads were generated by Illumina's next-generation sequencing approach using five types of P. lobata tissue, followed by CLC de novo assembly methods, ultimately yielding about 83,041 contigs in total. Then BLASTx similarity searches against the NCBI NR database and UniProtKB database were conducted. Once the duplicates among BLASTx hits were eliminated, ID mapping against the UniProt database was conducted online to retrieve Gene Ontology information. In search of the putative genes relevant to essential biosynthesis pathways, all 1,348 unique enzyme commission numbers were used to map pathways against the Kyoto Encyclopedia of Genes and Genomes. Enzymes related to the isoflavonoid and flavonoid biosynthesis pathways were focused for detailed investigation and subsequently, quantitative real-time reverse transcription polymerase chain reaction was conducted for biological validation. Metabolites of interest, puerarin and daidzin were studied by HPLC. The findings in this report may serve as a footstone for further research into this promising medicinal plant.

High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome.

Perilla frutescens var. crispa (Labiatae) has two chemo-varietal forms, i.e. red and green forms of perilla, that differ in the production of anthocyanins. To facilitate molecular biological and biochemical studies in perilla-specialized metabolism we used Illumina RNA-sequencing technology in our comprehensive comparison of the transcriptome map of the leaves of red and green forms of perilla. Sequencing generated over 1.2 billion short reads with an average length of 101 nt. De novo transcriptome assembly yielded 47,788 and 47,840 unigenes in the red and green forms of perilla plants, respectively. Comparison of the assembled unigenes and existing perilla cDNA sequences showed highly reliable alignment. All unigenes were annotated with gene ontology (GO) and Enzyme Commission numbers and entered into the Kyoto Encyclopedia of Genes and Genomes. We identified 68 differentially expressed genes (DEGs) in red and green forms of perilla. GO enrichment analysis of the DEGs showed that genes involved in the anthocyanin metabolic process were enriched. Differential expression analysis revealed that the transcript level of anthocyanin biosynthetic unigenes encoding flavonoid 3'-hydroxylase, dihydroflavonol 4-reductase, and anthocyanidin synthase was significantly higher in red perilla, while the transcript level of unigenes encoding limonene synthase was significantly higher in green perilla. Our data serve as a basis for future research on perilla bio-engineering and provide a shortcut for the characterization of new functional genes in P. frutescens.

Transcriptome Analysis of Nine Tissues to Discover Genes Involved in the Biosynthesis of Active Ingredients in Sophora flavescens.

Sophora flavescens AITON (kurara) has long been used to treat various diseases. Although several research findings revealed the biosynthetic pathways of its characteristic chemical components as represented by matrine, insufficient analysis of transcriptome data hampered in-depth analysis of the underlying putative genes responsible for the biosynthesis of pharmaceutical chemical components. In this study, more than 200 million fastq format reads were generated by Illumina's next-generation sequencing approach using nine types of tissue from S. flavescens, followed by CLC de novo assembly, ultimately yielding 83,325 contigs in total. By mapping the reads back to the contigs, reads per kilobase of the transcript per million mapped reads values were calculated to demonstrate gene expression levels, and overrepresented gene ontology terms were evaluated using Fisher's exact test. In search of the putative genes relevant to essential metabolic pathways, all 1350 unique enzyme commission numbers were used to map pathways against the Kyoto Encyclopedia of Genes and Genomes. By analyzing expression patterns, we proposed some candidate genes involved in the biosynthesis of isoflavonoids and quinolizidine alkaloids. Adopting RNA-Seq analysis, we obtained substantially credible contigs for downstream work. The preferential expression of the gene for putative lysine/ornithine decarboxylase committed in the initial step of matrine biosynthesis in leaves and stems was confirmed in semi-quantitative polymerase chain reaction (PCR) analysis. The findings in this report may serve as a stepping-stone for further research into this promising medicinal plant.

Study of factors involved in tongue color diagnosis by kampo medical practitioners using the farnsworth-munsell 100 hue test and tongue color images.

In traditional Japanese medicine (Kampo medicine), tongue color is important in discerning a patient's constitution and medical conditions. However, tongue color diagnosis is susceptible to the subjective factors of the observer. To investigate factors involved in tongue color diagnosis, both color discrimination and tongue color diagnosis were researched in 68 Kampo medical practitioners. Color discrimination was studied by the Farnsworth-Munsell 100 Hue test, and tongue color diagnosis was studied by 84 tongue images. We found that overall color discrimination worsened with aging. However, the color discrimination related to tongue color regions was maintained in subjects with 10 or more years of Kampo experience. On the other hand, tongue color diagnosis significantly differed between subjects with <10 years of experience and ≥10 years of experience. Practitioners with ≥10 years of experience could maintain a consistent diagnosis of tongue color regardless of their age.

Increased thiol biosynthesis of transgenic poplar expressing a wheat O-acetylserine(thiol) lyase enhances resistance to hydrogen sulfide and sulfur dioxide toxicity.

O-acetylserine(thiol) lyase (OASTL), a key enzyme of the plant sulfur assimilatory pathway, catalyses the formation of cysteine from sulfide and O-acetylserine. Transgenic hybrid poplar (Populus sieboldi x P. grandidentata 'Y63') plants expressing cys1, encoding a wheat cytosolic OASTL, were developed in order to examine the role of this enzyme in thiol production following hydrogen sulfide or sulfur dioxide exposure and in the extent of damage induced in the plants by these pollutants. The transgenic cys1 plants accumulated up to several-fold higher cysteine and glutathione levels and were significantly more resistant in terms of foliar damage to the pollutants than WT plants. The transgenic poplar also showed higher tolerance to sulfite and hydrogen peroxide and, interestingly, accumulated several-fold higher sulfite reductase transcripts than WT plants in response to sulfur dioxide. These data clearly demonstrate the important role of OASTL and the sulfur reduction pathway in sulfur and oxidative stress amelioration, and support the notion that transgenic trees resistant to such pollutants can be generated for phytoremediation strategies.

Heavy metal tolerance of transgenic tobacco plants over-expressing cysteine synthase.

Cysteine synthase [O-acetyl-L-serine(thiol)lyase] catalyzes the final step for L-cysteine biosynthesis in plants. The tolerance of transgenic tobacco plants over-expressing cysteine synthase cDNA in cytosol (3F), chloroplasts (4F) and in both organelles (F1) was investigated towards heavy metals such as Cd, Se, Ni, Pb and Cu. The transgenic plants were significantly more tolerant than wild-type plants in agar medium containing Cd, Se and Ni. The F1 transgenic plants had a higher resistance than other transgenic lines towards these metals and could enhance accumulation of Cd in shoot. These results suggest that the transgenic plants over-expressing cysteine synthase both in cytosol and chloroplasts can be applicable to phyto-remediation of Cd from contaminated soils.