Comprehensive metabolic and transcriptomic profiling of various tissues provide insights for saponin biosynthesis in the medicinally important Asparagus racemosus

Shatavari supplementation in postmenopausal women alters the skeletal muscle proteome and pathways involved in training adaptation

PURPOSE

Shatavari is an understudied, widely available herbal supplement. It contains steroidal saponins and phytoestrogens. We previously showed that six weeks of shatavari supplementation improved handgrip strength and increased markers of myosin contractile function. Mechanistic insights into shatavari's actions are limited. Therefore, we performed proteomics on vastus lateralis (VL) samples that remained from our original study.

METHODS

In a randomised double-blind trial, women (68.5 ± 6 years) ingested either placebo or shatavari (equivalent to 26,500 mg/d fresh weight) for six weeks. Tandem mass tag global proteomic analysis of VL samples was conducted (N = 7 shatavari, N = 5 placebo). Data were normalized to total peptides and scaled using a reference sample. Data were filtered using a 5% FDR. For each protein, the pre to post supplementation difference was expressed as log2 fold change. Welch's t tests with Benjamini-Hochberg corrections were performed for each protein. Pathway enrichment (PADOG, CAMERA) was interrogated in Reactome (v85).

RESULTS

No individual protein was significantly different between supplementation conditions. Both PADOG and CAMERA indicated that pathways related to (1) Integrin/MAPK signalling, (2) metabolism/insulin secretion; (3) cell proliferation/senescence/DNA repair/cell death; (4) haemostasis/platelets/fibrin; (5) signal transduction; (6) neutrophil degranulation and (7) chemical synapse function were significantly upregulated. CAMERA indicated pathways related to translation/amino acid metabolism, viral infection, and muscle contraction were downregulated.

CONCLUSION

Our analyses indicate that shatavari may support muscle adaptation responses to exercise. These data provide useful signposts for future investigation of shatavari's utility in conserving and enhancing musculoskeletal function in older age.

TRIAL REGISTRATION

NCT05025917 30/08/21, retrospectively registered.

De novo sequencing, assembly, and characterization of Asparagus racemosus transcriptome and analysis of expression profile of genes involved in the flavonoid biosynthesis pathway

Asparagus racemosus is known for its diverse content of secondary metabolites, i.e., saponins, alkaloids, and a wide range of flavonoids. Flavonoids, including phenols and polyphenols, have a significant role in plant physiology and are synthesized in several tissues. Despite the diverse role of flavonoids, genetic information is limited for flavonoid biosynthesis pathways in A. racemosus. The current study explores full-scale functional genomics information of A. racemosus by de novo transcriptome sequencing using Illumina paired-end sequencing technology to elucidate the genes involved in flavonoid biosynthesis pathways. The de novo assembly of high-quality paired-end reads resulted in ∼2.3 million high-quality reads with a pooled transcript of 45,647 comprising ∼76 Mb transcriptome with a mean length (bp) of 1,674 and N50 of 1,868bp. Furthermore, the coding sequence (CDS) prediction analysis from 45,647 pooled transcripts resulted in 45,444 CDS with a total length and mean length of 76,398,686 and 1,674, respectively. The Gene Ontology (GO) analysis resulted in a high number of CDSs assigned to 25,342 GO terms, which grouped the predicted CDS into three main domains, i.e., Biological Process (19,550), Molecular Function (19,873), and Cellular Component (14,577). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database was used to categorize 6,353 CDS into 25 distinct biological pathway categories, in which the majority of mapped CDS were shown to be related to translation (645), followed by signal transduction (532), carbohydrate metabolism (524), folding, sorting, and degradation (522). Among these, only ∼64 and 14 CDSs were found to be involved in the phenylpropanoid and flavonoid biosynthesis pathways, respectively. Quantitative Real-time PCR was used to check the expression profile of fourteen potential flavonoid biosynthesis pathway genes. The qRT-PCR analysis result matches the transcriptome sequence data validating the Illumina sequence results. Moreover, a large number of genes associated with the flavonoids biosynthesis pathway were found to be upregulated under the induction of methyl jasmonate. The present-day study on transcriptome sequence data of A. racemosus can be utilized for characterizing genes involved in flavonoid biosynthesis pathways and for functional genomics analysis in A. racemosus using the reverse genetics approach (CRISPR/Cas9 technology).

Unravelling the seasonal dynamics of the metabolome of white asparagus spears using untargeted metabolomics

INTRODUCTION

The white asparagus season lasts 4 months while the harvest period per field is 8 weeks. Different varieties are better suited for harvesting early or late in the season. Little is known of the dynamics of secondary metabolites of white asparagus during the production season.

OBJECTIVE

Characterization of the metabolome of white asparagus spears covering volatile and non-volatile composition in relation to quality aspects.

METHODS

Eight varieties, harvested repeatedly during two consecutive seasons were analysed following an untargeted metabolomics workflow using SPME GC-MS and LC-MS. Linear regression, cluster and network analyses were used to explore the profile dynamics, unravel patterns and study the influence of genotype and environment.

RESULTS

The metabolite profiles were influenced by the harvest moment and genetic background. Metabolites that significantly changed over time were distributed across seven clusters based on their temporal patterns. Two clusters including monoterpenes, benzenoids and saponins showed the most prominent seasonal changes. The changes depicted by the other five clusters were mainly ≤ 2-fold relative to the harvest start. Known asparagus aroma compounds were found to be relatively stable across the season/varieties. Heat-enhanced cultivation appeared to yield spears early in season with a similar metabolome to those harvested later.

CONCLUSION

The dynamics of the white asparagus metabolome is influenced by a complex relationship between the onset of spear development, the moment of harvest and the genetic background. The typical perceived asparagus flavour profile is unlikely to be significantly affected by these dynamics.

Multi-omics profiling reveals comprehensive microbe-plant-metabolite regulation patterns for medicinal plant Glycyrrhiza uralensis Fisch

Glycyrrhiza uralensis Fisch is a medicinal plant widely used to treat multiple diseases in Europe and Asia, and its efficacy largely depends on liquiritin and glycyrrhizic acid. The regulatory pattern responsible for the difference in efficacy between wild and cultivated G. uralensis remains largely undetermined. Here, we collected roots and rhizosphere soils from wild (WT) G. uralensis as well as those farmed for 1 year (C1) and 3 years (C3), generated metabolite and transcript data for roots, microbiota data for rhizospheres and conducted comprehensive multi-omics analyses. We updated gene structures for all 40 091 genes in G. uralensis, and based on 52 differentially expressed genes, we charted the route-map of both liquiritin and glycyrrhizic acid biosynthesis, with genes BAS, CYP72A154 and CYP88D6 critical for glycyrrhizic acid biosynthesis being significantly expressed higher in wild G. uralensis than in cultivated G. uralensis. Additionally, multi-omics network analysis identified that Lysobacter was strongly associated with CYP72A154, which was required for glycyrrhizic acid biosynthesis. Finally, we developed a holistic multi-omics regulation model that confirmed the importance of rhizosphere microbial community structure in liquiritin accumulation. This study thoroughly decoded the key regulatory mechanisms of liquiritin and glycyrrhizic acid, and provided new insights into the interactions of the plant's key metabolites with its transcriptome, rhizosphere microbes and environment, which would guide future cultivation of G. uralensis.

Effects of Mulching on Early-spring Green Asparagus Yield and Quality under Cultivation in Plastic Tunnels

Mulching significantly increases the crop yield and quality by positively affecting the physical features of the soil. The effect of multiple mulching treatments on soil temperature, yield, and nutrient composition of green asparagus grown in a plastic tunnel was assessed. Two mulch materials: transparent plastic film (PF) and rice husk (RH), were applied and compared with non-mulching treatment (CK). The soil temperatures at the soil surface and 10 cm below it were generally higher in the PF mulch than in the CK during the spring. PF mulch accelerated early spear emergence and growth, which led to harvesting 16 days earlier than in the CK. Under the PF mulch, the early yield of spears increased by 26.6% from January to the end of March, and the annual gross income by 14.8% because of the higher price resulting from the significantly higher marketable spear length and diameter; however, they were reduced in the RH mulch. Most nutrient compositions, such as soluble sugar, ascorbic acid, rutin, flavonoid content, and total antioxidant activity, were significantly increased in the PF mulch treatment. PF mulch might benefit green asparagus production during early spring because of its ability to promote early spear emergence and growth.

Glycosyltransferases: Mining, engineering and applications in biosynthesis of glycosylated plant natural products

UDP-Glycosyltransferases (UGTs) catalyze the transfer of nucleotide-activated sugars to specific acceptors, among which the GT1 family enzymes are well-known for their function in biosynthesis of natural product glycosides. Elucidating GT function represents necessary step in metabolic engineering of aglycone glycosylation to produce drug leads, cosmetics, nutrients and sweeteners. In this review, we systematically summarize the phylogenetic distribution and catalytic diversity of plant GTs. We also discuss recent progress in the identification of novel GT candidates for synthesis of plant natural products (PNPs) using multi-omics technology and deep learning predicted models. We also highlight recent advances in rational design and directed evolution engineering strategies for new or improved GT functions. Finally, we cover recent breakthroughs in the application of GTs for microbial biosynthesis of some representative glycosylated PNPs, including flavonoid glycosides (fisetin 3-O-glycosides, astragalin, scutellarein 7-O-glucoside), terpenoid glycosides (rebaudioside A, ginsenosides) and polyketide glycosides (salidroside, polydatin).

In vitro antidermatophytic activity of bioactive compounds from selected medicinal plants

Fungal infections are among the most difficult diseases to manage in humans. Eukaryotic fungal pathogens share many similarities with their host cells, which impairs the development of antifungal compounds. Therefore, it is desirable to harness the pharmaceutical potential of medicinal plants for antifungal drug discovery. In this study, the antifungal activity of sixteen plant extracts was investigated against selected dermatophytic fungi. Of the sixteen plants, the cladode (leaf) of Asparagus racemosus, and seed extract of Cassia occidentalis showed antifungal activity against Microsporum gypseum, Microsporum nanum, Trichophyton mentagrophytes and Trichophyton terrestre. The plant antifungal compounds were located by direct bioassay against Cladosporium herbarum. IR and NMR spectrometry analyses of these compounds identified the presence of saponin (in A. racemosus) and hydroxy anthraquinone (in C. occidentalis) in these antifungal compounds. The antidermatophytic activity of plant anthraquinone and saponins with reports of little or no hemolytic activity, makes these compounds ideal for alternative antifungal therapy and warrants further in-depth investigation in vivo.

Unveiling sugarcane defense response to Mythimna separata herbivory by a combination of transcriptome and metabolic analyses

BACKGROUND

Sugarcane is the most important sugar crop in the world. Like other crops, sugarcane suffers from herbivorous insect attack. The oriental armyworm Mythimna separata is a devastating pest of various crops in northeast Asia and an outbreak of this pest can result in substantial yield loss for sugarcane. However, the plant defense response situation is widely acquisition in model crops, but there is little information about how sugarcane plants defend themselves against this herbivore at the molecular and biochemical levels.

RESULTS

We combined transcriptome and metabolomic analysis to investigate the changes in gene expression and metabolic processes that occurred in sugarcane plants after continuous feeding by M. separata larvae for 12 and 24 h. We identified 13 662 genes and 55 metabolites that were differentially regulated in sugarcane plants fed on by M. separata. The genes involved in phytohormones, transcription factors, and kinase-related were activated and metabolism compounds such as carbohydrate, amino acid, ferulic substances and glutathione were detected regulated in sugarcane defense response. Comparable analyses showed a close correspondence relationship among pathways of phenylalanine metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis in transcript and metabolite profiles. Furthermore, a bioassay experiment was conducted to test the influence of up-regulated metabolites on M. separata growth and found chlorogenic acid had a lethal effect.

CONCLUSION

The results of our study greatly enhanced the understanding of the sugarcane-induced defense response mechanism against herbivore infestation at the transcriptional and metabolic levels. Also make contributions to provide clues for development of green pest control method. © 2021 Society of Chemical Industry.

The Plausible Role of Indian Traditional Medicine in Combating Corona Virus (SARS-CoV 2): A Mini-Review

SARS-CoV 2 is a novel virus strain of Coronavirus, reported in China in late December 2019. Its highly contagious nature in humans has prompted WHO to designate the ongoing pandemic as a Public Health Emergency of International Concern. At this moment, there is no specific treatment and the therapeutic strategies to deal with the infection are only supportive, with prevention aimed at reducing community transmission. A permanent solution for the pandemic, which has brought the world economy to the edge of collapse, is the need of the hour. This situation has brought intense research in traditional systems of medicine. Indian Traditional System, Ayurveda, has a clear concept of the cause and treatment of pandemics. Through this review, information on the potential antiviral traditional medicines along with their immunomodulatory pathways are discussed. We have covered the seven most important Indian traditional plants with antiviral properties: Withania somnifera (L.) Dunal (family: Solanaceae), Tinospora cordifolia (Thunb.) Miers (family: Menispermaceae), Phyllanthus emblica L. (family: Euphorbiaceae), Asparagus racemosus L. (family: Liliaceae), Glycyrrhiza glabra L. (family: Fabaceae), Ocimum sanctum L. (family: Lamiaceae) and Azadirachta indica A. Juss (family: Meliaceae) in this review. An attempt is also made to bring into limelight the importance of dietary polyphenol, Quercetin, which is a potential drug candidate in the making against the SARS-CoV2 virus.

Comparative Metabolome and Transcriptome Analyses of Susceptible Asparagus officinalis and Resistant Wild A. kiusianus Reveal Insights into Stem Blight Disease Resistance

Phomopsis asparagi is one of the most serious fungal pathogens, which causes stem blight disease in Asparagus officinalis (AO), adversely affecting its production worldwide. Recently, the development of novel asparagus varieties using wild Asparagus genetic resources with natural P. asparagi resistance has become a priority in Japan due to the lack of resistant commercial AO cultivars. In this study, comparative metabolome and transcriptome analyses of susceptible AO and resistant wild Asparagus kiusianus (AK) 24 and 48 h postinoculated (AOI_24 hpi, AOI_48 hpi, AKI_24 hpi and AKI_48 hpi, respectively) with P. asparagi were conducted to gain insights into metabolic and expression changes associated with AK species. Following infection, the resistant wild AK showed rapid metabolic changes with increased levels of flavonoids and steroidal saponins and decreased asparagusic acid glucose ester content, compared with the susceptible AO plants. Transcriptome data revealed a total of 21  differentially expressed genes (DEGs) as the core gene set that displayed upregulation in the resistant AK versus susceptible AO after infection with P. asparagi. Kyoto Encyclopedia of Genes and Genomes pathway analysis of these DEGs identified 11 significantly enriched pathways, including flavonoid biosynthesis and primary metabolite metabolism, in addition to plant signaling and defense-related pathways. In addition, comparative single-nucleotide polymorphism and Indel distributions in susceptible AO and resistant AK plants were evaluated using the latest AO reference genome Aspof.V1. The data generated in this study are important resources for advancing Asparagus breeding programs and for investigations of genetic linkage mapping, phylogenetic diversity and plant defense-related genes.

Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.)

BACKGROUND

Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially cultivated species of jute. Gene expression is spatiotemporal and is influenced by many factors. Therefore, to understand the molecular mechanisms of tissue development, it is necessary to study tissue-specific gene expression and regulation. We used weighted gene coexpression network analysis, to predict the functional roles of gene coexpression modules and individual genes, including those underlying the development of different tissue types. Although several transcriptome studies have been conducted on C. capsularis, there have not yet been any systematic and comprehensive transcriptome analyses for this species.

RESULTS

There was significant variation in gene expression between plant tissues. Comparative transcriptome analysis and weighted gene coexpression network analysis were performed for different C. capsularis tissues at different developmental stages. We identified numerous tissue-specific differentially expressed genes for each tissue, and 12 coexpression modules, comprising 126 to 4203 genes, associated with the development of various tissues. There was high consistency between the genes in modules related to tissues, and the candidate upregulated genes for each tissue. Further, a gene network including 21 genes directly regulated by transcription factor OMO55970.1 was discovered. Some of the genes, such as OMO55970.1, OMO51203.1, OMO50871.1, and OMO87663.1, directly involved in the development of stem bast tissue.

CONCLUSION

We identified genes that were differentially expressed between tissues of the same developmental stage. Some genes were consistently up- or downregulated, depending on the developmental stage of each tissue. Further, we identified numerous coexpression modules and genes associated with the development of various tissues. These findings elucidate the molecular mechanisms underlying the development of each tissue, and will promote multipurpose molecular breeding in jute and other fiber crops.