Comprehensive RNA sequencing and co-expression network analysis to complete the biosynthetic pathway of coumestrol, a phytoestrogen

Deciphering the regulatory networks involved in mild and severe salt stress responses in the roots of wild grapevine Vitis vinifera spp. sylvestris

Transcriptional regulatory networks are pivotal components of plant's response to salt stress. However, plant adaptation strategies varied as a function of stress intensity, which is mainly modulated by climate change. Here, we determined the gene regulatory networks based on transcription factor (TF) TF_gene co-expression, using two transcriptomic data sets generated from the salt-tolerant "Tebaba" roots either treated with 50 mM NaCl (mild stress) or 150 mM NaCl (severe stress). The analysis of these regulatory networks identified specific TFs as key regulatory hubs as evidenced by their multiple interactions with different target genes related to stress response. Indeed, under mild stress, NAC and bHLH TFs were identified as central hubs regulating nitrogen storage process. Moreover, HSF TFs were revealed as a regulatory hub regulating various aspects of cellular metabolism including flavonoid biosynthesis, protein processing, phenylpropanoid metabolism, galactose metabolism, and heat shock proteins. These processes are essentially linked to short-term acclimatization under mild salt stress. This was further consolidated by the protein-protein interaction (PPI) network analysis showing structural and plant growth adjustment. Conversely, under severe salt stress, dramatic metabolic changes were observed leading to novel TF members including MYB family as regulatory hubs controlling isoflavonoid biosynthesis, oxidative stress response, abscisic acid signaling pathway, and proteolysis. The PPI network analysis also revealed deeper stress defense changes aiming to restore plant metabolic homeostasis when facing severe salt stress. Overall, both the gene co-expression and PPI network provided valuable insights on key transcription factor hubs that can be employed as candidates for future genetic crop engineering programs.

Differentially Expressed Genes Related to Isoflavone Biosynthesis in a Soybean Mutant Revealed by a Comparative Transcriptomic Analysis

Soybean [Glycine max (L.) Merr.] isoflavones, which are secondary metabolites with various functions, are included in food, cosmetics, and medicine. However, the molecular mechanisms regulating the glycosylation and malonylation of isoflavone glycoconjugates remain unclear. In this study, we conducted an RNA-seq analysis to compare soybean genotypes with different isoflavone contents, including Danbaek and Hwanggeum (low-isoflavone cultivars) as well as DB-088 (high-isoflavone mutant). The transcriptome analysis yielded over 278 million clean reads, representing 39,156 transcripts. The analysis of differentially expressed genes (DEGs) detected 2654 up-regulated and 1805 down-regulated genes between the low- and high-isoflavone genotypes. The putative functions of these 4459 DEGs were annotated on the basis of GO and KEGG pathway enrichment analyses. These DEGs were further analyzed to compare the expression patterns of the genes involved in the biosynthesis of secondary metabolites and the genes encoding transcription factors. The examination of the relative expression levels of 70 isoflavone biosynthetic genes revealed the HID, IFS, UGT, and MAT expression levels were significantly up/down-regulated depending on the genotype and seed developmental stage. These expression patterns were confirmed by quantitative real-time PCR. Moreover, a gene co-expression analysis detected potential protein-protein interactions, suggestive of common functions. The study findings provide valuable insights into the structural genes responsible for isoflavone biosynthesis and accumulation in soybean seeds.

Alterations in the root phenylpropanoid pathway and root-shoot vessel system as main determinants of the drought tolerance of a soybean genotype

Climate change increases precipitation variability, particularly in savanna environments. We have used integrative strategies to understand the molecular mechanisms of drought tolerance, which will be crucial for developing improved genotypes. The current study compares the molecular and physiological parameters between the drought-tolerant Embrapa 48 and the sensitive BR16 genotypes. We integrated the root-shoot system's transcriptome, proteome, and metabolome to understand drought tolerance. The results indicated that Embrapa 48 had a greater capacity for water absorption due to alterations in length and volume. Drought tolerance appears to be ABA-independent, and IAA levels in the leaves partially explain the higher root growth. Proteomic profiles revealed up-regulated proteins involved in glutamine biosynthesis and proteolysis, suggesting osmoprotection and explaining the larger root volume. Dysregulated proteins in the roots belong to the phenylpropanoid pathways. Additionally, PR-like proteins involved in the biosynthesis of phenolics may act to prevent oxidative stress and as a substrate for modifying cell walls. Thus, we concluded that alterations in the root-shoot conductive vessel system are critical in promoting drought tolerance. Moreover, photosynthetic parameters from reciprocal grafting experiments indicated that the root system is more essential than the shoots in the drought tolerance mechanism. Finally, we provided a comprehensive overview of the genetic, molecular, and physiological traits involved in drought tolerance mechanisms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01307-7.

Bioprospecting microbes and enzymes for the production of pterocarpans and coumestans

The isoflavonoid derivatives, pterocarpans and coumestans, are explored for multiple clinical applications as osteo-regenerative, neuroprotective and anti-cancer agents. The use of plant-based systems to produce isoflavonoid derivatives is limited due to cost, scalability, and sustainability constraints. Microbial cell factories overcome these limitations in which model organisms such as Saccharomyces cerevisiae offer an efficient platform to produce isoflavonoids. Bioprospecting microbes and enzymes can provide an array of tools to enhance the production of these molecules. Other microbes that naturally produce isoflavonoids present a novel alternative as production chassis and as a source of novel enzymes. Enzyme bioprospecting allows the complete identification of the pterocarpans and coumestans biosynthetic pathway, and the selection of the best enzymes based on activity and docking parameters. These enzymes consolidate an improved biosynthetic pathway for microbial-based production systems. In this review, we report the state-of-the-art for the production of key pterocarpans and coumestans, describing the enzymes already identified and the current gaps. We report available databases and tools for microbial bioprospecting to select the best production chassis. We propose the use of a holistic and multidisciplinary bioprospecting approach as the first step to identify the biosynthetic gaps, select the best microbial chassis, and increase productivity. We propose the use of microalgal species as microbial cell factories to produce pterocarpans and coumestans. The application of bioprospecting tools provides an exciting field to produce plant compounds such as isoflavonoid derivatives, efficiently and sustainably.

Phytoestrogen Coumestrol Selectively Inhibits Monoamine Oxidase-A and Amyloid β Self-Aggregation

Pueraria lobata leaves contain a variety of phytoestrogens, including flavonoids, isoflavonoids, and coumestan derivatives. In this study, we aimed to identify the active ingredients of P. lobata leaves and to elucidate their function in monoamine oxidase (MAO) activation and Aβ self-aggregation using in vitro and in silico approaches. To the best of our knowledge, this is the first study to elucidate coumestrol as a selective and competitive MAO-A inhibitor. We identified that coumestrol, a coumestan-derivative, exhibited a selective inhibitory effect against MAO-A (IC₅₀ = 1.99 ± 0.68 µM), a key target protein for depression. In a kinetics analysis with 0.5 µg MAO-A, 40–160 µM substrate, and 25 °C reaction conditions, coumestrol acts as a competitive MAO-A inhibitor with an inhibition constant of 1.32 µM. During an in silico molecular docking analysis, coumestrol formed hydrogen bonds with FAD and pi–pi bonds with hydrophobic residues at the active site of the enzyme. Moreover, based on thioflavin-T-based fluorometric assays, we elucidated that coumestrol effectively prevented self-aggregation of amyloid beta (Aβ), which induces an inflammatory response in the central nervous system (CNS) and is a major cause of Alzheimer’s disease (AD). Therefore, coumestrol could be used as a CNS drug to prevent diseases such as depression and AD by the inhibition of MAO-A and Aβ self-aggregation.

Mass Biosynthesis of Coumestrol Derivatives and Their Isomers via Soybean Adventitious Root Cultivation in Bioreactors

Coumestrol (CMS) derivatives are unique compounds, which function as phytoalexins; they are derived from soybean roots, following abiotic and biotic stresses. As a phytoalexin, CMS forms a defense system that enables plants to maintain their viability. However, it is still challenging to achieve the mass production of phytoalexins, which exhibit pharmacological values, via plant breeding. Here, the synthesis of CMS derivatives from the seedling, plant, and adventitious root (AR) of Glycine max were investigated under artificial light, as well as via a chemical elicitor treatment. In the presence of constant light, as well as under treatment with methyl jasmonate, the CMS monoglucoside (coumestrin; CMSN) and malonyl CMSN (M-CMSN) contents of the AR culture (4 weeks) increased drastically. The two CMS derivatives, CMSN and M-CMSN, were obtained as a mixture of isomers, which were identified via nuclear magnetic resonance analysis. These derivatives were also observed in a soybean plant that was grown on artificial soil (AS; 5 weeks) and a Petri dish (9 days) although in considerably lesser quantities than those observed in the AR culture. Compared with the two other media (AS and the Petri dish), the AR culture achieved the superior synthesis of CMSN and M-CMSN within a relatively short cultivation period (<1 month) in laboratory-scale (3 L) and pilot-scale (1,000 L) bioreactors. The isoflavone content of AR under the constant light conditions was three-fold that under dark conditions. Significant quantities of malonyl daidzin and malonyl genistin were produced in the root of AS and the seedling of Petri dish, respectively. Flavonol glycosides were not produced in the AR culture under the dark and light conditions, as well as in AS under the dark condition. However, significant contents of kaempferol glycosides were produced in the leaves of AS and seedling of Petri dish, following the light treatment. Thus, we proposed that the established soybean AR-cultivation approach represented a better method for biosynthesizing phytoalexins, such as the CMS derivatives, as plant-derived functional materials.

Screening of Carbonic Anhydrase, Acetylcholinesterase, Butyrylcholinesterase, and α-Glycosidase Enzyme Inhibition Effects and Antioxidant Activity of Coumestrol

Coumestrol (3,9-dihydroxy-6-benzofuran [3,2-c] chromenone) as a phytoestrogen and polyphenolic compound is a member of the Coumestans family and is quite common in plants. In this study, antiglaucoma, antidiabetic, anticholinergic, and antioxidant effects of Coumestrol were evaluated and compared with standards. To determine the antioxidant activity of coumestrol, several methods—namely N,N-dimethyl-p-phenylenediamine dihydrochloride radical (DMPD^•+)-scavenging activity, 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulphonate) radical (ABTS^•+)-scavenging activity, 1,1-diphenyl-2-picrylhydrazyl radical (DPPH^•)-scavenging activity, potassium ferric cyanide reduction ability, and cupric ion (Cu²⁺)-reducing activity—were performed. Butylated hydroxyanisole (BHA), Trolox, α-Tocopherol, and butylated hydroxytoluene (BHT) were used as the reference antioxidants for comparison. Coumestrol scavenged the DPPH radical with an IC₅₀ value of 25.95 μg/mL (r²: 0.9005) while BHA, BHT, Trolox, and α-Tocopherol demonstrated IC₅₀ values of 10.10, 25.95, 7.059, and 11.31 μg/mL, respectively. When these results evaluated, Coumestrol had similar DPPH^•-scavenging effect to BHT and lower better than Trolox, BHA and α-tocopherol. In addition, the inhibition effects of Coumestrol were tested against the metabolic enzymes acetylcholinesterase (AChE), butyrylcholinesterase (BChE), carbonic anhydrase II (CA II), and α-glycosidase, which are associated with some global diseases such as Alzheimer’s disease (AD), glaucoma, and diabetes. Coumestrol exhibited K_i values of 10.25 ± 1.94, 5.99 ± 1.79, 25.41 ± 1.10, and 30.56 ± 3.36 nM towards these enzymes, respectively.

Transcriptome analysis of Kentucky bluegrass subject to drought and ethephon treatment

Kentucky bluegrass (Poa pratensis L.) is an excellent cool-season turfgrass utilized widely in Northern China. However, turf quality of Kentucky bluegrass declines significantly due to drought. Ethephon seeds-soaking treatment has been proved to effectively improve the drought tolerance of Kentucky bluegrass seedlings. In order to investigate the effect of ethephon leaf-spraying method on drought tolerance of Kentucky bluegrass and understand the underlying mechanism, Kentucky bluegrass plants sprayed with and without ethephon are subjected to either drought or well watered treatments. The relative water content and malondialdehyde conent were measured. Meanwhile, samples were sequenced through Illumina. Results showed that ethephon could improve the drought tolerance of Kentucky bluegrass by elevating relative water content and decreasing malondialdehyde content under drought. Transcriptome analysis showed that 58.43% transcripts (254,331 out of 435,250) were detected as unigenes. A total of 9.69% (24,643 out of 254,331) unigenes were identified as differentially expressed genes in one or more of the pairwise comparisons. Differentially expressed genes due to drought stress with or without ethephon pre-treatment showed that ethephon application affected genes associated with plant hormone, signal transduction pathway and plant defense, protein degradation and stabilization, transportation and osmosis, antioxidant system and the glyoxalase pathway, cell wall and cuticular wax, fatty acid unsaturation and photosynthesis. This study provides a theoretical basis for revealing the mechanism for how ethephon regulates drought response and improves drought tolerance of Kentucky bluegrass.

Effective methods for increasing coumestrol in soybean sprouts

Coumestrol (CM), a biologically active compound found in Leguminosae plants, provides various human health benefits. To identify easy and effective methods to increase CM content in vegetables, we developed a quantitative analysis method using high-performance liquid chromatography (HPLC). Using this method, we found that soybean sprouts (1.76 ± 0.13 μg/g) have high CM contents among nine vegetables and evaluated the difference in CM contents between two organs of the sprouts: cotyledons and hypocotyls. Next, soybean sprouts were cultivated under different light, temperature, and water conditions and their CM contents were evaluated. CM content was higher in hypocotyls (4.11 ± 0.04 μg/g) than in cotyledons. Cultivating soybean sprouts at 24°C enhanced CM content regardless of light conditions, the growth of fungi and bacteria, and sprout color. Thus, we identified methods of soybean sprout cultivation to increase CM content, which may provide health benefits and enhance value.

The Induction of the Isoflavone Biosynthesis Pathway Is Associated with Resistance to Common Bacterial Blight in Phaseolus vulgaris L

Xanthomonas axonopodis infects common bean (Phaseolus vulgaris L.) causing the disease common bacterial blight (CBB). The aim of this study was to investigate the molecular and metabolic mechanisms underlying CBB resistance in P. vulgaris. Trifoliate leaves of plants of a CBB-resistant P. vulgaris recombinant inbred line (RIL) and a CBB-susceptible RIL were inoculated with X. axonopodis or water (mock treatment). Leaves sampled at defined intervals over a 48-h post-inoculation (PI) period were monitored for alterations in global transcript profiles. A total of 800 genes were differentially expressed between pathogen and mock treatments across both RILs; approximately half were differentially expressed in the CBB-resistant RIL at 48 h PI. Notably, there was a 4- to 32-fold increased transcript abundance for isoflavone biosynthesis genes, including several isoflavone synthases, isoflavone 2'-hydroxylases and isoflavone reductases. Ultra-high performance liquid chromatography-tandem mass spectrometry assessed leaf metabolite levels as a function of the PI period. The concentrations of the isoflavones daidzein and genistein and related metabolites coumestrol and phaseollinisoflavan were increased in CBB-resistant RIL plant leaves after exposure to the pathogen. Isoflavone pathway transcripts and metabolite profiles were unaffected in the CBB-susceptible RIL. Thus, induction of the isoflavone pathway is associated with CBB-resistance in P. vulgaris.

Recent Advances in Heterologous Synthesis Paving Way for Future Green-Modular Bioindustries: A Review With Special Reference to Isoflavonoids

Isoflavonoids are well-known plant secondary metabolites that have gained importance in recent time due to their multiple nutraceutical and pharmaceutical applications. In plants, isoflavonoids play a role in plant defense and can confer the host plant a competitive advantage to survive and flourish under environmental challenges. In animals, isoflavonoids have been found to interact with multiple signaling pathways and have demonstrated estrogenic, antioxidant and anti-oncologic activities in vivo. The activity of isoflavonoids in the estrogen pathways is such that the class has also been collectively called phytoestrogens. Over 2,400 isoflavonoids, predominantly from legumes, have been identified so far. The biosynthetic pathways of several key isoflavonoids have been established, and the genes and regulatory components involved in the biosynthesis have been characterized. The biosynthesis and accumulation of isoflavonoids in plants are regulated by multiple complex environmental and genetic factors and interactions. Due to this complexity of secondary metabolism regulation, the export and engineering of isoflavonoid biosynthetic pathways into non-endogenous plants are difficult, and instead, the microorganisms Saccharomyces cerevisiae and Escherichia coli have been adapted and engineered for heterologous isoflavonoid synthesis. However, the current ex-planta production approaches have been limited due to slow enzyme kinetics and traditionally laborious genetic engineering methods and require further optimization and development to address the required titers, reaction rates and yield for commercial application. With recent progress in metabolic engineering and the availability of advanced synthetic biology tools, it is envisaged that highly efficient heterologous hosts will soon be engineered to fulfill the growing market demand.

Review: Biological functions of major latex-like proteins in plants

Major latex-like proteins (MLPs) have been identified in dicots and monocots. They are members of the birch pollen allergen Bet v 1 family as well as pathogenesis-related proteins class 10. MLPs have two main features. One is binding affinity toward various hydrophobic compounds, such as long-chain fatty acids, steroids, and systemic acquired resistance signals, via its internal hydrophobic cavity or hydrophobic residues on its surface. MLPs transport such compounds to other organs via phloem and xylem vessels and contribute to the expression of physiologically important ligands' activity in the particular organs. The second feature is responses to abiotic and biotic stresses. MLPs are involved in drought and salt tolerance through the mediation of plant hormone signaling pathways. MLPs generate resistance against pathogens by the induction of pathogenesis-related protein genes. Therefore, MLPs play crucial roles in drought and salt tolerance and resistance against pathogens. However, knowledge of MLPs is fragmented, and an overview of them is needed. Herein, we summarize the current knowledge of the biological functions of MLPs, which to our knowledge, is the first review about MLPs that has been reported.

A Potential Role of Coumestrol in Soybean Leaf Senescence and Its Interaction With Phytohormones

Coumestrol is a natural organic compound synthesized in soy leaves and functions as a phytoalexin. The coumestrol levels in plants are reported to increase upon insect attack. This study investigates the correlation between coumestrol, senescence, and the effect of phytohormones on the coumestrol levels in soybean leaves. Our analysis involving high-performance liquid chromatography and 2-D gel electrophoresis indicated a significant difference in the biochemical composition of soybean leaves at various young and mature growth stages. Eight chemical compounds were specifically detected in young leaves (V1) only, whereas three different coumestans isotrifoliol, coumestrol, and phaseol were detected only in mature, yellow leaves of the R6 and R7 growth stage. MALDI-TOF-MS analysis was used to identify two proteins 3,9 -dihydroxypterocarpan 6A-monooxygenase (CYP93A1) and isoflavone reductase homolog 2 (IFR2) only in mature leaves, which are key components of the coumestrol biosynthetic pathway. This indicates that senescence in soybean is linked to the accumulation of coumestrol. Following the external application of coumestrol, the detached V1-stage young leaves turned yellow and showed an interesting development of roots at the base of the midrib. Additionally, the application of phytohormones, including SA, methyl jasmonate (MeJA), and ethephon alone and in various combinations induced yellowing within 5 days of the application with a concomitant significant increase in endogenous coumestrol accumulation. This was also accompanied by a significant increase in the expression of genes CYP81E28 (Gm08G089500), CYP81E22 (Gm16G149300), GmIFS1, and GmIFS2. These results indicate that various coumestans, especially coumestrol, accumulate during leaf maturity, or senescence in soybean.

Candidate Domestication-Related Genes Revealed by Expression Quantitative Trait Loci Mapping of Narrow-Leafed Lupin (Lupinus angustifolius L.)

The last century has witnessed rapid domestication of the narrow-leafed lupin (Lupinus angustifolius L.) as a grain legume crop, exploiting discovered alleles conferring low-alkaloid content (iucundus), vernalization independence (Ku and Julius), and reduced pod shattering (lentus and tardus). In this study, a L. angustifolius mapping population was subjected to massive analysis of cDNA ends (MACE). The MACE yielded 4185 single nucleotide polymorphism (SNP) markers for linkage map improvement and 30,595 transcriptomic profiles for expression quantitative trait loci (eQTL) mapping. The eQTL highlighted a high number of cis- and trans-regulated alkaloid biosynthesis genes with gene expression orchestrated by a regulatory agent localized at iucundus locus, supporting the concept that ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR RAP2-7 may control low-alkaloid phenotype. The analysis of Ku shed light on the vernalization response via FLOWERING LOCUS T and FD regulon in L. angustifolius, providing transcriptomic evidence for the contribution of several genes acting in C-repeat binding factor (CBF) cold responsiveness and in UDP-glycosyltransferases pathways. Research on lentus selected a DUF1218 domain protein as a candidate gene controlling the orientation of the sclerified endocarp and a homolog of DETOXIFICATION14 for purplish hue of young pods. An ABCG transporter was identified as a hypothetical contributor to sclerenchyma fortification underlying tardus phenotype.

Is Chickpea a Potential Substitute for Soybean? Phenolic Bioactives and Potential Health Benefits

Legume seeds are rich sources of protein, fiber, and minerals. In addition, their phenolic compounds as secondary metabolites render health benefits beyond basic nutrition. Lowering apolipoprotein B secretion from HepG2 cells and decreasing the level of low-density lipoprotein (LDL)-cholesterol oxidation are mechanisms related to the prevention of cardiovascular diseases (CVD). Likewise, low-level chronic inflammation and related disorders of the immune system are clinical predictors of cardiovascular pathology. Furthermore, DNA-damage signaling and repair are crucial pathways to the etiology of human cancers. Along CVD and cancer, the prevalence of obesity and diabetes is constantly increasing. Screening the ability of polyphenols in inactivating digestive enzymes is a good option in pre-clinical studies. In addition, in vivo studies support the role of polyphenols in the prevention and/or management of diabetes and obesity. Soybean, a well-recognized source of phenolic isoflavones, exerts health benefits by decreasing oxidative stress and inflammation related to the above-mentioned chronic ailments. Similar to soybeans, chickpeas are good sources of nutrients and phenolic compounds, especially isoflavones. This review summarizes the potential of chickpea as a substitute for soybean in terms of health beneficial outcomes. Therefore, this contribution may guide the industry in manufacturing functional foods and/or ingredients by using an undervalued feedstock.