Structure and function of enzymes involved in the biosynthesis of phenylpropanoids

Insight into the role of clathrin-mediated endocytosis inhibitors in SARS-CoV-2 infection

Emergence of SARS-CoV-2 variants warrants sustainable efforts to upgrade both the diagnostic and therapeutic protocols. Understanding the details of cellular and molecular basis of the virus-host cell interaction is essential for developing variant-independent therapeutic options. The internalization of SARS-CoV-2, into lung epithelial cells, is mediated by endocytosis, especially clathrin-mediated endocytosis (CME). Although vaccination is the gold standard strategy against viral infection, selective inhibition of endocytic proteins, complexes, and associated adaptor proteins may present a variant-independent therapeutic strategy. Although clathrin and/or dynamins are the most important proteins involved in CME, other endocytic mechanisms are clathrin and/or dynamin independent and rely on other proteins. Moreover, endocytosis implicates some subcellular structures, like plasma membrane, actin and lysosomes. Also, physiological conditions, such as pH and ion concentrations, represent an additional factor that mediates these events. Accordingly, endocytosis related proteins are potential targets for small molecules that inhibit endocytosis-mediated viral entry. This review summarizes the potential of using small molecules, targeting key proteins, participating in clathrin-dependent and -independent endocytosis, as variant-independent antiviral drugs against SARS-CoV-2 infection. The review takes two approaches. The first outlines the potential role of endocytic inhibitors in preventing endocytosis-mediated viral entry and its mechanism of action, whereas in the second computational analysis was implemented to investigate the selectivity of common inhibitors against endocytic proteins in SARS-CoV-2 endocytosis. The analysis revealed that remdesivir, methyl-β-cyclodextrin, rottlerin, and Bis-T can effectively inhibit clathrin, HMG-CoA reductase, actin, and dynamin I GTPase and are more potent in inhibiting SARS-CoV-2 than chloroquine. CME inhibitors for SARS-CoV-2 infection remain understudied.

Genome-wide studies of PAL genes in sorghum and their responses to aphid infestation

Phenylalanine ammonia-lyase (PAL, EC 4.3.1.25) plays a crucial role in plant adaptation to biotic and abiotic stresses. However, the current knowledge about PAL proteins in sorghum is essentially lacking. Thus, in this study we aimed to analyze the PAL family genes in sorghum using a genome-wide approach and to explore the role of PAL genes in host plant resistance to aphids via SA-mediated defense signaling. Here, we report gene structural features of 8 PAL (SbPAL) genes in sorghum (Sorghum bicolor), their phylogeny, protein motifs and promoter analysis. Furthermore, we demonstrated that the SbPAL genes were induced by sugarcane aphid (SCA) infestation and SbPAL exhibited differential gene expression in susceptible and resistant genotypes. PAL activity assays further validated upregulated expression of the SbPAL genes in a resistant genotype. In addition, exogenous application of SA reduced plant damage and suppressed aphid population growth and fecundity in susceptible genotype, suggesting that those SbPAL genes act as positive regulator of the SA-mediated defense signaling pathway to combat aphid pests in sorghum. This study provides insights for further examination of the defense role of PAL in sorghum against other pests and pathogens.

Effect of Heavy Metal Stress on Phenolic Compounds Accumulation in Winter Wheat Plants

Heavy metal stress can lead to many adverse effects that inhibit cellular processes at various levels of metabolism, causing a decrease in plant productivity. In response to environmental stressors, phenolic compounds fulfill significant molecular and biochemical functions in plants. Increasing the biosynthesis of phenolic compounds in plants subjected to heavy metal stress helps protect plants from oxidative stress. A pot experiment was carried out to determine the effect of the accumulation of copper (Cu) and lead (Pb) salts at concentrations of 200, 500, and 1000 ppm on seed germination, the activity of enzymes in the phenylalanine ammonia-lyase pathway (PAL) and tyrosine ammonia-lyase (TAL), along with the total phenol and flavonoid contents in seedlings of hybrid Triticum aestivum L. (winter wheat) cultivars. The accumulation of heavy metals, especially Cu, had a negative impact on the seed germination process. The cultivar "Hyacinth" reacted most strongly to heavy metal stress, which was confirmed by obtaining the lowest values of the germination parameters. Heavy metal stress caused an increase in the activity of PAL and TAL enzymes and an increase in the accumulation of phenolic compounds. Under the influence of Cu, the highest activity was shown in cv. "Hyvento" (especially at 200 ppm) and, due to the accumulation of Pb, in cv. "Hyacinth" (1000 ppm) and cv. "Hyking" (200 ppm). The cultivar "Hyking" had the highest content of phenolic compounds, which did not increase with the application of higher concentrations of metals. In other cultivars, the highest content of total phenols and flavonoids was usually observed at the lowest concentration (200 ppm) of the tested heavy metals, Cu and Pb.

Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics

Docynia delavayi (Franch.) Schneid is an evergreen tree with multiple benefits and high development and utilization value. The fruit is consumed as fresh and dry fruit, juices, and other products. However, it is unknown the chemical changes that occur upon fruit maturation. The metabolite content of unripe and ripe fruit was examined using UPLC-MS/MS technology based on a broadly targeted metabolome. We identified 477 metabolites, of which 130 differed between ripe and unripe fruit. These compounds are primarily involved in the biosynthesis of secondary metabolites, such as pantothenic acid, flavonoids, and amino acids. Moreover, in ripe fruit, there are 94 metabolites that are upregulated, particularly flavonoids and terpenoids. In comparison, compounds associated with sour flavors (amino acids, phenolic acids, organic acids) are down-regulated. Remarkably, these metabolites have a strong relationship with the medicinal properties of D. delavayi. This study provides a global perspective of the D. delavayi fruit metabolome and a comprehensive analysis of metabolomic variations during fruit development, thereby increasing the knowledge of the metabolic basis of important fruit quality traits in D. delavayi fruit.

Phenylalanine Ammonia Lyase GmPAL1.1 Promotes Seed Vigor under High-Temperature and -Humidity Stress and Enhances Seed Germination under Salt and Drought Stress in Transgenic Arabidopsis

Seed vigor is an important agronomic attribute, essentially associated with crop yield. High-temperature and humidity (HTH) stress directly affects seed development of plants, resulting in the decrease of seed vigor. Therefore, it is particularly important to discover HTH-tolerant genes related to seed vigor. Phenylalanine ammonia lyase (PAL, EC 4.3.1.24) is the first rate-limiting enzyme in the phenylpropanoid biosynthesis pathway and a key enzyme involved in plant growth and development and environmental adaptation. However, the biological function of PAL in seed vigor remains unknown. Here, GmPAL1.1 was cloned from soybean, and its protein was located in the cytoplasm and cell membrane. GmPAL1.1 was significantly induced by HTH stress in developing seeds. The overexpression of GmPAL1.1 in Arabidopsis (OE) accumulated lower level of ROS in the developing seeds and in the leaves than the WT at the physiological maturity stage under HTH stress, and the activities of SOD, POD, and CAT and flavonoid contents were significantly increased, while MDA production was markedly reduced in the leaves of the OE lines than in those of the WT. The germination rate and viability of mature seeds of the OE lines harvested after HTH stress were higher than those of the WT. Compared to the control, the overexpression of GmPAL1.1 in Arabidopsis enhanced the tolerance to salt and drought stresses during germination. Our results suggested the overexpression of GmPAL1.1 in Arabidopsis promoted seed vigor at the physiological maturation period under HTH stress and increased the seeds' tolerance to salt and drought during germination.

Recent Updates on Source, Biosynthesis, and Therapeutic Potential of Natural Flavonoid Luteolin: A Review

Nature gives immense resources that are beneficial to humankind. The natural compounds present in plants provide primary nutritional values to our diet. Apart from food, plants also provide chemical compounds with therapeutic values. The importance of these plant secondary metabolites is increasing due to more studies revealing their beneficial properties in treating and managing various diseases and their symptoms. Among them, flavonoids are crucial secondary metabolite compounds present in most plants. Of the reported 8000 flavonoid compounds, luteolin is an essential dietary compound. This review discusses the source of the essential flavonoid luteolin in various plants and its biosynthesis. Furthermore, the potential health benefits of luteolins such as anti-cancer, anti-microbial, anti-inflammatory, antioxidant, and anti-diabetic effects and their mechanisms are discussed in detail. The activity of luteolin and its derivatives are diverse, as they help to prevent and control many diseases and their life-threatening effects. This review will enhance the knowledge and recent findings regarding luteolin and its therapeutic effects, which are certainly useful in potentially utilizing this natural metabolite.

Flooding and herbivory: the effect of concurrent stress factors on plant volatile emissions and gene expression in two heirloom tomato varieties

BACKGROUND

In nature and in cultivated fields, plants encounter multiple stress factors. Nonetheless, our understanding of how plants actively respond to combinatorial stress remains limited. Among the least studied stress combination is that of flooding and herbivory, despite the growing importance of these stressors in the context of climate change. We investigated plant chemistry and gene expression changes in two heirloom tomato varieties: Cherokee Purple (CP) and Striped German (SG) in response to flooding, herbivory by Spodoptera exigua, and their combination.

RESULTS

Volatile organic compounds (VOCs) identified in tomato plants subjected to flooding and/or herbivory included several mono- and sesquiterpenes. Flooding was the main factor altering VOCs emission rates, and impacting plant biomass accumulation, while different varieties had quantitative differences in their VOC emissions. At the gene expression levels, there were 335 differentially expressed genes between the two tomato plant varieties, these included genes encoding for phenylalanine ammonia-lyase (PAL), cinnamoyl-CoA-reductase-like, and phytoene synthase (Psy1). Flooding and variety effects together influenced abscisic acid (ABA) signaling genes with the SG variety showing higher levels of ABA production and ABA-dependent signaling upon flooding. Flooding downregulated genes associated with cytokinin catabolism and general defense response and upregulated genes associated with ethylene biosynthesis, anthocyanin biosynthesis, and gibberellin biosynthesis. Combining flooding and herbivory induced the upregulation of genes including chalcone synthase (CHS), PAL, and genes encoding BAHD acyltransferase and UDP-glucose iridoid glucosyltransferase-like genes in one of the tomato varieties (CP) and a disproportionate number of heat-shock proteins in SG. Only the SG variety had measurable changes in gene expression due to herbivory alone, upregulating zeatin, and O-glucosyltransferase and thioredoxin among others.

CONCLUSION

Our results suggest that both heirloom tomato plant varieties differ in their production of secondary metabolites including phenylpropanoids and terpenoids and their regulation and activation of ABA signaling upon stress associated with flooding. Herbivory and flooding together had interacting effects that were evident at the level of plant chemistry (VOCs production), gene expression and biomass markers. Results from our study highlight the complex nature of plant responses to combinatorial stresses and point at specific genes and pathways that are affected by flooding and herbivory combined.

Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region

Cyanobacteria are diverse photosynthetic microorganisms able to produce a myriad of bioactive chemicals. To make possible the rational exploitation of these microorganisms, it is fundamental to know their metabolic capabilities and to have genomic resources. In this context, the main objective of this research was to determine the genome features and the biochemical profile of Synechococcus sp. UCP002. The cyanobacterium was isolated from the Peruvian Amazon Basin region and cultured in BG-11 medium. Growth parameters, genome features, and the biochemical profile of the cyanobacterium were determined using standardized methods. Synechococcus sp. UCP002 had a specific growth rate of 0.086 ± 0.008 μ and a doubling time of 8.08 ± 0.78 h. The complete genome of Synechococcus sp. UCP002 had a size of ∼3.53 Mb with a high coverage (∼200x), and its quality parameters were acceptable (completeness = 99.29%, complete and single-copy genes = 97.5%, and contamination = 0.35%). Additionally, the cyanobacterium had six plasmids ranging from 24 to 200 kbp. The annotated genome revealed ∼3,422 genes, ∼ 3,374 protein-coding genes (with ∼41.31% hypothetical protein-coding genes), two CRISPR Cas systems, and 61 non-coding RNAs. Both the genome and plasmids had the genes for prokaryotic defense systems. Additionally, the genome had genes coding the transcription factors of the metalloregulator ArsR/SmtB family, involved in sensing heavy metal pollution. The biochemical profile showed primary nutrients, essential amino acids, some essential fatty acids, pigments (e.g., all-trans-β-carotene, chlorophyll a, and phycocyanin), and phenolic compounds. In conclusion, Synechococcus sp. UCP002 shows biotechnological potential to produce human and animal nutrients and raw materials for biofuels and could be a new source of genes for synthetic biological applications.

Apigenin and its dermatological applications: A comprehensive review

Apigenin is one of the abundant flavonoids in fruits and vegetables of human diet with several demonstrated health benefits. The aim of the present study is to provide an overview of the current evidence regarding the effect of apigenin on different dermatological complications. Electronic databases including PubMed, Scopus, and Web of Science were searched to retrieve all papers assessing the dermatological effects of apigenin. Preclinical studies support beneficial effects of apigenin on UV-induced skin damage, vitiligo, dermatitis, wounds, skin aging, and some types of skin cancer. The compound mostly acts via inhibition of inflammation through suppression of pro-inflammatory cytokines and intracellular inflammatory mediators, as well as antioxidant properties such as improvement of endogenous antioxidant defense mechanisms. There are also some studies for the design and development of novel drug delivery systems for apigenin to improve its oral and topical bioavailability. Nevertheless, no clinical study has evaluated apigenin as a natural supplement for skin conditions. Considering the benefits of apigenin in preclinical models of dermatological disorders, as well as the acceptable safety of this compound, apigenin may be a future candidate to be used in dermatological disorders. Future clinical studies are needed to further confirm the safety and efficacy of apigenin in skin care products.

Sirex noctilio infestation led to inevitable pine death despite activating pathways involved in tolerance

Defense-related metabolome traits in pine species after infestation by Sirex noctilio are largely unknown, despite, in most cases, trees being overwhelmed. Using LC-MS-based untargeted metabolomics, we revealed the systemic metabolic changes induced by this insect in 14-year-old Pinus radiata trees, the most affected species worldwide. An immediate metabolome alteration was expressed in needles after infestation, including the up-regulation of flavonols, flavan-3-ols, oxyneolignans, auxins, proline, and tryptophan, among others. The flavan-3-ols (catechin and procyanidin B1) suggested a rapidly induced photoprotection mechanism aided by diverting proline as an alternative substrate for respiration to compensate for the progressive chlorosis that degrades photosystems. Meanwhile, glutathione, glutamate, and ascorbate levels significantly dropped in needles, which may indicate the critical oxidative stress that trees had to face since the onset of the infestation. They were not fully replenished after long-term infestation, and redox homeostasis was probably not achieved, compromising tree survival. Nevertheless, a huge auxins overexpression detected in needles throughout the infestation may reflect tolerance against the premature senescence caused by the woodwasp venom. In contrast, the metabolome of wood tissues remained initially unchanged, although it seems to collapse after three months. Overall, the metabolomics strategy adopted in this work evidenced its usefulness in uncovering the fundamental roles of plants' chemical defense that govern interactions with specific stressors.

Wall-associated kinase-like gene RL1 contributes to red leaves in sorghum

Red leaves are common in trees but rare in cereal crops. Red leaves can be used as raw materials for anthocyanin extraction and may have some adaptive significance for plants. In this study, we discovered a red leaf phenotype in the F₁ hybrids derived from a cross between two sorghum accessions with green leaf. Histological analysis of red leaves and green leaves showed that red compounds accumulate in mesophyll cells and gradually spreads to the entire leaf blade. In addition, we found chloroplasts degraded more quickly in red leaves than in green leaves based on transmission electron microscopy. Metabolic analysis revealed that flavonoids including six anthocyanins are more abundant in red leaves. Moreover, transcriptome analysis revealed that expression of flavonoid biosynthesis genes was upregulated in red leaves. These observations indicate that flavonoids and anthocyanins in particular, are ideal candidates for the red compounds accumulating in red leaves. Segregation analysis of the red leaf phenotype suggested a genetic architecture consisting of three dominant genes, one (RL1 for RED LEAF1) of which we mapped to a 55-kb region on chromosome 7 containing seven genes. Sequencing, reverse transcription-polymerase chain reaction, and transcriptome analysis suggested Sobic.007G214300, encoding a wall-associated kinase, as the most likely candidate for RL1. Fine mapping the red leaf gene and identifying the metabolites that cause red leaf in sorghum provide us with a better understanding of the red leaf phenotype in the natural population of sorghum.

Integrative Analysis of the Metabolome and Transcriptome Provides Insights into the Mechanisms of Flavonoid Biosynthesis in Quinoa Seeds at Different Developmental Stages

Quinoa (Chenopodium quinoa Willd.) is a crop with high nutritional and health benefits. Quinoa seeds are rich in flavonoid compounds; however, the mechanisms behind quinoa flavonoid biosynthesis remain unclear. We independently selected the high-generation quinoa strain ‘Dianli-3260′, and used its seeds at the filling, milk ripening, wax ripening, and mature stages for extensive targeted metabolome analysis combined with joint transcriptome analysis. The results showed that the molecular mechanism of flavonoid biosynthesis in quinoa seeds was mainly concentrated in two pathways: “flavonoid biosynthesis pathway” and “flavone and flavonol biosynthesis pathway”. Totally, 154 flavonoid-related metabolites, mainly flavones and flavonols, were detected in the four development stages. Moreover, 39,738 genes were annotated with KEGG functions, and most structural genes of flavonoid biosynthesis were differentially expressed during grain development. We analyzed the differential flavonoid metabolites and transcriptome changes between the four development stages of quinoa seeds and found that 11 differential flavonoid metabolites and 22 differential genes were the key factors for the difference in flavonoid biosynthesis. This study provides important information on the mechanisms underlying quinoa flavonoid biosynthesis, the screening of potential quinoa flavonoid biosynthesis regulation target genes, and the development of quinoa products.

Impact of the Flavonoid Quercetin on β-Amyloid Aggregation Revealed by Intrinsic Fluorescence

We report the effects of quercetin, a flavonoid present in the human diet, on early stage beta-amyloid (Aβ) aggregation, a seminal event in Alzheimer's disease. Molecular level changes in Aβ arrangements are monitored by time-resolved emission spectral (TRES) measurements of the fluorescence of Aβ's single tyrosine intrinsic fluorophore (Tyr). The results suggest that quercetin binds β-amyloid oligomers at early stages of their aggregation, which leads to the formation of modified oligomers and hinders the creation of β-sheet structures, potentially preventing the onset of Alzheimer's disease.

Extraction Techniques and Analytical Methods for Isolation and Characterization of Lignans

Lignans are a group of natural polyphenols present in medicinal plants and in plants which are a part of the human diet for which more and more pharmacological activities, such as antimicrobial, anti-inflammatory, hypoglycemic, and cytoprotective, are being reported. However, it is their cytotoxic activities that are best understood and which have shed light on this group. Two anticancer drugs, etoposide, and teniposide, were derived from a potent cytotoxic agent—podophyllotoxin from the roots of Podophyllum peltatum. The evidence from clinical and observational studies suggests that human microbiota metabolites (enterolactone, enterodiol) of dietary lignans (secoisolariciresinol, pinoresinol, lariciresinol, matairesinol, syringaresinol, medioresinol, and sesamin) are associated with a reduced risk of some hormone-dependent cancers. The biological in vitro, pharmacological in vivo investigations, and clinical studies demand significant amounts of pure compounds, as well as the use of well-defined and standardized extracts. That is why proper extract preparation, optimization of lignan extraction, and identification are crucial steps in the development of lignan use in medicine. This review focuses on lignan extraction, purification, fractionation, separation, and isolation methods, as well as on chromatographic, spectrometric, and spectroscopic techniques for their qualitative and quantitative analysis.

Comparative Transcriptomic and Metabolic Analyses Reveal the Coordinated Mechanisms in Pinus koraiensis under Different Light Stress Conditions

Light is one of the most important environmental cues that affects plant development and regulates its behavior. Light stress directly inhibits physiological responses and plant tissue development and even induces mortality in plants. Korean pine (Pinus koraiensis) is an evergreen conifer species widely planted in northeast China that has important economic and ecological value. However, the effects of light stress on the growth and development of Korean pine are still unclear. In this study, the effects of different shading conditions on physiological indices, molecular mechanisms and metabolites of Korean pine were explored. The results showed that auxin, gibberellin and abscisic acid were significantly increased under all shading conditions compared with the control. The contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoid also increased as the shading degree increased. Moreover, a total of 8556, 3751 and 6990 differentially expressed genes (DEGs) were found between the control and HS (heavy shade), control and LS (light shade), LS vs. HS, respectively. Notably, most DEGs were assigned to pathways of phytohormone signaling, photosynthesis, carotenoid and flavonoid biosynthesis under light stress. The transcription factors MYB-related, AP2-ERF and bHLH specifically increased expression during light stress. A total of 911 metabolites were identified, and 243 differentially accumulated metabolites (DAMs) were detected, among which flavonoid biosynthesis (naringenin chalcone, dihydrokaempferol and kaempferol) metabolites were significantly different under light stress. These results will provide a theoretical basis for the response of P. koraiensis to different light stresses.

Phenylalanine suppresses cell death caused by loss of fumarylacetoacetate hydrolase in Arabidopsis

Fumarylacetoacetate hydrolase (FAH) catalyzes the final step of Tyrosine (Tyr) degradation pathway essential to animals and the deficiency of FAH causes an inborn lethal disease. In plants, a role of this pathway was unknown until we found that mutation of Short-day Sensitive Cell Death1 (SSCD1), encoding Arabidopsis FAH, results in cell death under short day. Phenylalanine (Phe) could be converted to Tyr and then degraded in both animals and plants. Phe ingestion in animals worsens the disease caused by FAH defect. However, in this study we found that Phe represses cell death caused by FAH defect in plants. Phe treatment promoted chlorophyll biosynthesis and suppressed the up-regulation of reactive oxygen species marker genes in the sscd1 mutant. Furthermore, the repression of sscd1 cell death by Phe could be reduced by α-aminooxi-β-phenylpropionic acid but increased by methyl jasmonate, which inhibits or activates Phe ammonia-lyase catalyzing the first step of phenylpropanoid pathway, respectively. In addition, we found that jasmonate signaling up-regulates Phe ammonia-lyase 1 and mediates the methyl jasmonate enhanced repression of sscd1 cell death by Phe. These results uncovered the relation between chlorophyll biosynthesis, phenylpropanoid pathway and jasmonate signaling in regulating the cell death resulting from loss of FAH in plants.

Flavonoid 4,4'-dimethoxychalcone induced ferroptosis in cancer cells by synergistically activating Keap1/Nrf2/HMOX1 pathway and inhibiting FECH

Flavonoids are widely distributed in plants as secondary metabolites and have various biological benefits such as anti-tumor, anti-oxidant, anti-inflammatory and anti-aging. We previously reported that 4,4'-dimethoxychalcone (DMC) suppressed cancer cell proliferation by aggravating oxidative stress and inducing G2/M cell cycle arrest. In the present study, we explored the underlying mechanisms by which DMC inhibited cancer cell growth. Given that ferrochelatase (FECH) is a potential target of DMC identified by thermal proteome profiling (TPP) method, herein, we confirmed that DMC inhibited the enzymatic activity of FECH. Furthermore, we proved that DMC induced Keap1 degradation via ubiquitin-proteasome system, which led to the nuclear translocation of Nrf2 and upregulated Nrf2 targeted gene HMOX1. FECH inhibition and HMOX1 upregulation resulted in iron overload and triggered ferroptosis in cancer cells. Collectively, we revealed that DMC induced ferroptosis by synergistically activating Keap1/Nrf2/HMOX1 pathway and inhibiting FECH. Our findings indicate that FECH contributes to the non-canonical ferroptosis induction, shed light on the mechanisms of DMC inhibiting cancer cell growth, and set an example for studying biological functions of flavonoids.

Constitutive expression of VviNAC17 transcription factor significantly induces the synthesis of flavonoids and other phenolics in transgenic grape berry cells

VviNAC17 is a grapevine transcription factor activated by ABA. Because ABA has been proposed as the main signal modulating the secondary metabolism in grape berry skins, here we postulated VviNAC17 as a positive regulator of secondary metabolism in grape cells. To validate the hypothesis, VviNAC17 was constitutively and stably overexpressed in grape berry suspension-cultured cells of Gamay Fréaux cv. by Agrobacterium-mediated transformation. Targeted transcriptional analyses by qPCR showed that several genes involved the phenylpropanoid (VviPAL1), stilbenoid (VviSTS1) and flavonoid pathways (VviDFR, VviLAR1, VviANR, VviLDOX, and VviUFGT1), as well as anthocyanin vacuolar transport and accumulation (VviGST4 and VvMATE1) were significantly upregulated in VviNAC17-overexpressing transgenic cells, which translated in the stimulation of a number of enzymatic activities in those pathways. This was the case of phenylalanine ammonia lyase (PAL) and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT) that were about 2-fold and 3.5-fold higher in VviNAC17-overexpressing cells than in control cells. VviNAC17-overexpressing cells accumulated significantly higher amounts of anthocyanins, proanthocyanidins, total flavonoids and total phenolics. These findings confirmed that VviNAC17 is an important positive regulator of secondary metabolism in grapevine contributing to the accumulation of important berry quality-related secondary metabolites.

Exogenous Melatonin Treatment Induces Disease Resistance against Botrytis cinerea on Post-Harvest Grapes by Activating Defence Responses

Botrytis cinerea seriously affects the value of post-harvest grapes. Melatonin can act as an exogenous regulator in the resistance of exogenous pathogens due to its antioxidant activity. An artificial inoculation trial was conducted to research the induced resistance mechanism of melatonin treatment using the table grape “Muscat Hamburg” (Vitis vinifera L. cv). Grapes were immersed with 0.02, 0.2, and 2 mmol/L melatonin, followed by B. cinerea suspension injections after 48 h. The results showed that the mycelial growth and spore germination of B. cinerea was not significantly inhibited by melatonin at different concentrations (0.02–2 mmol/L). However, post-harvest melatonin treatment inhibited the increase of disease incidence and severity of grey mould, induced the synthesis and accumulation of total phenols and flavonoids, reduced malondialdehyde generation, and inhibited an increase in cell membrane permeability. Meanwhile, defensive enzyme activities, including superoxide dismutase (SOD), peroxidize (POD), catalase (CAT), phenylalanine ammonia-lyase (PAL), polyphenol oxidase (PPO), chitinase (CHI), and β-1,3-glucanase, were significantly increased in fruits treated with exogenous melatonin. These results suggested that exogenous melatonin treatment could activate defence responses to combat the infection of B. cinerea in post-harvest grapes.

Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L

Dioscorea cirrhosa is a plant that is used as a dye as well as in medicine. Many metabolites with pharmacological activity exist in the tubers of D. cirrhosa. However, little is known about the mechanism regulating biosynthesis in these metabolites. In this study, transcriptome and metabolome profiling were performed in four color tubers. A total of 531 metabolites, including 62 flavonoids, were identified. Epicatechin and proanthocyanin B2 were the key metabolites that exhibited high content levels in the four tubers. These metabolites were divided into nine classes with distinct change patterns. A total of 22,865 differentially expressed genes (DEGs) were identified by transcriptome analysis. Among these DEGs, we identified 67 candidate genes related to the flavonoid biosynthesis pathway and three genes that played pivotal roles in proanthocyanin (PA) synthesis. A weighted gene co-expression network analysis (WGCNA) revealed that the two modules, "MEblue" and "MEblack," were two key gene sets strongly associated with phenylpropanoid and flavonoid biosynthesis. We also found that the plant hormone signal transduction biological process exhibited activity in the late stage of tuber color formation. Additionally, we identified 37 hub transcript factors related to flavonoid biosynthesis, of which 24 were found to be highly associated with flavonoid pathway genes. In addition to the MYB-bHLH-WD40 (MBW) genes, we found that the plant hormone gene families exhibited high expression levels. This study provides a reference for understanding the synthesis of D. cirrhosa tuber metabolites at the molecular level and provides a foundation for the further development of D. cirrhosa related plant pigments as well as its further use in the pharmaceutical industry.

Integrated transcriptome and metabolome analyses revealed regulatory mechanisms of flavonoid biosynthesis in Radix Ardisia

Background

Radix Ardisia (Jab Bik Lik Jib) is a common Miao medicine and is widely distributed in the Guizhou region of southern China. The botanical origin of Radix Ardisia includes the dry root and rhizome of Ardisia Crenata Sims (ACS) or Ardisia Crispa (Thunb.) A.DC. (AC), which are closely related species morphologically. However, the secondary metabolites in their roots are different from one another, especially the flavonoids, and these differences have not been thoroughly explored at the molecular level. This project preliminarily identified regulatory molecular mechanisms in the biosynthetic pathways of the flavonoids between ACS and AC using a multi-omics association analysis.

Methods

In this study, we determined the total levels of saponin, flavonoid, and phenolic in Radix Ardisia from different origins. Integrated transcriptome and metabolome analyses were used to identify the differentially expressed genes (DEGs) and differentially expressed metabolites (DEM). We also performed conjoint analyses on DEGs and DEMs to ascertain the degree pathways, and explore the regulation of flavonoid biosynthesis.

Results

The total flavonoid and phenolic levels in ACS were significantly higher than in AC (P < 0.05). There were 17,685 DEGs between ACS vs. AC, 8,854 were upregulated and 8,831 were downregulated. Based on this, we continued to study the gene changes in the flavonoid biosynthesis pathway, and 100 DEGs involving flavonoid biosynthesis were differentially expressed in ACS and AC. We validated the accuracy of the RNA-seq data using qRT-PCR. Metabolomic analyses showed that 11 metabolites were involved in flavonoid biosynthesis including: Naringenin, Luteolin, Catechin, and Quercetin. A conjoint analysis of the genome-wide connection network revealed the differences in the types and levels of flavonoid compounds between ACS and AC. The correlation analysis showed that Naringenin, Luteolin, Catechin, and Quercetin were more likely to be key compounds in the flavonoid biosynthesis pathway also including 4CL, AOMT, CHS, CHI, DFR, F3'5'H, FLS, and LAR.

Conclusions

This study provides useful information for revealing the regulation of flavonoid biosynthesis and the regulatory relationship between metabolites and genes in the flavonoid biosynthesis pathway in Radix Ardisia from different origins.

The Small-Molecule Language of Dynamic Microbial Interactions

Although microbes are routinely grown in monocultures in the laboratory, they are almost never encountered as single species in the wild. Our ability to detect and identify new microorganisms has advanced significantly in recent years, but our understanding of the mechanisms that mediate microbial interactions has lagged behind. What makes this task more challenging is that microbial alliances can be dynamic, consisting of multiple phases. The transitions between phases, and the interactions in general, are often mediated by a chemical language consisting of small molecules, also referred to as secondary metabolites or natural products. In this microbial lexicon, the molecules are like words and through their effects on recipient cells they convey meaning. The current review highlights three dynamic microbial interactions in which some of the words and their meanings have been characterized, especially those that mediate transitions in selected multiphasic associations. These systems provide insights into the principles that govern microbial symbioses and a playbook for interrogating similar associations in diverse ecological niches. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Ethylene-responsive factor ERF114 mediates fungal pathogen effector PevD1-induced disease resistance in Arabidopsis thaliana

APETALA2/ethylene-responsive factor (AP2/ERF) family transcription factors are well-documented in plant responses to a wide range of biotic and abiotic stresses, but their roles in mediating elicitor-induced disease resistance remains largely unexplored. PevD1 is a Verticillium dahliae secretory effector that can induce disease resistance in cotton and tobacco plants. In our previous work, Nicotiana benthamiana ERF114 (NbERF114) was identified in a screen of genes differentially expressed in response to PevD1 infiltration. Here, we found that the ortholog of NbERF114 in Arabidopsis thaliana (ERF114) also strongly responded to PevD1 treatment and transcripts were induced by Pseudomonas syringae pv. tomato (Pst) DC3000 infection. Loss of ERF114 function caused impaired disease resistance, while overexpressing ERF114 (OE-ERF114) enhanced resistance to Pst DC3000. Moreover, ERF114 mediated PevD1-induced disease resistance. RNA-sequencing analysis revealed that the transcript level of phenylalanine ammonia-lyase1 (PAL1) and its downstream genes were significantly suppressed in erf114 mutants compared with A. thaliana Col-0. Reverse transcription-quantitative PCR (RT-qPCR) analysis further confirmed that the PAL1 mRNA level was significantly elevated in overexpressing OE-ERF114 plants but reduced in erf114 mutants compared with Col-0. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) and electrophoretic mobility shift assay verified that ERF114 directly bound to the promoter of PAL1. The gene expression profiles of ERF114 and PAL1 in oestradiol-inducible transgenic plants confirmed ERF114 could activate PAL1 transcriptional expression. Further investigation revealed that ERF114 positively modulated PevD1-induced lignin and salicylic acid accumulation, probably by activating PAL1 transcription.

High-quality chromosome-level genome assembly of Litsea coreana L. provides insights into Magnoliids evolution and flavonoid biosynthesis

The magnoliid Litsea coreana has been the subject of a substantial amount of research owing to its production of many flavonoid metabolites, high food processing value, and a controversial phylogenetic position. For this study, we assembled a high-grade genome at the chromosome scale and annotation of L. coreana that was anchored to 12 chromosomes. The total genome was 1139.45 Mb, while the N50 scaffold was 97.18 Mb long. The analysis of phylogenetic trees constructed by different methods show that the phylogeny of Magnoliids is inconsistent, indicating that the differentiation process of monocots, eudicots, and Magnoliids still remains in dispute. An ancient whole-genome duplication (WGD) event was shown to have occurred before the Magnoliales and Laurels had differentiated. Subsequently, an independent WGD appeared in the Lauralean lineage. A total of 27 types of flavonoids were detected in all five tissues of L. coreana. Chalcone synthases (CHSs) that are responsible for production of flavonoids have been validated at the bioinformatics level. The retention of comparative genomic analyses of the CHS gene family showed that this family had contracted significantly in L. coreana. Our research further elaborated the evolution of Lauraceae and perfected the genetic basis of flavonoid biosynthesis in L. coreana. SIGNIFICANCE STATEMENT: Provides evidence that determines the evolutionary status of Magnoliids. The chalcone synthase gene family was significantly contracted in Litsea coreana.

The role of key gut microbial metabolites in the development and treatment of cancer

In recent years, the role of gut microbial metabolites on the inhibition and progression of cancer has gained significant interest in anticancer research. It has been established that the gut microbiome plays a pivotal role in the development, treatment and prognosis of different cancer types which is often mediated through the gut microbial metabolites. For instance, gut microbial metabolites including bacteriocins, short-chain fatty acids and phenylpropanoid-derived metabolites have displayed direct and indirect anticancer activities through different molecular mechanisms. Despite the reported anticancer activity, some gut microbial metabolites including secondary bile acids have exhibited pro-carcinogenic properties. This review draws a critical summary and assessment of the current studies demonstrating the carcinogenic and anticancer activity of gut microbial metabolites and emphasises the need to further investigate the interactions of these metabolites with the immune system as well as the tumour microenvironment in molecular mechanistic and clinical studies.

Heinz-resistant tomato cultivars exhibit a lignin-based resistance to field dodder (Cuscuta campestris) parasitism

Cuscuta species (dodders) are agriculturally destructive, parasitic angiosperms. These parasitic plants use haustoria as physiological bridges to extract nutrients and water from hosts. Cuscuta campestris has a broad host range and wide geographical distribution. While some wild tomato relatives are resistant, cultivated tomatoes are generally susceptible to C. campestris infestations. However, some specific Heinz tomato (Solanum lycopersicum) hybrid cultivars exhibit resistance to dodders in the field, but their defense mechanism was previously unknown. Here, we discovered that the stem cortex in these resistant lines responds with local lignification upon C. campestris attachment, preventing parasite entry into the host. Lignin Induction Factor 1 (LIF1, an AP2-like transcription factor), SlMYB55, and Cuscuta R-gene for Lignin-based Resistance 1, a CC-NBS-LRR (CuRLR1) are identified as factors that confer host resistance by regulating lignification. SlWRKY16 is upregulated upon C. campestris infestation and potentially negatively regulates LIF1 function. Intriguingly, CuRLR1 may play a role in signaling or function as an intracellular receptor for receiving Cuscuta signals or effectors, thereby regulating lignification-based resistance. In summary, these four regulators control the lignin-based resistance response in specific Heinz tomato cultivars, preventing C. campestris from parasitizing resistant tomatoes. This discovery provides a foundation for investigating multilayer resistance against Cuscuta species and has potential for application in other essential crops attacked by parasitic plants.

Fabaceae: a significant flavonoid source for plant and human health

The Fabaceae is recognized as the third largest and one of the most influential families among the flowering plants. Furthermore, its name is linked to “Legumes”, which represent a vast group of angiosperms in the continents utilized as crops, forages, and green manures. It is recognized for diverse constituents, covering both primary metabolites include lectins, chitinases, various proteases, and α-amylase inhibitors, as well as secondary metabolites include flavonoids, alkaloids, terpenoids, tannins, and phenolics. Fabaceae flavonoid plays an important role in the legumes’ adaptability to biological surroundings as defensive agents (phytoalexins) and as chemical signals in a symbiotic relationship with a bacterial species known as rhizobia. Considering their important role in plant defense and benefits to human healthiness, a number of studies on the Fabaceae plant have been performed, namely isolation and screening of the purified compounds and their biological activity. This study outlines specified issues on the chemical structure, biosynthesis, biological activities, and medicinal uses of Fabaceae compounds.

Heterorhabditis and Photorhabdus Symbiosis: A Natural Mine of Bioactive Compounds

Phylum Nematoda is of great economic importance. It has been a focused area for various research activities in distinct domains across the globe. Among nematodes, there is a group called entomopathogenic nematodes, which has two families that live in symbiotic association with bacteria of genus Xenorhabdus and Photorhabdus, respectively. With the passing years, researchers have isolated a wide array of bioactive compounds from these symbiotically associated nematodes. In this article, we are encapsulating bioactive compounds isolated from members of the family Heterorhabditidae inhabiting Photorhabdus in its gut. Isolated bioactive compounds have shown a wide range of biological activity against deadly pathogens to both plants as well as animals. Some compounds exhibit lethal effects against fungi, bacteria, protozoan, insects, cancerous cell lines, neuroinflammation, etc., with great potency. The main aim of this article is to collect and analyze the importance of nematode and its associated bacteria, isolated secondary metabolites, and their biomedical potential, which can serve as potential leads for further drug discovery.

OsSPLs Regulate Male Fertility in Response to Different Temperatures by Flavonoid Biosynthesis and Tapetum PCD in PTGMS Rice

Photoperiod and thermo-sensitive genic male sterile (PTGMS) rice is an important resource for two line hybrid rice production. The SQUAMOSA–promoter binding, such as the (SPL) gene family, encode the plant specific transcription factors that regulate development and defense responses in plants. However, the reports about SPLs participating in male fertility regulation are limited. Here, we identified 19 OsSPL family members and investigated their involvement in the fertility regulation of the PTGMS rice lines, PA2364S and PA2864S, with different fertility transition temperatures. The results demonstrated that OsSPL2, OsSPL4, OsSPL16 and OsSPL17 affect male fertility in response to temperature changes through the MiR156-SPL module. WGCNA (weighted gene co-expression network analysis) revealed that CHI and APX1 were co-expressed with OsSPL17. Targeted metabolite and flavonoid biosynthetic gene expression analysis revealed that OsSPL17 regulates the expression of flavonoid biosynthesis genes CHI, and the up regulation of flavanones (eriodictvol and naringenin) and flavones (apigenin and luteolin) content contributed to plant fertility. Meanwhile, OsSPL17 negatively regulates APX1 to affect APX (ascorbate peroxidase) activity, thereby regulating ROS (reactive oxygen species) content in the tapetum, controlling the PCD (programmed cell death) process and regulating male fertility in rice. Overall, this report highlights the potential role of OsSPL for the regulation of male fertility in rice and provides a new insight for the further understanding of fertility molecular mechanisms in PTGMS rice.

Methoxyacrylate Fungicide Candidate CL-15C Also Functions as a Plant Elicitor in Arabidopsis thaliana and Oryza sativa L

Unlike traditional fungicides targeting fungi, plant elicitors usually lack direct fungicidal activity but improve the plant immune system to resist fungi infection, which has gained increasing attention for better fungi resistance management and environment protection. (E)-methyl-2-(2-((((Z)-(amino-(3,4-dichloroisothiazol-5-yl)methylene)amino)oxy)methyl)phenyl)-2-(methoxyimino)acetate (CL-15C) was found to be a fungicide candidate with a broad spectrum. Here, we studied its immune-inducing ability and mechanism to strengthen the resistance of Arabidopsis thaliana against Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) and Oryza sativa L. against Magnaporthe oryzae. CL-15C promoted a 2.20- and 1.47-fold increase in phenylalanine ammonia-lyase (PAL) activity in A. thaliana and O. sativa, respectively. It also facilitated a 1.89- and 1.32-fold increase in accumulation of salicylic acid (SA) in A. thaliana and O. sativa, respectively. Differential genes were clustered in the SA signaling pathway at 24 h after a CL-15C treatment in A. thaliana. Because PAL is a rate-limiting enzyme in the phenylalanine metabolic pathway, after a CL-15C treatment, a pal1(PAL 1) mutant was more susceptible to Pst DC3000 when compared with the wild type. Bacterial counts in leaves after a CL-15C treatment showed a 1.11-fold reduction in the pal1 mutant and a 1.54-fold reduction in the wild type. The effect of CL-15C on the PAL enzyme activity and SA content was attenuated in the pal1 mutant. Present experimental data implied that the immune-inducing activity of CL-15C was dependent on PAL gene-mediated synthesis of SA.

Bioactive Constituents of Iris hybrida (Iridaceae): processing effect

Iris genus plants are a valuable source of bioactive compounds, which are an important component for pharmaceutical development. The present article shows the potential of mineral nutrition with applied of magnesium sulfate, iron chelates, and potassium oxide on affecting the phenolic compounds content in Iris hybrida 'Tsikavynka', I. hybrida 'Tambo', and I. hybridа 'Widecombe Fire'. The effect of mineral processing was specific to plant organs and varied in the components composition. The Irises rhizomes had an increased total phenolic compounds content after treatment (up to 10% of the total isoflavonoids content, up to 8% of phenolic acids; up to 5% of γ-pyrones; up to 13% of flavonoids) by UV-Vis spectroscopy method. A positive effect of nutrition on the biosynthesis and content of individual isoflavonoids (tectoridin, nigricin D-glucoside, genistin, iristectorigenin B, nigricin, irigenin, irisolidone) and xanthone mangiferin in Irises rhizomes by HPLC has been established. In addition, an increase of chlorogenic acid amount in Irises leaves was noted. The results demonstrate the sensitivity of Iris phenylpropanoid metabolism to mineral nutrition and can be used for predicted medical plant cultivation with increased content of bioactive constituents.

Floral Scents and Fruit Aromas: Functions, Compositions, Biosynthesis, and Regulation

Floral scents and fruit aromas are crucial volatile organic compounds (VOCs) in plants. They are used in defense mechanisms, along with mechanisms to attract pollinators and seed dispersers. In addition, they are economically important for the quality of crops, as well as quality in the perfume, cosmetics, food, drink, and pharmaceutical industries. Floral scents and fruit aromas share many volatile organic compounds in flowers and fruits. Volatile compounds are classified as terpenoids, phenylpropanoids/benzenoids, fatty acid derivatives, and amino acid derivatives. Many genes and transcription factors regulating the synthesis of volatiles have been discovered. In this review, we summarize recent progress in volatile function, composition, biosynthetic pathway, and metabolism regulation. We also discuss unresolved issues and research perspectives, providing insight into improvements and applications of plant VOCs.

Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida

Background

Seed germination is a series of ordered physiological and morphogenetic processes and a critical stage in plant life cycle. Tamarix hispida is one of the most salt-tolerant plant species; however, its seed germination has not been analysed using combined transcriptomics and metabolomics.

Results

Transcriptomic sequencing and widely targeted metabolomics were used to detect the transcriptional metabolic profiles of T. hispida at different stages of seed germination and young seedling growth. Transcriptomics showed that 46,538 genes were significantly altered throughout the studied development period. Enrichment study revealed that plant hormones, such as auxin, ABA, JA and SA played differential roles at varying stages of seed germination and post-germination. Metabolomics detected 1022 metabolites, with flavonoids accounting for the highest proportion of differential metabolites. Combined analysis indicated that flavonoid biosynthesis in young seedling growth, such as rhoifolin and quercetin, may improve the plant’s adaptative ability to extreme desert environments.

Conclusions

The differential regulation of plant hormones and the accumulation of flavonoids may be important for the seed germination survival of T. hispida in response to salt or arid deserts. This study enhanced the understanding of the overall mechanism in seed germination and post-germination. The results provide guidance for the ecological value and young seedling growth of T. hispida.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08341-x.

Integrated Analysis of Metabolome and Transcriptome Data for Uncovering Flavonoid Components of Zanthoxylum bungeanum Maxim. Leaves Under Drought Stress

Zanthoxylum bungeanum Maxim. leaves (ZBLs) are rich in flavonoids and have become popular in nutrition, foods and medicine. However, the flavonoid components in ZBLs and the mechanism of flavonoid biosynthesis under drought stress have received little attention. Here, we performed an integrative analysis of the metabolome and transcriptome of ZBLs from HJ (Z. bungeanum cv. “Hanjiao”) and FJ (Z. bungeanum cv. “Fengjiao”) at four drought stages. A total of 231 individual flavonoids divided into nine classes were identified and flavones and flavonols were considered the most abundant flavonoid components in ZBLs. The total flavonoid content of ZBLs was higher in FJ; it increased in FJ under drought stress but decreased in HJ. Nine-quadrant analysis identified five and eight differentially abundant flavonoids in FJ and HJ leaves, respectively, under drought stress. Weighted gene correlation network analysis (WGCNA) identified nine structural genes and eight transcription factor genes involved in the regulation of flavonoid biosynthesis. Moreover, qRT-PCR results verified the accuracy of the transcriptome data and the reliability of the candidate genes. Taken together, our results reveal the flavonoid components of ZBLs and document changes in flavonoid metabolism under drought stress, providing valuable information for nutrition value and food utilization of ZBLs.

Metabolic Profiling and Transcriptome Analysis Reveal the Key Role of Flavonoids in Internode Coloration of Phyllostachys violascens cv. Viridisulcata

Bamboo, being an ornamental plant, has myriad aesthetic and economic significance. Particularly, Phyllostachys violascens cv. Viridisulcata contains an internode color phenotype in variation in green and yellow color between the sulcus and culm, respectively. This color variation is unique, but the underlying regulatory mechanism is still unknown. In this study, we used metabolomic and transcriptomic strategies to reveal the underlying mechanism of variation in internode color. A total of 81 metabolites were identified, and among those, prunin as a flavanone and rhoifolin as a flavone were discovered at a high level in the culm. We also found 424 differentially expressed genes and investigated three genes (PvGL, PvUF7GT, and PvC12RT1) that might be involved in prunin or rhoifolin biosynthesis. Their validation by qRT-PCR confirmed high transcript levels in the culm. The results revealed that PvGL, PvUF7GT, and PvC12RT1 might promote the accumulation of prunin and rhoifolin which were responsible for the variation in internode color of P. violascens. Our study also provides a glimpse into phenotypic coloration and is also a valuable resource for future studies.

Biochemical composition of the pericarp cell wall of popcorn inbred lines with different popping expansion

The popping expansion is a characteristic that is positively related with the quality of popcorn. A positive correlation between the volume of expansion and the thickness of the pericarp, and between the proportion of the opaque/shiny endosperm and the grain weight and volume, were postulated. However, there are no reports in the literature that address the importance of cell wall components in the popping expansion. Here, we investigate the biochemical composition of the pericarp cell walls of three inbred lines of popcorn with different popping expansion. Inbred lines GP12 (expansion volume >40 mL g⁻¹), P11 (expansion volume 30 mL g⁻¹) and P16 (expansion volume 14 mL g⁻¹) were used for the analysis and quantification of monosaccharides by HPAEC-PAD, and ferulic and p-coumaric acids and lignin by HPLC. Our hypothesis is that the biochemical composition of the pericarp cell walls may be related to greater or lesser popping expansion. Our data suggest that the lignin content and composition contribute to popping expansion. The highest concentration of lignin (129.74 μg mg⁻¹; 12.97%) was detected in the pericarp cell wall of the GP12 inbred line with extremely high popping expansion, and the lowest concentration (113.52 μg mg⁻¹; 11.35%) was observed in the P16 inbred line with low popping expansion. These findings may contribute to indicating the quantitative trait locus for breeding programs and to developing other methods to improve the popping expansion of popcorn.

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Biochemical composition of the pericarp cell wall was related to popcorn expansion.

•Three lineages of popcorn with different expansion capacities were analyzed.

•Monosaccharides, ferulic and p-coumaric acids and lignin were quantified.

•Xylose was detected in the highest concentration in the three lineages of popcorn.

•The lignin content and composition contributed to popcorn grain expansion capacity.

Plant Flavonoids in Mediterranean Species: A Focus on Flavonols as Protective Metabolites under Climate Stress

Flavonoids are specialized metabolites largely widespread in plants where they play numerous roles including defense and signaling under stress conditions. These compounds encompass several chemical subgroups such as flavonols which are one the most represented classes. The most studied flavonols are kaempferol, quercetin and myricetin to which research attributes antioxidative properties and a potential role in UV-defense through UV-screening mechanisms making them critical for plant adaptation to climate change. Despite the great interest in flavonol functions in the last decades, some functional aspects remain under debate. This review summarizes the importance of flavonoids in plant defense against climate stressors and as signal molecules with a focus on flavonols in Mediterranean plant species. The review emphasizes the relationship between flavonol location (at the organ, tissue and cellular scales) and their function as defense metabolites against climate-related stresses. It also provides evidence that biosynthesis of flavonols, or flavonoids as a whole, could be a crucial process allowing plants to adapt to climate change, especially in the Mediterranean area which is considered as one of the most sensitive regions to climate change over the globe.

The Rhizobium-Legume Symbiosis: Co-opting Successful Stress Management

The interaction of bacteria with plants can result in either a positive, negative, or neutral association. The rhizobium-legume interaction is a well-studied model system of a process that is considered a positive interaction. This process has evolved to require a complex signal exchange between the host and the symbiont. During this process, rhizobia are subject to several stresses, including low pH, oxidative stress, osmotic stress, as well as growth inhibiting plant peptides. A great deal of work has been carried out to characterize the bacterial response to these stresses. Many of the responses to stress are also observed to have key roles in symbiotic signaling. We propose that stress tolerance responses have been co-opted by the plant and bacterial partners to play a role in the complex signal exchange that occurs between rhizobia and legumes to establish functional symbiosis. This review will cover how rhizobia tolerate stresses, and how aspects of these tolerance mechanisms play a role in signal exchange between rhizobia and legumes.

Global Transcriptome Analysis Revealed the Molecular Regulation Mechanism of Pigment and Reactive Oxygen Species Metabolism During the Stigma Development of Carya cathayensis

Hickory (Carya cathayensis Sarg.) is a monoecious plant of the genus Carya of the Juglandaceae family. Its nuts contain a number of nutritional compounds and are deeply loved by consumers. Interestingly, it was observed that the color of hickory stigma changed obviously from blooming to mature. However, the molecular mechanism underlying color formation during stigma development and the biological significance of this phenomenon was mostly unknown. In this work, pigment content, reactive oxygen species (ROS) removal capacity, and transcriptome analysis of developing stigma of hickory at 4 differential sampling time points (S1, S2, S3, and S4) were performed to reveal the dynamic changes of related pigment, antioxidant capacity, and its internal molecular regulatory mechanism. It was found that total chlorophyll content was decreased slightly from S1 to S4, while total carotenoids content was increased from S1 to S3 but decreased gradually from S3 to S4. Total anthocyanin content continued to increase during the four periods of stigma development, reaching the highest level at the S4. Similarly, the antioxidant capacity of stigma was also gradually improved from S1 to S4. Furthermore, transcriptome analysis of developing hickory stigma identified 31,027 genes. Time-series analysis of gene expressions showed that these genes were divided into 12 clusters. Cluster 5 was enriched with some genes responsible for porphyrin and chlorophyll metabolism, carotenoid metabolism, and photosynthesis. Meanwhile, cluster 10 was enriched with genes related to flavonoid metabolism, including anthocyanin involved in ROS scavenging, and its related genes were mainly distributed in cluster 12. Based on the selected threshold values, a total of 10432 differentially expressed genes were screened out and enriched in the chlorophyll, carotenoid, anthocyanin, and ROS metabolism. The expression trends of these genes provided plausible explanations for the dynamic change of color and ROS level of hickory stigma with development. qRT-PCR analyses were basically consistent with the results of RNA-seq. The gene co-regulatory networks of pigment and ROS metabolism were further constructed and MYB113 (CCA0887S0030) and WRKY75 (CCA0573S0068) were predicted to be two core transcriptional regulators. These results provided in-depth evidence for revealing the molecular mechanism of color formation in hickory stigma and its biological significance.

Melatonin-induced physiology and transcriptome changes in banana seedlings under salt stress conditions

Soil salinization poses a serious threat to the ecological environment and agricultural production and is one of the most common abiotic stresses in global agricultural production. As a salt-sensitive plant, the growth, development, and production of bananas (Musa acuminata L.) are restricted by salt stress. Melatonin is known to improve the resistance of plants to stress. The study analyzed the effects of 100 μM melatonin on physiological and transcriptome changes in banana varieties (AAA group cv. Cavendish) under 60 mmol/l of NaCl salt stress situation. The phenotypic results showed that the application of exogenous melatonin could maintain banana plants' health growth and alleviate the damage caused by salt stress. The physiological data show that the application of exogenous melatonin can enhance salt tolerance of banana seedlings by increasing the content of proline content and soluble protein, slowing down the degradation of chlorophyll, reducing membrane permeability and recovery of relative water content, increasing the accumulation of MDA, and enhancing antioxidant defense activity. Transcriptome sequencing showed that melatonin-induced salt tolerance of banana seedlings involved biological processes, molecular functions, and cellular components. We also found that differentially expressed genes (DEGs) are involved in a variety of metabolic pathways, including amino sugar and nucleotide sugar metabolism, phenylalanine metabolism, cyanoamino acid metabolism, starch and sucrose metabolism, and linoleic acid metabolism. These major metabolism and biosynthesis may be involved in the potential mechanism of melatonin under salt stress. Furthermore, some members of the transcription factor family, such as MYB, NAC, bHLH, and WRKY, might contribute to melatonin alleviating salt stress tolerance of the banana plant. The result laid a basis for further clarifying the salt stress resistance mechanism of bananas mediated by exogenous melatonin and provides theoretical bases to utilize melatonin to improve banana salt tolerance in the future.

Comparative Transcriptome Analysis Identifies Key Regulatory Genes Involved in Anthocyanin Metabolism During Flower Development in Lycoris radiata

Lycoris is used as a garden flower due to the colorful and its special flowers. Floral coloration of Lycoris is a vital trait that is mainly regulated via the anthocyanin biosynthetic pathway. In this study, we performed a comparative transcriptome analysis of Lycoris radiata petals at four different flower development stages. A total of 38,798 differentially expressed genes (DEGs) were identified by RNA sequencing, and the correlation between the expression level of the DEGs and the anthocyanin content was explored. The identified DEGs are significantly categorized into 'flavonoid biosynthesis,' 'phenylpropanoid biosynthesis,' 'Tropane, piperidine and pyridine alkaloid biosynthesis,' 'terpenoid backbone biosynthesis' and 'plant hormone signal transduction' by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The candidate genes involved in anthocyanin accumulation in L. radiata petals during flower development stages were also identified, which included 56 structural genes (especially LrDFR1 and LrFLS) as well as 27 key transcription factor DEGs (such as C3H, GATA, MYB, and NAC). In addition, a key structural gene namely LrDFR1 of anthocyanin biosynthesis pathway was identified as a hub gene in anthocyanin metabolism network. During flower development stages, the expression level of LrDFR1 was positively correlated with the anthocyanin content. Subcellular localization revealed that LrDFR1 is majorly localized in the nucleus, cytoplasm and cell membrane. Overexpression of LrDFR1 increased the anthocyanin accumulation in tobacco leaves and Lycoris petals, suggesting that LrDFR1 acts as a positively regulator of anthocyanin biosynthesis. Our results provide new insights for elucidating the function of anthocyanins in L. radiata petal coloring during flower development.

Early detection of Huanglongbing with EESI-MS indicates a role of phenylpropanoid pathway in citrus

Huanglongbing (HLB), a devastating disease for citrus worldwide, is caused by Candidatus Liberibacter asiaticus (CLas). In this study, we employed a novel extractive electrospray ionization-mass spectrometry (EESI-MS) method to analyze the metabolites in leaves of uninfected and HLB-infected Newhall navel orange. The results showed that uninfected and HLB-infected leaves could be readily distinguished based on EESI-MS combined by multivariable analysis. Nine phenolic compounds involved in phenylpropanoid pathway, such as p-coumaric acid, naringin, and apigenin, were principal components to distinguish the leaves of uninfected and HLB-infected Newhall navel orange. Gene expression was also conducted to further explore the molecular mechanism of phenylpropanoid branch pathway in HLB. The expression of genes (4CL, HCT, CHI, CHS, CYP, and C12R) involved in phenylpropanoid branch pathway was increased in asymptomatic and early period of HLB-infected leaves, while decreased in later period of HLB-infected leaves. This study provides a novel method for early detection of citrus HLB and suggests the regulation mechanism of phenylpropanoid pathway in the interaction between citrus and CLas.

Cold Plasma Processing on Fruits and Fruit Juices: A Review on the Effects of Plasma on Nutritional Quality

This review aims to present the effects of cold plasma technology on the nutritional quality of fruits and fruit juices. This review focuses on the chemical changes induced by plasma on several bioactive compounds, such as sugars, starch, lipids, vitamins, phenolic compounds, carotenoids, and anthocyanins. The main plasma-reacting species that reacts with fruit compounds are presented and discussed. The review presents the mechanisms that lead to the improvement and degradation of the main compounds, showing both the advantages and disadvantages of cold plasma technology.