Drought Resistance in Qingke Involves a Reprogramming of the Phenylpropanoid Pathway and UDP-Glucosyltransferase Regulation of Abiotic Stress Tolerance Targeting Flavonoid Biosynthesis

The introgression of BjMYB113 from Brassica juncea leads to purple leaf trait in Brassica napus

The purple leaves of Brassica napus are abundant in anthocyanins, which are renowned for their role in conferring distinct colors, stress tolerance, and health benefits, however the genetic basis of this trait in B. napus remains largely unelucidated. Herein, the purple leaf B. napus (PL) exhibited purple pigments in the upper epidermis and a substantial increase in anthocyanin accumulation, particularly of cyanidin, compared to green leaf B. napus (GL). The genetic control of the purple leaf trait was attributed to a semi-dominant gene, pl, which was mapped to the end of chromosome A03. However, sequencing of the fragments amplified by the markers linked to pl indicated that they were all mapped to chromosome B05 from B. juncea. Within this B05 chromosomal segment, the BjMYB113 gene-specific marker showed perfect co-segregation with the purple leaf trait in the F2 population, suggesting that the BjMYB113 introgression from B. juncea was the candidate gene for the purple leaf trait in B. napus. To further verify the function of candidate gene, CRISPR/Cas9 was performed to knock out the BjMYB113 gene in PL. The three myb113 mutants exhibited evident green leaf phenotype, absence of purple pigments in the adaxial epidermis, and a significantly reduced accumulation of anthocyanin compared to PL. Additionally, the genes involved in positive regulatory (TT8), late anthocyanin biosynthesis (DFR, ANS, UFGT), as well as transport genes (TT19) were significantly suppressed in the myb113 mutants, further confirming that BjMYB113 was response for the anthocyanin accumulation in purple leaf B. napus. This study contributes to an advanced understanding of the regulation mechanism of anthocyanin accumulation in B. napus.

UGT gene family identification and functional analysis of HvUGT1 under drought stress in wild barley

Drought stress poses a significant threat to global agriculture, highlighting the urgent need to elucidate the molecular mechanisms underlying plant drought tolerance. The UDP-glycosyltransferase (UGT) gene family plays crucial roles in diverse biological processes in plants. In this study, we conducted a comprehensive analysis of the UGT gene family in wild barley EC_S1, focusing on gene characteristics, subcellular localization, phylogenetic relationships, and protein structure. A total of 175 UGT gene family members were identified, exhibiting diverse patterns in protein length, molecular weight, isoelectric point, hydrophilicity, and subcellular localization. Most genes are located at chromosome ends. Phylogenetic analysis grouped the UGT genes into seven clusters, with barley-specific group E. Expression analysis across barley tissues showed upregulation in roots and senescent leaves, implying diverse roles. Under drought stress, expression patterns varied, with drought-tolerant varieties showing fewer changes than sensitive ones. Clustering analysis revealed distinct expression patterns, suggesting regulatory functions in barley's drought response. As a case, the HvUGT1 was cloned. Overexpression of HvUGT1 in Arabidopsis enhanced drought tolerance, with increased water retention, reduced cell damage, and elevated flavonoid levels. Conversely, HvUGT1 silencing in wild barley decreased drought tolerance, accompanied by reduced antioxidant enzyme activity and flavonoid content. These results highlight HvUGT1's importance in enhancing plant drought tolerance, possibly through flavonoid-mediated ROS clearance. The research provides gene resources and valuable insights for the development of drought-resistant crops through targeted genetic manipulation strategies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01487-w.

Biosynthesized Selenium Nanoparticles as an Effective Tool to Combat Soil Metal Stresses in Rice (Oryza sativa L.)

Nanotechnology has demonstrated significant potential to improve agricultural production and increase crop tolerance to abiotic stress including exposure to heavy metals. The present study investigated the mechanisms by which aloe vera extract gel-biosynthesized (AVGE) selenium nanoparticles (Se NPs) alleviated cadmium (Cd)-induced toxicity to rice (Oryza sativa L.). AVGE Se NPs, chemically synthesized bare Se NPs, and NaSeO3 as an ionic control were applied to Cd-stressed rice seedlings via root exposure in both hydroponic and soil systems. Upon exposure to AVGE Se NPs at 15 mg Se/L, the fresh root biomass was significantly increased by 100.7% and 19.5% as compared to Cd control and conventional bare Se NPs. Transcriptional analyses highlighted that AVGE Se NPs activated stress signaling and defense related pathways, including glutathione metabolism, phenylpropanoid biosynthesis and plant hormone signal transduction. Specifically, exposure to AVGE Se NPs upregulated the expression of genes associated with the gibberellic acid (GA) biosynthesis by and 4.79- and 3.29-fold as compared to the Cd-alone treatment and the untreated control, respectively. Importantly, AVGE Se NPs restored the composition of the endophyte community and recruit of beneficial species under Cd exposure; the relative abundance of Azospirillum was significantly increased in roots, shoots, and the rhizosphere soil by 0.73-, 4.58- and 0.37-fold, respectively, relative to the Cd-alone treatment. Collectively, these findings highlight the significant potential of AVGE Se NPs to enhance plant growth and to minimize the Cd-induced toxicity in rice and provide a promising nanoenabled strategy to enhance food safety upon crop cultivation in contaminated agricultural soils.

Effects and mechanisms of proanthocyanidins-derived carbon dots on alleviating salt stress in rice by muti-omics analysis

Carbon dots (CDs) with different structures were prepared by electrolysis (PE-CDs) and hydrothermal (PH-CDs) methods using proanthocyanidins as precursors. The smaller size and lower zeta potential enabled the PE-CDs treated rice seedlings to exhibit greater resistance to salt stress. The fresh weight of rice seedlings under salt stress was significantly increased by spraying CDs every other day for two weeks. PE-CDs treated group exhibited a faster electron transport rate, and the SOD activity and flavonoid content were 2.5-fold and 0.23-fold higher than those of the salt stress-treated group. Furthermore, the metabolomics and transcriptomics analysis revealed that the PsaC gene of photosystem I was significantly up-regulated under PE-CDs treatment, which accelerated electron transfer in photosystem I. The up-regulation of BX1 and IGL genes encoding indole synthesis allowed rice to enhance stress tolerance through tryptophan and benzoxazine biosynthesis pathways. These findings offer help in purposefully synthesizing CDs and boosting food production.

Integrated analysis of transcriptomics and metabolomics of garden asparagus (Asparagus officinalis L.) under drought stress

BACKGROUND

Drought is a leading environmental factor affecting plant growth. To explore the drought tolerance mechanism of asparagus, this study analyzed the responses of two asparagus varieties, namely, 'Jilv3' (drought tolerant) and 'Pacific Early' (drought sensitive), to drought stress using metabolomics and transcriptomics.

RESULTS

In total, 2,567 and 7,187 differentially expressed genes (DEGs) were identified in 'Pacific Early' and 'Jilv3', respectively, by comparing the transcriptome expression patterns between the normal watering treatment and the drought stress treatment. These DEGs were significantly enriched in the amino acid biosynthesis, carbon metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways. In 'Jilv3', DEGs were also enriched in the following energy metabolism-related pathways: citrate cycle (TCA cycle), glycolysis/gluconeogenesis, and pyruvate metabolism. This study also identified 112 and 254 differentially accumulated metabolites (DAMs) in 'Pacific Early' and 'Jilv3' under drought stress compared with normal watering, respectively. The amino acid, flavonoid, organic acid, and soluble sugar contents were more significantly enhanced in 'Jilv3' than in 'Pacific Early'. According to the metabolome and transcriptome analysis, in 'Jilv3', the energy supply of the TCA cycle was improved, and flavonoid biosynthesis increased. As a result, its adaptability to drought stress improved.

CONCLUSIONS

These findings help to better reveal the molecular mechanism underlying how asparagus responds to drought stress and improve researchers' ability to screen drought-tolerant asparagus varieties as well as breed new varieties.

Exploration the interaction of cadmium and copper toxic effects in pakchoi (Brassica chinensis L) roots through combinatorial transcriptomic and weighted gene co-expression network analysis

The interaction between cadmium(Cd) and copper(Cu) during combined pollution can lead to more complex toxic effects on humans and plants.However, there is still a lack of sufficient understanding regarding the types of interactions at the plant molecular level and the response strategies of plants to combined pollution. To assess this, we investigated the phenotypic and transcriptomic patterns of pakchoi (Brassica chinensis L) roots in response to individual and combined pollution of Cd and Cu. The results showed that compared to single addition, the translocation factor of heavy metals in roots significantly decreased (p < 0.05) under the combined addition, resulting in higher accumulation of Cd and Cu in the roots. Transcriptomic analysis of pakchoi roots revealed that compared to single pollution, there were 312 and 1926 differentially expressed genes (DEGs) specifically regulated in the Cd2Cu20 and Cd2Cu100 combined treatments, respectively. By comparing the expression of these DEGs among different treatments, we found that the combined pollution of Cd and Cu mainly affected the transcriptome of the roots in an antagonistic manner. Enrichment analysis indicated that pakchoi roots upregulated the expression of genes involved in glucosetransferase activity, phospholipid homeostasis, proton transport, and the biosynthesis of phenylpropanoids and flavonoids to resist Cd and Cu combined pollution. Using weighted gene co-expression network analysis (WGCNA), we identified hub genes related to the accumulation of Cd and Cu in the roots, which mainly belonged to the LBD, thaumatin-like protein, ERF, MYB, WRKY, and TCP transcription factor families. This may reflect a transcription factor-driven trade-off strategy between heavy metal accumulation and growth in pakchoi roots. Additionally, compared to single metal pollution, the expression of genes related to Nramp, cation/H+ antiporters, and some belonging to the ABC transporter family in the pakchoi roots was significantly upregulated under combined pollution. This could lead to increased accumulation of Cd and Cu in the roots. These findings provide new insights into the interactions and toxic mechanisms of multiple metal combined pollution at the molecular level in plants.

Anatomical and Metabolome Features of Haloxylon aphyllum and Haloxylon persicum Elucidate the Resilience against Gall-Forming Insects

Globally, gall-forming insects significantly contribute to the degradation of desert ecosystems. Recent studies have demonstrated that Haloxylon persicum suffers less damage from gall-formers compared to Haloxylon aphyllum. However, the mechanisms driving the long-term metabolic responses of these species to gall-forming biotic stress in their natural environment remain unclear. The current study comparatively analyzes the anatomical features and metabolomic changes in H. aphyllum and H. persicum damaged by gall-forming insects. This research aimed to uncover potential metabolic tolerance mechanisms through GC-MS analysis. The study findings indicate that gall-forming insects cause a reduction in nearly all the anatomical structures of Haloxylon shoots, with the effects being less severe in H. persicum than in H. aphyllum. Thus, the metabolic pathways responsible for the biosynthesis of biologically active substances that enhance resistance to gall inducers were different, specifically in H. aphyllum-the biosynthesis of fatty acids (+their derivatives) and γ-tocopherol (vitamin E) and H. persicum-the biosynthesis of fatty acids (+their derivatives), dialkyl ethers, carbohydrates (+their derivatives), aromatic acid derivatives, phytosterols, γ-tocopherol (vitamin E), phenols, and terpenoids. The results suggest that the modulation of metabolic pathways under biotic stress plays a crucial role in the enhanced survival and growth of H. persicum.

Analysis Transcriptome and Phytohormone Changes Associated with the Allelopathic Effects of Ginseng Hairy Roots Induced by Different-Polarity Ginsenoside Components

The allelopathic autotoxicity of ginsenosides is an important cause of continuous cropping obstacles in ginseng planting. There is no report on the potential molecular mechanism of the correlation between polarity of ginsenoside components and their allelopathic autotoxicity. This study applied a combination of metabolomics and transcriptomics analysis techniques, combined with apparent morphology, physiological indexes, and cell vitality detection of the ginseng hairy roots, through which the molecular mechanism of correlation between polarity and allelopathic autotoxicity of ginsenosides were comprehensively studied. The hairy roots of ginseng presented more severe cell apoptosis under the stress of low-polarity ginsenoside components (ZG70). ZG70 exerted allelopathic autotoxicity by regulating the key enzyme genes of cis-zeatin (cZ) synthesis pathway, indole-3-acetic acid (IAA) synthesis pathway, and jasmonates (JAs) signaling transduction pathway. The common pathway for high-polarity ginsenoside components (ZG50) and ZG70 to induce the development of allelopathic autotoxicity was through the expression of key enzymes in the gibberellin (GA) signal transduction pathway, thereby inhibiting the growth of ginseng hairy roots. cZ, indole-3-acetamid (IAM), gibberellin A1 (GA1), and jasmonoyl-L-isoleucine (JA-ILE) were the key response factors in this process. It could be concluded that the polarity of ginsenoside components were negatively correlated with their allelopathic autotoxicity.

Integrated Full-Length Transcriptomics and Metabolomics Reveal Glycosyltransferase Involved in the Biosynthesis of Flavonol Glycosides in Laportea bulbifera

Many species of the Urticaceae family are important cultivated fiber plants that are known for their economic and industrial values. However, their secondary metabolite profiles and associated biosynthetic mechanisms have not been well-studied. Using Laportea bulbifera as a model, we conducted widely targeted metabolomics, which revealed 523 secondary metabolites, including a unique accumulation of flavonol glycosides in bulblet. Through full-length transcriptomic and RNA-seq analyses, the related genes in the flavonoid biosynthesis pathway were identified. Finally, weighted gene correlation network analysis and functional characterization revealed four LbUGTs, including LbUGT78AE1, LbUGT72CT1, LbUGT71BX1, and LbUGT71BX2, can catalyze the glycosylation of flavonol aglycones (kaempferol, myricetin, gossypetin, and quercetagetin) using UDP-Gal and UDP-Glu as the sugar donors. LbUGT78AE1 and LbUGT72CT1 showed substrate promiscuity, whereas LbUGT71BX1 and LbUGT71BX2 exhibited different substrate and sugar donor selectivity. These results provide a genetic resource for studying Laportea in the Urticaceae family, as well as key enzymes responsible for the metabolism of valuable flavonoid glycosides.

Leveraging Unidentified Metabolic Features for Key Pathway Discovery: Chemical Classification-driven Network Analysis in Untargeted Metabolomics

Untargeted metabolomics using liquid chromatography-electrospray ionization-high-resolution tandem mass spectrometry (UPLC-ESI-MS/MS) provides comprehensive insights into the dynamic changes of metabolites in biological systems. However, numerous unidentified metabolic features limit its utilization. In this study, a novel approach, the Chemical Classification-driven Molecular Network (CCMN), was proposed to unveil key metabolic pathways by leveraging hidden information within unidentified metabolic features. The method was demonstrated by using the herbivore-induced metabolic response in corn silk as a case study. Untargeted metabolomics analysis using UPLC-MS/MS was performed on wild corn silk and two genetically modified lines (pre- and postinsect treatment). Global annotation initially identified 256 (ESI-) and 327 (ESI+) metabolites. MS/MS-based classifications predicted 1939 (ESI-) and 1985 (ESI+) metabolic features into the chemical classes. CCMNs were then constructed using metabolic features shared classes, which facilitated the structure- or class annotation for completely unknown metabolic features. Next, 844/713 significantly decreased and 1593/1378 increased metabolites in ESI-/ESI+ modes were defined in response to insect herbivory, respectively. Method validation on a spiked maize sample demonstrated an overall class prediction accuracy rate of 95.7%. Potential key pathways were prescreened by a hypergeometric test using both structure- and class-annotated differential metabolites. Subsequently, CCMN was used to deeply amend and uncover the pathway metabolites deeply. Finally, 8 key pathways were defined, including phenylpropanoid (C6-C3), flavonoid, octadecanoid, diterpenoid, lignan, steroid, amino acid/small peptide, and monoterpenoid. This study highlights the effectiveness of leveraging unidentified metabolic features. CCMN-based key pathway analysis reduced the bias in conventional pathway enrichment analysis. It provides valuable insights into complex biological processes.

Transcriptome and Metabolome Analyses Reflect the Molecular Mechanism of Drought Tolerance in Sweet Potato

Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most widely cultivated crops in the world, with outstanding stress tolerance, but drought stress can lead to a significant decrease in its yield. To reveal the response mechanism of sweet potato to drought stress, an integrated physiological, transcriptome and metabolome investigations were conducted in the leaves of two sweet potato varieties, drought-tolerant zhenghong23 (Z23) and a more sensitive variety, jinong432 (J432). The results for the physiological indexes of drought showed that the peroxidase (POD) and superoxide dismutase (SOD) activities of Z23 were 3.68 and 1.21 times higher than those of J432 under severe drought, while Z23 had a higher antioxidant capacity. Transcriptome and metabolome analysis showed the importance of the amino acid metabolism, respiratory metabolism, and antioxidant systems in drought tolerance. In Z23, amino acids such as asparagine participated in energy production during drought by providing substrates for the citrate cycle (TCA cycle) and glycolysis (EMP). A stronger respiratory metabolism ability could better maintain the energy supply level under drought stress. Drought stress also activated the expression of the genes encoding to antioxidant enzymes and the biosynthesis of flavonoids such as rutin, resulting in improved tolerance to drought. This study provides new insights into the molecular mechanisms of drought tolerance in sweet potato.

Integrated Transcriptomics and Metabolomics Analyses Provide Insights into Qingke in Response to Cold Stress

The survival and productivity of qingke in high altitude (>4300 m, average yearly temperature <0 °C) of the Tibetan Plateau are significantly impacted by low-temperature stress. Uncovering the mechanisms underlying low-temperature stress response in cold-tolerant qingke varieties is crucial for qingke breeding. Herein, we conducted a comprehensive transcriptomic and metabolomic analysis on cold-sensitive (ZQ) and cold-tolerant (XL) qingke varieties under chilling and freezing treatments and identified lipid metabolism pathways as enriched in response to freezing treatment. Additionally, a significant positive correlation was observed between the expression of C-repeat (CRT) binding factor 10A (HvCBF10A) and Gly-Asp-Ser-Leu-motif lipase (HvGDSL) and the accumulation of multiple lipids. Functional analysis confirmed that HvCBF10A directly binds to HvGDSL, and silencing HvCBF10A resulted in a significant decrease in both HvGDSL and lipid levels, consequently impairing the cold tolerance. Overall, HvCBF10A and HvGDSL are functional units in actively regulating lipid metabolism to enhance freezing stress tolerance in qingke.

Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana Using Short Gradient Multi-CV FAIMSpro BoxCar DIA

A major limitation when undertaking quantitative proteomic time-course experimentation is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity and high dynamic range sample types, such as plant extracts, balance between resolution and time is especially apparent. To address this, we evaluate multiple compensation voltage (CV) high field asymmetric waveform ion mobility spectrometry (FAIMSpro) settings using the latest label-free single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply quantify the Arabidopsis thaliana seedling proteome. Using a BoxCarDIA acquisition workflow with a -30 -50 -70 CV FAIMSpro setting, we were able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-min gradient, facilitating the analysis of ∼42 samples per day. Utilizing this acquisition approach, we then quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress, to identify early and late stress response proteins and reveal stress response overlaps. Here, we successfully quantify >6400 shoot and >8500 root protein groups, respectively, quantifying nearly ∼9700 unique protein groups in total across the study. Collectively, we pioneer a short gradient, multi-CV FAIMSpro BoxCarDIA acquisition workflow that represents an exciting new analysis approach for undertaking quantitative proteomic time-course experimentation in plants.

Research progress and applications of colorful Brassica crops

MAIN CONCLUSION

We review the application and the molecular regulation of anthocyanins in colorful Brassica crops, the creation of new germplasm resources, and the development and utilization of colorful Brassica crops. Brassica crops are widely cultivated: these include oilseed crops, such as rapeseed, mustards, and root, leaf, and stem vegetable types, such as turnips, cabbages, broccoli, and cauliflowers. Colorful variants exist of these crop species, and asides from increased aesthetic appeal, these may also offer advantages in terms of nutritional content and improved stress resistances. This review provides a comprehensive overview of pigmentation in Brassica as a reference for the selection and breeding of new colorful Brassica varieties for multiple end uses. We summarize the function and molecular regulation of anthocyanins in Brassica crops, the creation of new colorful germplasm resources via different breeding methods, and the development and multifunctional utilization of colorful Brassica crop types.

Metabolomic Analysis of the Response of Haloxylon ammodendron and Haloxylon persicum to Drought

Haloxylon ammodendron and Haloxylon persicum, as typical desert plants in arid areas, show strong drought tolerance and environmental adaptability and are therefore ideal model plants for studying the molecular mechanisms of drought tolerance. A metabolomic analysis of H. ammodendron and H. persicum in their natural environment is lacking, and their metabolic response to drought therefore remains unclear. To elucidate the response of H. ammodendron and H. persicum to drought at the metabolic level, a non-targeted metabolomics analysis was carried out herein. Under a dry environment, H. ammodendron exhibited 296 and 252 differentially expressed metabolites (DEMs) in the positive and negative ion modes, respectively, whereas 452 and 354 DEMs were identified in the positive and negative ion modes in H. persicum, respectively. The results indicated that H. ammodendron responds to drought by increasing the content of organic nitrogen compounds and lignans, neolignans, and related compounds, and reducing the content of alkaloids and derivatives. By contrast, H. persicum adapts to the dry environment by increasing the content of organic acids and their derivatives and reducing the content of lignans, neolignans, and related compounds. In addition, H. ammodendron and H. persicum improved their osmoregulation ability, reactive oxygen species detoxification ability, and cell membrane stability by regulating the key metabolic pathways and anabolism of associated metabolites. This is the first metabolomics report on the response of H. ammodendron and H. persicum to drought in their natural environment, providing a foundation for the further study of their regulatory mechanisms under drought stress.

Advances in the study of the function and mechanism of the action of flavonoids in plants under environmental stresses

MAIN CONCLUSION

This review summarizes the anti-stress effects of flavonoids in plants and highlights its role in the regulation of polar auxin transport and free radical scavenging mechanism. As secondary metabolites widely present in plants, flavonoids play a vital function in plant growth, but also in resistance to stresses. This review introduces the classification, structure and synthetic pathways of flavonoids. The effects of flavonoids in plant stress resistance were enumerated, and the mechanism of flavonoids in plant stress resistance was discussed in detail. It is clarified that plants under stress accumulate flavonoids by regulating the expression of flavonoid synthase genes. It was also determined that the synthesized flavonoids are transported in plants through three pathways: membrane transport proteins, vesicles, and bound to glutathione S-transferase (GST). At the same time, the paper explores that flavonoids regulate polar auxin transport (PAT) by acting on the auxin export carrier PIN-FORMED (PIN) in the form of ATP-binding cassette subfamily B/P-glycoprotein (ABCB/PGP) transporter, which can help plants to respond in a more dominant form to stress. We have demonstrated that the number and location of hydroxyl groups in the structure of flavonoids can determine their free radical scavenging ability and also elucidated the mechanism by which flavonoids exert free radical removal in cells. We also identified flavonoids as signaling molecules to promote rhizobial nodulation and colonization of arbuscular mycorrhizal fungi (AMF) to enhance plant-microbial symbiosis in defense to stresses. Given all this knowledge, we can foresee that the in-depth study of flavonoids will be an essential way to reveal plant tolerance and enhance plant stress resistance.

Multi-Omics Analysis Provides Crucial Insights into the Drought Adaptation of Glycyrrhiza uralensis Fisch

Drought adaptation of plants is closely related to resistance and tolerance to drought stress as well as the ability to recover after the elimination of the stress. Glycyrrhiza uralensis Fisch is a commonly applied herb whose growth and development are greatly affected by drought. Here, we provide the first comprehensive analysis of the transcriptomic, epigenetic, and metabolic responses of G. uralensis to drought stress and rewatering. The hyper-/hypomethylation of genes may lead to up-/downregulated gene expression, and epigenetic changes can be regarded as an important regulatory mechanism of G. uralensis under drought stress and rewatering. Moreover, integrated transcriptome and metabolome analysis revealed that genes and metabolites involved in pathways of antioxidation, osmoregulation, phenylpropanoid biosynthesis, and flavonoid biosynthesis may regulate the drought adaptation of G. uralensis. This work provides crucial insights into the drought adaptation of G. uralensis and offers epigenetic resources for cultivating G. uralensis with high drought adaptation.

A novel TF molecular switch-mechanism found in two contrasting ecotypes of a psammophyte, Agriophyllum squarrosum, in regulating transcriptional drought memory

BACKGROUND

Prior drought stress may change plants response patterns and subsequently increase their tolerance to the same condition, which can be referred to as "drought memory" and proved essential for plants well-being. However, the mechanism of transcriptional drought memory in psammophytes remains unclear. Agriophyllum squarrosum, a pioneer species on mobile dunes, is widely spread in Northern China's vast desert areas with outstanding ability of water use efficiency. Here we conducted dehydration-rehydration treatment on A. squarrosum semi-arid land ecotype AEX and arid land ecotype WW to dissect the drought memory mechanism of A. squarrosum, and to determine the discrepancy in drought memory of two contrasting ecotypes that had long adapted to water heterogeneity.

RESULT

Physiological traits monitoring unveiled the stronger ability and longer duration in drought memory of WW than that of AEX. A total of 1,642 and 1,339 drought memory genes (DMGs) were identified in ecotype AEX and WW, respectively. Furthermore, shared DMGs among A. squarrosum and the previously studied species depicted that drought memory commonalities in higher plants embraced pathways like primary and secondary metabolisms; while drought memory characteristics in A. squarrosum were mainly related to response to heat, high light intensity, hydrogen peroxide, and dehydration, which might be due to local adaptation to desert circumstances. Heat shock proteins (HSPs) occupied the center of the protein-protein interaction (PPI) network in drought memory transcription factors (TF), thus playing a key regulatory role in A. squarrosum drought memory. Co-expression analysis of drought memory TFs and DMGs uncovered a novel regulating module, whereby pairs of TFs might function as molecular switches in regulating DMG transforming between high and low expression levels, thus promoting drought memory reset.

CONCLUSION

Based on the co-expression analysis, protein-protein interaction prediction, and drought memory metabolic network construction, a novel regulatory module of transcriptional drought memory in A. squarrosum was hypothesized here, whereby recurrent drought signal is activated by primary TF switches, then amplified by secondary amplifiers, and thus regulates downstream complicated metabolic networks. The present research provided valuable molecular resources on plants' stress-resistance basis and shed light on drought memory in A. squarrosum.

Integrated metabolomics and proteomics analysis to study the changes in Scutellaria baicalensis at different growth stages

Scutellaria baicalensis is a functional food that has the potential to treat various diseases. Scutellaria baicalensis can be divided into two types: Ziqin (strip types) and (rotten xylem). Ziqin is used to clear lower energizer large intestine heat syndrome, while Kuqin is used for the treatment of upper energizer lung heat syndrome. At present, the substance basis of the differences between Ziqin and Kuqin is not clear. The changes in metabolite accumulation and protein expression between them were analyzed by the non-targeted metabolomic technique in combination with the label-free proteomics approach. The results showed that the differentially accumulated metabolites and abundant proteins were mainly enriched in the pathways of phenylalanine, tyrosine and tryptophan biosynthesis, phenylpropanoid biosynthesis, flavonoid biosynthesis, flavone and flavonol biosynthesis, isoflavonoid biosynthesis, and anthocyanin biosynthesis. Collectively, these results reveal the changes of Scutellaria baicalensis in different growth years and provide a reference for selecting the appropriate harvest period.

Cajanus platycarpus Flavonoid 3'5' Hydroxylase_2 (CpF3'5'H_2) Confers Resistance to Helicoverpa armigera by Modulating Total Polyphenols and Flavonoids in Transgenic Tobacco

Pod borer Helicoverpa armigera, a polyphagus herbivorous pest, tremendously incurs crop damage in economically important crops. This necessitates the identification and utility of novel genes for the control of the herbivore. The present study deals with the characterization of a flavonoid 3'5' hydroxylase_2 (F3'5'H_2) from a pigeonpea wild relative Cajanus platycarpus, possessing a robust chemical resistance response to H. armigera. Though F3'5'H_2 displayed a dynamic expression pattern in both C. platycarpus (Cp) and the cultivated pigeonpea, Cajanus cajan (Cc) during continued herbivory, CpF3'5'H_2 showed a 4.6-fold increase vis a vis 3-fold in CcF3'5'H_2. Despite similar gene copy numbers in the two Cajanus spp., interesting genic and promoter sequence changes highlighted the stress responsiveness of CpF3'5'H_2. The relevance of CpF3'5'H_2 in H. armigera resistance was further validated in CpF3'5'H_2-overexpressed transgenic tobacco based on reduced leaf damage and increased larval mortality through an in vitro bioassay. As exciting maiden clues, CpF3'5'H_2 deterred herbivory in transgenic tobacco by increasing total flavonoids, polyphenols and reactive oxygen species (ROS) scavenging capacity. To the best of our knowledge, this is a maiden attempt ascertaining the role of F3'5'H_2 gene in the management of H. armigera. These interesting leads suggest the potential of this pivotal branch-point gene in biotic stress management programs.

Genetic architecture of inducible and constitutive metabolic profile related to drought resistance in qingke (Tibetan hulless barley)

Qingke (Tibetan hulless barley, Hordeum vulgare L. var. nudum) is the primary food crop on the Tibet Plateau, the long-term drought and other harsh environments makes qingke an important resource for the study of abiotic resistance. Here, we evaluated the drought sensitivity of 246 qingke varieties. Genome-wide association studies (GWAS) found that root-specific expressed gene CYP84 may be involved in the regulation of drought resistance. Based on widely targeted metabolic profiling, we identified 2,769 metabolites in qingke leaves, of which 302 were significantly changed in response to drought stress, including 4-aminobutyric acid (GABA), proline, sucrose and raffinose. Unexpectedly, these drought-induced metabolites changed more violently in drought-sensitive qingkes, while the constitutive metabolites that had little response to drought stress, such as C-glycosylflavonoids and some amino acids, accumulated excessively in drought-resistant qingkes. Combined with metabolite-based genome-wide association study (mGWAS), a total of 1,006 metabolites under optimal condition and 1,031 metabolites under mild drought stress had significant associated loci. As a marker metabolite induced by drought stress, raffinose was significantly associated with two conservatively adjacent α-galactosidase genes, qRT-PCR suggests that these two genes may jointly regulate the raffinose content in qingke. Besides, as constituent metabolites with stable differences between drought-sensitive and drought-resistant qingkes, a class of C-glycosylflavonoids are simultaneously regulated by a UDP-glucosyltransferase gene. Overall, we performed GWAS for sensitivity and widely targeted metabolites during drought stress in qingke for the first time, which provides new insights into the response mechanism of plant drought stress and drought resistance breeding.

Integrative metabolomic and transcriptomic analyses reveal the mechanisms of Tibetan hulless barley grain coloration

Cereal grains accumulate anthocyanin during developmental process. The anthocyanin content increases at grain filling stages to develop grain coloration in cereals. However, anthocyanin biosynthesis responsible for grain coloring and its regulatory mechanisms controlled by structural and functional genes remain unclear. Therefore, this study aimed to explore the global map of metabolic changes linked to grain coloration of Tibetan hulless barley (qingke) using an integrative metabolome and transcriptome approach. Grains from three colored qingke cultivars at different developmental stages were considered for molecular and metabolic investigations. A total of 120 differentially accumulated metabolites (DAMs) and 8,327 differentially expressed genes (DEGs) were filtered. DEGs were mainly enriched in the phenylpropanoid and flavonoid pathways. The transcript levels of anthocyanin biosynthesis genes (PAL, C4H, 4CL, CHS, FLS, F3H, F3'H, DFR, ANS, GT, OMT, and MAT) significantly upregulate in colored qingke compared to the non-colored variety. During grain development and maturation, the strong correlation of HvMYC2 expression with anthocyanin contents and anthocyanin biosynthesis genes suggested it as a critical gene in anthocyanin accumulation. Further results confirmed that HvMYC2 could be activated by HvMYB and be a positive regulator of UV-B and cold tolerance in qingke. In addition, verification based on enzymatic assays indicated that six key modifier enzymes could catalyze glycosylation, malonylation, and methylation of anthocyanins, thereby dissecting the major anthocyanin modification pathway in colored qingke. Overall, our study provides global insight into anthocyanin accumulation and the mechanism underlying grain coloration in qingke.

Leaf-transcriptome profiles of phoebe bournei provide insights into temporal drought stress responses

Phoebe bournei (Hemsl.) Yang is used as a commercial wood in China and is enlisted as a near-threatened species. Prolonged droughts pose a serious threat to young seedlings (1-2 years old). A transcriptome sequencing approach, together with the measurement of growth parameters and biochemical analyses were used to understand P. bournei's drought responses on 15d, 30d, and 45d of drought stress treatment. The stem and root dry weights decreased significantly with drought stress duration. Activities of antioxidative enzymes i.e., peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) increased significantly with the increase in drought stress duration. A total of 13,274, 15,648, and 9,949 genes were differentially expressed in CKvs15d, CKvs30d, and CKvs45d, respectively. The differential expression analyses showed that photosystem I and II underwent structural changes, chlorophyll biosynthesis, and photosynthesis were reduced. The genes annotated as POD, SOD, and CAT were upregulated in drought-treated leaves as compared to control. Additionally, plant-hormone signal transduction, MAPK signaling-plant, phenylpropanoid biosynthesis, flavonoid biosynthesis, and starch and sucrose metabolism pathways showed large-scale expression changes in major genes. We also found that members of 25 transcription factor families were differentially expressed. Our study presents and discusses these transcriptome signatures. Overall, our findings represent key data for breeding towards drought stress tolerance in P. bournei.

Nitrogen addition modifies the relative gene expression level and accumulation of carbon-based bioactive substances in Cyclocarya paliurus

In China, lots of Cyclocarya paliurus plantations have been established for tea and functional food production on nitrogen (N)-limited land. The optimum N levels require for biosynthesis and accumulation of carbon-based bioactive substances vary among plant species. This study integrated field trial with hydroponic culture to assess impact of nitrogen addition on accumulation and relative gene expression level of carbon-based secondary metabolites in C. paliurus. N addition significantly influenced not only contents of polyphenols, flavonoids and triterpenoids and relative gene expression levels of their biosynthetic pathway in C. paliurus leaves but also leaf biomass production and the bioactive substance accumulations. An intermediate N addition induced the highest contents of polyphenols, flavonoids and triterpenoids in leaves, but the optimized accumulation of these bioactive substances in the leaves was the trade-off between their contents and leaf biomass production. Correlation analysis showed that related gene expression levels were closely correlated with contents of their leaf corresponding secondary metabolites. Compared with ratios of carbon/N (C/N) and carbon/phosphorus (C/P) in the soil, ratios of C/N and C/P in the leaves were more strongly related to the contents and accumulations of polyphenols, flavonoids and triterpenoids. To obtain higher yields of targeted phytochemicals, the threshold ratios of C/N and C/P in the leaves are recommended for N and P fertilization at similar sites. Overall, our findings would provide the theoretical basis and technical support for manipulating N fertilization in C. paliurus plantations to obtain higher accumulations of targeted bioactive substances.

Molecular mechanisms of flavonoid accumulation in germinating common bean (Phaseolus vulgaris) under salt stress

Flavonoids are important secondary metabolites, active biomolecules in germinating beans, and have prominent applications in food and medicine due to their antioxidant effects. Rutin is a plant flavonoid with a wide biological activity range. In this study, flavonoid (rutin) accumulation and its related molecular mechanisms in germinating common bean (Phaseolus vulgaris) were observed at different time points (0–120 h) under salt stress (NaCl). The rutin content increased from germination onset until 96 h, after which a reducing trend was observed. Metabolome analysis showed that salt stress alters flavonoid content by regulating phenylpropanoid (ko00940) and flavonoid (ko00941) biosynthesis pathways, as well as their enzyme activities, including cinnamyl-alcohol dehydrogenase (CAD), peroxidase (POD), chalcone isomerase (CHI), and flavonol synthase (FLS). The RNA-seq and quantitative real-time PCR (qRT-PCR) analyses also showed that these two pathways were linked to changes in flavonoid content following salt treatment. These results reveal that salt stress effectively enhanced rutin content accumulation in germinating beans, hence it could be employed to enhance the functional quality of germinating common beans.

Biosynthetic mechanisms of isoflavone accumulation affected by different growth patterns in Astragalus mongholicus products

BACKGROUND

At present, Astragalus mongholicus products on the market represent two growth patterns: imitative wild A. mongholicus (WAM) and cultivated A. mongholicus (CAM). The 6-year-old WAM (A6) and 2-year-old CAM (B2) products are often sold as commodities. This study aimed to explore the effects of the abovementioned growth patterns on the biosynthetic mechanisms of isoflavone accumulation in A. mongholicus products.

RESULTS

In this paper, the content of calycosin-7-O-β-D-glucoside in 6-year-old WAM (A6) was significantly higher than that in 2-year-old CAM (B2) based on high-performance liquid chromatography. Tissue anatomy indicated that A6 has developed phloem fibers, thickened secondary walls, and a more well-developed vascular system than B2. Thirteen differentially accumulated metabolites were found in A6 and B2 by UHPLC-ESI-Q-TOF-MS/MS, of which isoflavones were highly and significantly enriched in A6. By combining transcriptomics and metabolomics analysis, we found that the metabolomics profile was the same as the transcriptomics profile in both A6 and B2. In total, 11 novel isoflavone-related genes were isolated using BLAST and functional annotation through RNA-Seq and Iso-Seq. The results of integrated analysis, Short Time-series Expression Miner analysis, and Pearson correlation analysis showed that the regulation of four key enzymes, cinnamate 4-hydroxylase, 6-deoxychalcone synthase, chalcone reductase, and chalcone isomerase, led to the high accumulation of isoflavones in A6. In addition, AmUFGT (c778119) and AmUCGT (c303354) were predicted to be 7-O-glycosyltransferases by phylogenetic analysis; these genes catalyze formononetin and calycosin, respectively.

CONCLUSIONS

The findings of this work will clarify the differences in the biosynthetic mechanism of isoflavone accumulation between A6 and B2, which will guide the cultivation of A. mongholicus.

Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology

In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.

Gene Co-expression Network and Regression Analysis Identify the Transcriptomic, Physiological, and Biochemical Indicators of the Response of Alpine Woody Plant Rhododendron rex to Drought Stress

Increasing severity of drought stress due to global change and extreme weather has been affecting the biodiversity, function, and stability of forest ecosystems. However, despite being an important component in the alpine and subalpine vegetation in forest ecosystems, Rhododendron species have been paid rare attention in the study of molecular mechanism of tolerance or response to drought. Herein, we investigated the correlation of transcriptomic changes with the physiological and biochemical indicators of Rhododendron rex under drought stress by using the co-expression network approach and regression analysis. Compared with the control treatment, the number of significantly differentially expressed unigenes (DEGs) increased with the degree of drought stress. The DEGs were mainly enriched in the cell wall metabolic process, signaling pathways, sugar metabolism, and nitrogen metabolism. Coupled analysis of the transcriptome, physiological, and biochemical parameters indicated that the metabolic pathways were highly correlated with the physiological and biochemical indicators under drought stress, especially the chlorophyll fluorescence parameters, such as the actual photosynthetic efficiency of photosystem II, electron transport rate, photochemical quenching coefficient, and the maximum quantum efficiency of photosystem II photochemistry. The majority of the response genes related to the metabolic pathways, including photosynthesis, sugar metabolism, and phytohormone signal pathway, were highly expressed under drought stress. In addition, genes associated with cell wall, pectin, and galacturonan metabolism also played crucial roles in the response of R. rex to drought stress. The results provided novel insight into the molecular response of the alpine woody species under drought stress and may improve the understanding of the response of forest ecosystems to the global climate change.

The Roles of microRNA-Long Non-coding RNA-mRNA Networks in the Regulation of Leaf and Flower Development in Liriodendron chinense

The leaf and the flower are vital plant organs owing to their roles in photosynthesis and reproduction. Long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and transcription factors (TFs) are very important to the development of these organs. Liriodendron chinense is a common ornamental tree species in southern China with an unusual leaf shape and tulip-like flowers. The genetic mechanisms underlying leaf and flower development in L. chinense and the miRNA-lncRNA-TF regulatory networks are poorly studied. Through the integration and analysis of different types of sequencing data, we identified the miRNA-lncRNA-TF regulatory networks that were related to leaf and flower development. These networks contained 105 miRNAs, 258 lncRNAs, 393 TFs, and 22 endogenous target mimics. Notably, lch-lnc7374-miR156h-SPL3 and lch-lnc7374-miR156j-SPL9 were potential regulators of stamen and pistil development in L. chinense, respectively. miRNA-lncRNA-mRNA regulatory networks were shown to impact anther development, male and female fertility, and petal color by regulating the biosynthesis of phenylpropanoid metabolites. Phenylpropanoid metabolite biosynthesis genes and TFs that were targeted by miRNAs and lncRNAs were differentially expressed in the leaf and flower. Moreover, RT-qPCR analysis confirmed 22 differentially expressed miRNAs, among which most of them showed obvious leaf or flower specificity; miR157a-SPL and miR160a-ARF module were verified by using RLM-RACE, and these two modules were related to leaf and flower development. These findings provide insight into the roles of miRNA-lncRNA-mRNA regulatory networks in organ development and function in L. chinense, and will facilitate further investigation into the regulatory mechanisms of leaf and flower development in L. chinense.

Altitudinal Variation of Metabolites, Mineral Elements and Antioxidant Activities of Rhodiola crenulata (Hook.f. & Thomson) H.Ohba

Rhodiolacrenulata (Hook.f. & Thomson) H.Ohba is an alpine medicinal plant that can survive in extreme high altitude environments. However, its changes to extreme high altitude are not yet clear. In this study, the response of Rhodiola crenulata to differences in altitude gradients was investigated through chemical, ICP-MS and metabolomic methods. A targeted study of Rhodiola crenulata growing at three vertical altitudes revealed that the contents of seven elements Ca, Sr, B, Mn, Ni, Cu, and Cd, the phenolic components, the ascorbic acid, the ascorbic acid/dehydroascorbate ratio, and the antioxidant capacity were positively correlated with altitude, while the opposite was true for total ascorbic acid content. Furthermore, 1165 metabolites were identified: flavonoids (200), gallic acids (30), phenylpropanoids (237), amino acids (100), free fatty acids and glycerides (56), nucleotides (60), as well as other metabolites (482). The differential metabolite and biomarker analyses suggested that, with an increasing altitude: (1) the shikimic acid-phenylalanine-phenylpropanoids-flavonoids pathway was enhanced, with phenylpropanoids upregulating biomarkers much more than flavonoids; phenylpropanes and phenylmethanes upregulated, and phenylethanes downregulated; the upregulation of quercetin was especially significant in flavonoids; upregulation of condensed tannins and downregulation of hydrolyzed tannins; upregulation of shikimic acids and amino acids including phenylalanine. (2) significant upregulation of free fatty acids and downregulation of glycerides; and (3) upregulation of adenosine phosphates. Our findings provide new insights on the responses of Rhodiola crenulata to extreme high altitude adversity.

Potential of Producing Flavonoids Using Cyanobacteria As a Sustainable Chassis

Numerous plant secondary metabolites have remarkable impacts on both food supplements and pharmaceuticals for human health improvement. However, higher plants can only generate small amounts of these chemicals with specific temporal and spatial arrangements, which are unable to satisfy the expanding market demands. Cyanobacteria can directly utilize CO₂, light energy, and inorganic nutrients to synthesize versatile plant-specific photosynthetic intermediates and organic compounds in large-scale photobioreactors with outstanding economic merit. Thus, they have been rapidly developed as a "green" chassis for the synthesis of bioproducts. Flavonoids, chemical compounds based on aromatic amino acids, are considered to be indispensable components in a variety of nutraceutical, pharmaceutical, and cosmetic applications. In contrast to heterotrophic metabolic engineering pioneers, such as yeast and Escherichia coli, information about the biosynthesis flavonoids and their derivatives is less comprehensive than that of their photosynthetic counterparts. Here, we review both benefits and challenges to promote cyanobacterial cell factories for flavonoid biosynthesis. With increasing concerns about global environmental issues and food security, we are confident that energy self-supporting cyanobacteria will attract increasing attention for the generation of different kinds of bioproducts. We hope that the work presented here will serve as an index and encourage more scientists to join in the relevant research area.

Melatonin enhances drought stress tolerance in maize through coordinated regulation of carbon and nitrogen assimilation

Melatonin is a pleiotropic regulatory molecule in plants and is involved in regulating plant tolerance to drought stress. Here, we conducted transcriptomic and physiological analyses to identify metabolic processes associated with the enhanced tolerance of the melatonin-treated maize (Zea mays L.) seedlings to water deficit. Maize seedlings were foliar sprayed with either 50 μM melatonin or water and exposed to drought stress for 12 d in growth chambers. Drought stress significantly suppressed seedling growth, and melatonin application partially alleviated this growth inhibition. RNA-Seq analysis revealed that genes whose expression was significantly altered by melatonin were mainly related to carbon (C) and nitrogen (N) metabolism. Analysis of transcriptomics, enzyme activity, and metabolite content data, melatonin-treated plants exhibited a higher level of relatively stable C and N metabolism than untreated plants; this phenotype of melatonin-treated plants was associated with their higher photosynthesis, sucrose biosynthesis, N assimilation, and protein biosynthesis capacities under drought stress. Overall, our results suggest that melatonin enhances drought stress tolerance in maize through coordinated regulation of C and N metabolism.

Integrated analysis of miRNA-mRNA regulatory networks of potato (Solanum tuberosum L.) in response to cadmium stress

Cadmium (Cd) stress is a ubiquitous abiotic stress affecting plant growth worldwide and negatively impacting crop yield and food safety. Potato is the most important non-grain crop globally, but there is limited research available on the response of this crop to Cd stress. This study explored the coping mechanism for Cd stress in potato through analyses of miRNA and mRNA. Tissue culture seedlings (20-day-old) of potato variety 'Atlantic' were cultured for up to 48 h in liquid medium containing 5 mmol/L CdCl2, and phenotypic, physiological, and transcriptomic changes were observed at specific times. With the extension of Cd stress time, the potato leaves gradually wilted and curled, and root salicylic acid (SA), glutathione (GSH), and lignin contents and peroxidase (POD) activity increased, while indole-3-acetic acid (IAA) and zeatin (ZT) contents decreased. Using miRNA-seq, 161 existing miRNAs, 383 known miRNAs, and 7361 novel miRNAs were identified, and, 18 miRNAs were differentially expressed in response to Cd stress. Based on mRNA-seq, 7340 differentially expressed mRNAs (DEGs) were found. Through mRNA-miRNA integrated analysis, miRNA-target gene pairs consisting of 23 DEGs and 33 miRNAs were identified. Furthermore, "glutathione metabolism" "plant hormone signal transduction" and "phenylpropanoid biosynthesis" were established as crucial pathways in the Cd stress response of potato. Novel miRNAs novel-m3483-5p and novel-m2893-5p participate in these pathways through targeted regulation of cinnamic alcohol dehydrogenase (CAD; PG0005359) and alanine aminotransferase (POP; PG0024281), respectively. This study provides information that will help elucidate the complex mechanism of the Cd stress response in potato. Moreover, candidate miRNAs and mRNAs could yield new strategies for the development of Cd-tolerant potato breeding.