Enhanced metabolic process to indole alkaloids in Clematis terniflora DC. after exposure to high level of UV-B irradiation followed by the dark

Comprehensive transcriptomic meta-analysis unveils new responsive genes to methyl jasmonate and ethylene in Catharanthusroseus

In Catharanthus roseus, vital plant hormones, namely methyl jasmonate (MeJA) and ethylene, serve as abiotic triggers, playing a crucial role in stimulating the production of specific secondary compounds with anticancer properties. Understanding how plants react to various stresses, stimuli, and the pathways involved in biosynthesis holds significant promise. The application of stressors like ethylene and MeJA induces the plant's defense mechanisms, leading to increased secondary metabolite production. To delve into the essential transcriptomic processes linked to hormonal responses, this study employed an integrated approach combining RNA-Seq data meta-analysis and system biology methodologies. Furthermore, the validity of the meta-analysis findings was confirmed using RT-qPCR. Within the meta-analysis, 903 genes exhibited differential expression (DEGs) when comparing normal conditions to those of the treatment. Subsequent analysis, encompassing gene ontology, KEGG, TF, and motifs, revealed that these DEGs were actively engaged in multiple biological processes, particularly in responding to various stresses and stimuli. Additionally, these genes were notably enriched in diverse biosynthetic pathways, including those related to TIAs, housing valuable medicinal compounds found in this plant. Furthermore, by conducting co-expression network analysis, we identified hub genes within modules associated with stress response and the production of TIAs. Most genes linked to the biosynthesis pathway of TIAs clustered within three specific modules. Noteworthy hub genes, including Helicase ATP-binding domain, hbdA, and ALP1 genes within the blue, turquoise, and green module networks, are presumed to play a role in the TIAs pathway. These identified candidate genes hold potential for forthcoming genetic and metabolic engineering initiatives aimed at augmenting the production of secondary metabolites and medicinal compounds within C. roseus.

The Plant Metabolic Changes and the Physiological and Signaling Functions in the Responses to Abiotic Stress

Global climate change has altered, and will further alter, rainfall patterns and temperatures likely causing more frequent drought and heat waves, which will consequently exacerbate abiotic stresses of plants and significantly decrease the yield and quality of crops. On the one hand, the global demand for food is ever-increasing owing to the rapid increase of the human population. On the other hand, metabolic responses are one of the most important mechanisms by which plants adapt to and survive to abiotic stresses. Here we therefore summarize recent progresses including the plant primary and secondary metabolic responses to abiotic stresses and their function in plant resistance acting as antioxidants, osmoregulatory, and signaling factors, which enrich our knowledge concerning commonalities of plant metabolic responses to abiotic stresses, including their involvement in signaling processes. Finally, we discuss potential methods of metabolic fortification of crops in order to improve their abiotic stress tolerance.

UVB Irradiation-Induced Transcriptional Changes in Lignin- and Flavonoid Biosynthesis and Indole/Tryptophan-Auxin-Responsive Genes in Rice Seedlings

Global warming accelerates the destruction of the ozone layer, increasing the amount of UVB reaching the Earth’s surface, which in turn alters plant growth and development. The effects of UVB-induced alterations of plant secondary and cell wall metabolism were previously documented; however, there is little knowledge of its effects on rice seedlings during the developmental phase of leaves. In this study, we examined secondary metabolic responses to UVB stress using a transcriptomic approach, focusing on the biosynthetic pathways for lignin, flavonoid, and indole/tryptophan-auxin responses. As new leaves emerged, they were irradiated with UVB for 5 days (for 3 h/day⁻¹). The genes encoding the enzymes related to lignin (4CL, CAD, and POD) and flavonoid biosynthesis (CHS, CHI, and FLS) were highly expressed on day 1 (younger leaves) and day 5 (older leaves) after UVB irradiation. The expression of the genes encoding the enzymes related to tryptophan biosynthesis (AS, PRT, PRAI, IGPS, and TS) increased on day 3 of UVB irradiation, and the level of tryptophan increased and showed the same temporal pattern of occurrence as the expression of the cognate gene. Interestingly, the genes encoding BBX4 and BBX11, negative regulators of UVB signaling, and SAUR27 and SAUR55, auxin response enzymes, were downregulated on day 3 of UVB irradiation. When these results are taken together, they suggest that secondary metabolic pathways in rice seedlings are influenced by the interaction between UVB irradiation and the leaf developmental stage. Thus, the strategies of protection against, adaptation to, and mitigation of UVB might be delicately regulated, and, in this context, our data provide valuable information to understand UVB-induced secondary metabolism in rice seedlings.

Integration of the metabolome and transcriptome reveals indigo biosynthesis in Phaius flavus flowers under freezing treatment

Background

Indigo-containing plant tissues change blue after a freezing treatment, which is accompanied by changes in indigo and its related compounds. Phaius flavus is one of the few monocot plants containing indigo. The change to blue after freezing was described to explore the biosynthesis of indigo in P. flavus.

Methods

In this study, we surveyed the dynamic change of P. flavus flower metabolomics and transcriptomics.

Results

The non-targeted metabolomics and targeted metabolomics results revealed a total of 98 different metabolites, the contents of indole, indican, indigo, and indirubin were significantly different after the change to blue from the freezing treatment. A transcriptome analysis screened ten different genes related to indigo upstream biosynthesis, including three anthranilate synthase genes, two phosphoribosyl-anthranilate isomerase genes, one indole-3-glycerolphosphate synthase gene, five tryptophan synthase genes. In addition, we further candidate 37 cytochrome P450 enzyme genes, one uridine diphosphate glucosyltransferase gene, and 24 β-D-glucosidase genes were screened that may have participated in the downstream biosynthesis of indigo. This study explained the changes of indigo-related compounds at the metabolic level and gene expression level during the process of P. flavus under freezing and provided new insights for increasing the production of indigo-related compounds in P. flavus. In addition, transcriptome sequencing provides the basis for functional verification of the indigo biosynthesis key genes in P. flavus.

Morphophysiological and Proteomic Responses on Plants of Irradiation with Electromagnetic Waves

Electromagnetic energy is the backbone of wireless communication systems, and its progressive use has resulted in impacts on a wide range of biological systems. The consequences of electromagnetic energy absorption on plants are insufficiently addressed. In the agricultural area, electromagnetic-wave irradiation has been used to develop crop varieties, manage insect pests, monitor fertilizer efficiency, and preserve agricultural produce. According to different frequencies and wavelengths, electromagnetic waves are typically divided into eight spectral bands, including audio waves, radio waves, microwaves, infrared, visible light, ultraviolet, X-rays, and gamma rays. In this review, among these electromagnetic waves, effects of millimeter waves, ultraviolet, and gamma rays on plants are outlined, and their response mechanisms in plants through proteomic approaches are summarized. Furthermore, remarkable advancements of irradiating plants with electromagnetic waves, especially ultraviolet, are addressed, which shed light on future research in the electromagnetic field.

Effects of Light on Secondary Metabolite Biosynthesis in Medicinal Plants

Secondary metabolites (SMs) found in medicinal plants are one of main sources of drugs, cosmetics, and health products. With the increase in demand for these bioactive compounds, improving the content and yield of SMs in medicinal plants has become increasingly important. The content and distribution of SMs in medicinal plants are closely related to environmental factors, especially light. In recent years, artificial light sources have been used in controlled environments for the production and conservation of medicinal germplasm. Therefore, it is essential to elucidate how light affects the accumulation of SMs in different plant species. Here, we systematically summarize recent advances in our understanding of the regulatory roles of light quality, light intensity, and photoperiod in the biosynthesis of three main types of SMs (polyphenols, alkaloids, and terpenoids), and the underlying mechanisms. This article provides a detailed overview of the role of light signaling pathways in SM biosynthesis, which will further promote the application of artificial light sources in medicinal plant production.

Ionomic and metabolomic analyses reveal the resistance response mechanism to saline-alkali stress in Malus halliana seedlings

Saline-alkali stress is a major abiotic stress limiting plant growth. The selection of saline-alkali-tolerant rootstock is an effective strategy to reduce salinization-alkalization influence in apple production. M. halliana is a highly saline-alkali-resistant apple rootstock in northwestern China. However, few metabolic response studies have been conducted on this species. In plants under saline-alkali stress, the uptake of K, Mg and Zn in M. halliana leaves were inhibited, whereas the absorption of Fe²⁺, Cu²⁺ or Mn²⁺ were increased. Metabolic analysis revealed 140 differentially expressed metabolites, which were mainly involved in alkaloid biosynthesis, phenylalanine biosynthesis, ATP-binding cassette (ABC) transporters, and mineral absorption. Especially, the expression of sucrose, amino acids, alkaloids, flavonoids and carotenoids were significantly upregulated under saline-alkali stress. qRT-PCR analysis demonstrated that NHX8 and ZTP1 involved in Na⁺ and Fe²⁺ transport were upregulated, while AKT1, MRS2-4 and ZTP29 involved in K⁺, Mg²⁺ and Zn²⁺ transport were downregulated, respectively. ANT, ATP2A, CALM and SOS2 are involved in Ca²⁺ signal transduction, and ABCB1, ABCC10 and NatA are key transporters that maintain ionic homeostasis. M. halliana regulates Na⁺/K⁺ homeostasis by mediating Ca²⁺ signalling and ABC transporters. The accumulation of metabolites contributes to improving the saline-alkali resistance of M. halliana because of the scavenging of ROS. An increase in pheophorbide a content in porphyrin and chlorophyll metabolism leads to leaf senescence in M. halliana leaves, which contributes to a reduction in stress-induced injury. These findings provide important insights into the saline-alkali tolerance mechanism in apple, which also provides an important starting point for future research.

A metabolomic strategy revealed the role of JA and SA balance in Clematis terniflora DC. Response to UVB radiation and dark

Clematis terniflora DC. is a valuable resource with potential high pharmaceutical value. Proteomic, transcriptomic and metabolomic analyses of C. terniflora that has been exposed to high levels of UVB irradiation and dark conditions (HUVB + D) have revealed the mechanisms underlying its medicinal potential. However, the signal transduction pathways and the mechanisms of regulation for the accumulation of secondary metabolites remain unclear. In this study, we show that the jasmonic acid (JA) and salicylic acid (SA) signals were activated in C. terniflora in response to HUVB + D. Metabolomic analysis demonstrated that the perturbation in JA and SA balance led to additional reallocation of carbon and nitrogen resources. Evaluating the fold change ratios of differentially changed metabolites proved that JA signal enhanced the transformation of nitrogen to carbon through the 4-aminobutyric acid (GABA) shunt pathway, which increased the carbon reserve to be utilized in the production of secondary metabolites. However, SA signal induced the synthesis of proline, while avoiding the accumulation of secondary metabolites. Over all, the results indicate that the co-increase of JA and SA reconstructed the dynamic stability of transformation from nitrogen to carbon, which effectively enhanced the oxidative defense to HUVB + D in C. terniflora by increasing the secondary metabolites.

Integrated physiologic, proteomic, and metabolomic analyses of Malus halliana adaptation to saline-alkali stress

Saline-alkali stress is a severely adverse abiotic stress limiting plant growth. Malus halliana Koehne is an apple rootstock that is tolerant to saline-alkali stress. To understand the molecular mechanisms underlying the tolerance of M. halliana to saline-alkali stress, an integrated metabolomic and proteomic approach was used to analyze the plant pathways involved in the stress response of the plant and its regulatory mechanisms. A total of 179 differentially expressed proteins (DEPs) and 140 differentially expressed metabolites (DEMs) were identified. We found that two metabolite-related enzymes (PPD and PAO) were associated with senescence and involved in porphyrin and chlorophyll metabolism; six photosynthesis proteins (PSAH2, PSAK, PSBO2, PSBP1, and PSBQ2) were significantly upregulated, especially PSBO2, and could act as regulators of photosystem II (PSII) repair. Sucrose, acting as a signaling molecule, directly mediated the accumulation of D-phenylalanine, tryptophan, and alkaloid (vindoline and ecgonine) and the expression of proteins related to aspartate and glutamate (ASP3, ASN1, NIT4, and GLN1-1). These responses play a central role in maintaining osmotic balance and removing reactive oxygen species (ROS). In addition, sucrose signaling induced flavonoid biosynthesis by activating the expression of CYP75B1 to regulate the homeostasis of ROS and promoted auxin signaling by activating the expression of T31B5_170 to enhance the resistance of M. halliana to saline-alkali stress. The decrease in peroxidase superfamily protein (PER) and ALDH2C4 during lignin synthesis further triggered a plant saline-alkali response. Overall, this study provides an important starting point for improving saline-alkali tolerance in M. halliana via genetic engineering.

A perspective on ecologically relevant plant-UV research and its practical application

Plants perceive ultraviolet-B (UV-B) radiation through the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8), and initiate regulatory responses via associated signalling networks, gene expression and metabolic pathways. Various regulatory adaptations to UV-B radiation enable plants to harvest information about fluctuations in UV-B irradiance and spectral composition in natural environments, and to defend themselves against UV-B exposure. Given that UVR8 is present across plant organs and tissues, knowledge of the systemic signalling involved in its activation and function throughout the plant is important for understanding the context of specific responses. Fine-scale understanding of both UV-B irradiance and perception within tissues and cells requires improved application of knowledge about UV-attenuation in leaves and canopies, warranting greater consideration when designing experiments. In this context, reciprocal crosstalk among photoreceptor-induced pathways also needs to be considered, as this appears to produce particularly complex patterns of physiological and morphological response. Through crosstalk, plant responses to UV-B radiation go beyond simply UV-protection or amelioration of damage, but may give cross-protection over a suite of environmental stressors. Overall, there is emerging knowledge showing how information captured by UVR8 is used to regulate molecular and physiological processes, although understanding of upscaling to higher levels of organisation, i.e. organisms, canopies and communities remains poor. Achieving this will require further studies using model plant species beyond Arabidopsis, and that represent a broad range of functional types. More attention should also be given to plants in natural environments in all their complexity, as such studies are needed to acquire an improved understanding of the impact of climate change in the context of plant-UV responses. Furthermore, broadening the scope of experiments into the regulation of plant-UV responses will facilitate the application of UV radiation in commercial plant production. By considering the progress made in plant-UV research, this perspective highlights prescient topics in plant-UV photobiology where future research efforts can profitably be focussed. This perspective also emphasises burgeoning interdisciplinary links that will assist in understanding of UV-B effects across organisational scales and gaps in knowledge that need to be filled so as to achieve an integrated vision of plant responses to UV-radiation.

Defense potential of secondary metabolites in medicinal plants under UV-B stress

Ultraviolet-B (UV-B) radiation has, for many decades now, been widely studied with respect to its consequences on plant and animal health. Though according to NASA, the ozone hole is on its way to recovery, it will still be a considerable time before UV-B levels reach pre-industrial limits. Thus, for the present, excessive UV-B reaching the Earth is a cause for concern, and UV-B related human ailments are on the rise. Plants produce various secondary metabolites as one of the defense strategies under UV-B. They provide photoprotection via their UV-B screening effects and by quenching the reactive oxygen- and nitrogen species produced under UV-B influence. These properties of plant secondary metabolites (PSMs) are being increasingly recognized and made use of in sunscreens and cosmetics, and pharma- and nutraceuticals are gradually becoming a part of the regular diet. Secondary metabolites derived from medicinal plants (alkaloids, terpenoids, and phenolics) are a source of pharmaceuticals, nutraceuticals, as well as more rigorously tested and regulated drugs. These metabolites have been implicated in providing protection not only to plants under the influence of UV-B, but also to animals/animal cell lines, when the innate defenses in the latter are not adequate under UV-B-induced damage. The present review focuses on the defense potential of secondary metabolites derived from medicinal plants in both plants and animals. In plants, the concentrations of the alkaloids, terpenes/terpenoids, and phenolics have been discussed under UV-B irradiation as well as the fate of the genes and enzymes involved in their biosynthetic pathways. Their role in providing protection to animal models subjected to UV-B has been subsequently elucidated. Finally, we discuss the possible futuristic scenarios and implications for plant, animal, and human health pertaining to the defense potential of these secondary metabolites under UV-B radiation-mediated damages.

Comparative Proteomic Analysis Reveals Elevated Capacity for Photosynthesis in Polyphenol Oxidase Expression-Silenced Clematis terniflora DC. Leaves

Polyphenol oxidase (PPO) catalyzes the o-hydroxylation of monophenols and oxidation of o-diphenols to quinones. Although the effects of PPO on plant physiology were recently proposed, little has been done to explore the inherent molecular mechanisms. To explore the in vivo physiological functions of PPO, a model with decreased PPO expression and enzymatic activity was constructed on Clematis terniflora DC. using virus-induced gene silencing (VIGS) technology. Proteomics was performed to identify the differentially expressed proteins (DEPs) in the model (VC) and empty vector-carrying plants (VV) untreated or exposed to high levels of UV-B and dark (HUV-B+D). Following integration, it was concluded that the DEPs mainly functioned in photosynthesis, glycolysis, and redox in the PPO silence plants. Mapman analysis showed that the DEPs were mainly involved in light reaction and Calvin cycle in photosynthesis. Further analysis illustrated that the expression level of adenosine triphosphate (ATP) synthase, the content of chlorophyll, and the photosynthesis rate were increased in VC plants compared to VV plants pre- and post HUV-B+D. These results indicate that the silence of PPO elevated the plant photosynthesis by activating the glycolysis process, regulating Calvin cycle and providing ATP for energy metabolism. This study provides a prospective approach for increasing crop yield in agricultural production.

Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

Background

Clematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the “Queen of the Vines”. However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C. finetiana obtained using the Illumina paired-end sequencing technology.

Results

Sequences on a total of 71,900 high-quality unigenes with the mean length of 865 bp were produced in this study. There were 6192unigenes annotated and classified into 49 functional sub-groups in three main ontology categories in GO (Gen Ontology) database,14,022 unigenes mapped to COGs (Clusters of Orthologous Groups) database and classified into 25 functional categories, and 21,494 unigenes obtained and divided into 128 pathways of KEGG (Kyoto Encyclopedia of Genes) Database. A total of 7532 SSRs were discovered from 6337 unigenes. We randomly tested 210 primer pairs, of which 52 primer pairs were able to generate specific products, and 19 possessed polymorphism in the 13 wild populations of six species from Clematis, which were used as a test material.

Conclusions

The dataset of C. finetiana transcriptome and the identified new SSR markers will promote genetic research and breeding effort in Clematis.

Electronic supplementary material

The online version of this article (10.1186/s41065-018-0060-x) contains supplementary material, which is available to authorized users.

Measurement of metabolite variations and analysis of related gene expression in Chinese liquorice (Glycyrrhiza uralensis) plants under UV-B irradiation

Plants respond to UV-B irradiation (280–315 nm wavelength) via elaborate metabolic regulatory mechanisms that help them adapt to this stress. To investigate the metabolic response of the medicinal herb Chinese liquorice (Glycyrrhiza uralensis) to UV-B irradiation, we performed liquid chromatography tandem mass spectrometry (LC-MS/MS)-based metabolomic analysis, combined with analysis of differentially expressed genes in the leaves of plants exposed to UV-B irradiation at various time points. Fifty-four metabolites, primarily amino acids and flavonoids, exhibited changes in levels after the UV-B treatment. The amino acid metabolism was altered by UV-B irradiation: the Asp family pathway was activated and closely correlated to Glu. Some amino acids appeared to be converted into antioxidants such as γ-aminobutyric acid and glutathione. Hierarchical clustering analysis revealed that various flavonoids with characteristic groups were induced by UV-B. In particular, the levels of some ortho-dihydroxylated B-ring flavonoids, which might function as scavengers of reactive oxygen species, increased in response to UV-B treatment. In general, unigenes encoding key enzymes involved in amino acid metabolism and flavonoid biosynthesis were upregulated by UV-B irradiation. These findings lay the foundation for further analysis of the mechanism underlying the response of G. uralensis to UV-B irradiation.

Proteomic Contributions to Medicinal Plant Research: From Plant Metabolism to Pharmacological Action

Herbal medicine is a clinical practice of utilizing medicinal plant derivatives for therapeutic purposes. It has an enduring history worldwide and plays a significant role in the fight against various diseases. Herbal drug combinations often exhibit synergistic therapeutic action compared with single-constituent dosage, and can also enhance the cytotoxicity induced by chemotherapeutic drugs. To explore the mechanism underlying the pharmacological action of herbs, proteomic approaches have been applied to the physiology of medicinal plants and its effects on animals. This review article focuses on the existing proteomics-based medicinal plant research and discusses the following topics: (i) plant metabolic pathways that synthesize an array of bioactive compounds; (ii) pharmacological action of plants tested using in vivo and in vitro studies; and (iii) the application of proteomic approaches to indigenous plants with scarce sequence information. The accumulation of proteomic information in a biological or medicinal context may help in formulating the effective use of medicinal plants.