Comparative Transcriptome Analyses Reveal a Special Glucosinolate Metabolism Mechanism in Brassica alboglabra Sprouts

Developing multifunctional crops by engineering Brassicaceae glucosinolate pathways

Glucosinolates (GSLs), found mainly in species of the Brassicaceae family, are one of the most well-studied classes of secondary metabolites. Produced by the action of myrosinase on GSLs, GSL-derived hydrolysis products (GHPs) primarily defend against biotic stress in planta. They also significantly affect the quality of crop products, with a subset of GHPs contributing unique food flavors and multiple therapeutic benefits or causing disagreeable food odors and health risks. Here, we explore the potential of these bioactive functions, which could be exploited for future sustainable agriculture. We first summarize our accumulated understanding of GSL diversity and distribution across representative Brassicaceae species. We then systematically discuss and evaluate the potential of exploited and unutilized genes involved in GSL biosynthesis, transport, and hydrolysis as candidate GSL engineering targets. Benefiting from available information on GSL and GHP functions, we explore options for multifunctional Brassicaceae crop ideotypes to meet future demand for food diversification and sustainable crop production. An integrated roadmap is subsequently proposed to guide ideotype development, in which maximization of beneficial effects and minimization of detrimental effects of GHPs could be combined and associated with various end uses. Based on several use-case examples, we discuss advantages and limitations of available biotechnological approaches that may contribute to effective deployment and could provide novel insights for optimization of future GSL engineering.

Identification of key genes controlling soluble sugar and glucosinolate biosynthesis in Chinese cabbage by integrating metabolome and genome-wide transcriptome analysis

INTRODUCTION

Soluble sugar and glucosinolate are essential components that determine the flavor of Chinese cabbage and consumer preferences. However, the underlying regulatory networks that modulate the biosynthesis of soluble sugar and glucosinolate in Chinese cabbage remain largely unknown.

METHODS

The glucosinolate and carotene content in yellow inner-leaf Chinese cabbage were observed, followed by the combination of metabolome and transcriptome analysis to explore the metabolic basis of glucosinolate and soluble sugar.

RESULTS

This study observed high glucosinolate and carotene content in yellow inner-leaf Chinese cabbage, which showed a lower soluble sugar content. The differences between the yellow and the white inner-leaf Chinese cabbage were compared using the untargeted metabonomic and transcriptomic analyses in six cultivars of Chinese cabbage to explore the metabolic basis of glucosinolate and soluble sugar. Aliphatic glucosinolate and two soluble sugars (fructose and glucose) were the key metabolites that caused the difference in Chinese cabbage's glucosinolate and soluble sugar. By integrating soluble sugar and glucosinolate-associated metabolism and transcriptome data, we indicated BraA05gAOP1 and BraA04gAOP4, BraA03gHT7 and BraA01gHT4 were the glucosinolates and soluble sugar biosynthesis structural genes. Moreover, BraA01gCHR11 and BraA07gSCL1 were two vital transcription factors that regulate soluble sugar and glucosinolate biosynthesis.

DISCUSSION

These findings provide novel insights into glucosinolate and soluble sugar biosynthesis and a possible explanation for the significant difference in nutrients between yellow and white inner-leaf Chinese cabbage. Moreover, it will facilitate genetic modification to improve the Chinese cabbage's nutritional and health values.

Transcriptome Analysis of Glutathione Response: RNA-Seq Provides Insights into Balance between Antioxidant Response and Glucosinolate Metabolism

When being stressed, plants require a balance between the resistance pathway and metabolism. Glucosinolates (GS) are secondary metabolics that widely exist in Brassicaceae. Glutathione (GSH) not only participates in plant processing reactive oxygen species (ROS) but also directly participates in GS synthesis as a sulfur donor. Therefore, we used transcriptomic to identify antioxidant and GS metabolism responses in GSH-treated pakchoi. Our study elucidated that GSH can be used as priming to improve oxidative resistance and preferentially stimulate the expression of resistance genes such as CAT1. The reduction in transcription factor expression inhibits the key steps of the GS synthesis pathway. When ROS returned to normal level, the resistance gene decreased and returned to normal level, while GSH restored the gene expression of GS biosynthesis. This work puts forward the mechanism of GSH in regulating the antioxidant system and glucosinolate metabolic pathway, which provides a basis for further study on the relationship between environmental signals and plant metabolism and provides ideas for follow-up research.

Comparative transcriptomic analyses of glucosinolate metabolic genes during the formation of Chinese kale seeds

BACKGROUND

To understand the mechanism of glucosinolates (GSs) accumulation in the specific organs, combined analysis of physiological change and transcriptome sequencing were applied in the current study. Taking Chinese kale as material, seeds and silique walls were divided into different stages based on the development of the embryo in seeds and then subjected to GS analysis and transcriptome sequencing.

RESULTS

The main GS in seeds of Chinese kale were glucoiberin and gluconapin and their content changed with the development of the seed. During the transition of the embryo from torpedo- to the early cotyledonary-embryo stage, the accumulation of GS in the seed was accompanied by the salient decline of GS in the corresponding silique wall. Thus, the seed and corresponding silique wall at these two stages were subjected to transcriptomic sequencing analysis. 135 genes related to GS metabolism were identified, of which 24 genes were transcription factors, 81 genes were related to biosynthetic pathway, 25 genes encoded catabolic enzymes, and 5 genes matched with transporters. The expression of GS biosynthetic genes was detected both in seeds and silique walls. The high expression of FMOGS-OX and AOP2, which is related to the production of gluconapin by side modification, was noted in seeds at both stages. Interestingly, the expression of GS biosynthetic genes was higher in the silique wall compared with that in the seed albeit lower content of GS existed in the silique wall than in the seed. Combined with the higher expression of transporter genes GTRs in silique walls than in seeds, it was proposed that the transportation of GS from the silique wall to the seed is an important source for seed GS accumulation. In addition, genes related to GS degradation expressed abundantly in the seed at the early cotyledonary-embryo stage indicating its potential role in balancing seed GS content.

CONCLUSIONS

Two stages including the torpedo-embryo and the early cotyledonary-embryo stage were identified as crucial in GS accumulation during seed development. Moreover, we confirmed the transportation of GS from the silique wall to the seed and proposed possible sidechain modification of GS biosynthesis may exist during seed formation.

Induction of Glucoraphasatin Biosynthesis Genes by MYB29 in Radish (Raphanus sativus L.) Roots

Glucoraphasatin (GRH) is a specific aliphatic glucosinolate (GSL) that is only abundant in radish (Raphanus sativus L.). The gene expression regulating GRH biosynthesis in radish is still poorly understood. We employed a total of 59 radish accessions to analyze GSL profiles and showed that GRH was specific and predominant among the aliphatic GSLs in radish roots. We selected five accessions roots with high, moderate and low GSL biosynthesis, respectively, to conduct a comparative transcriptome analysis and the qRT-PCR of the biosynthesis genes for aliphatic GSLs. In this study, among all the accessions tested, roots with the accession RA157-74 had a high GRH content and showed a significant expression of the aliphatic GSL biosynthesis genes. We defined the genes involved in the GRH biosynthesis process and found that they were regulated by a transcription factor (RSG00789) at the MYB29 locus in radish roots. We found 13 aliphatic GSL biosynthesis genes regulated by the RSG00789 gene in the GRH biosynthesis pathway.

Physiological and transcriptomic responses of water spinach (Ipomoea aquatica) to prolonged heat stress

Background

Water spinach (Ipomoea aquatica) is an important heat-resistant leafy vegetable that can survive under long-time heat stress condition. However, the physiological characteristics and molecular changes in its response to heat stress are poorly understood.

Results

In this study the selected water spinach cultivars with different thermo resistance and their physiological response to heat stress were examined. Under prolonged heat stress, plant growth was inhibited in all tested cultivars. This inhibition was accompanied by the reduction of photosynthetic performance. The reactive oxygen species system in terms of superoxide and hydrogen peroxide contents, as well as antioxidant polyphenols, were evaluated. The results showed that prolonged heat stress caused reduced antioxidant capacity, but the role of antioxidant capacity in a prolonged thermotolerance was not predominant. Transcriptomic analysis of the water spinach subjected to heat stress revealed that 4145 transcripts were specifically expressed with 2420 up-regulated and 1725 down-regulated in heat-sensitive and heat-tolerant cultivars treated with 42 °C for 15 days. Enrichment analysis of these differentially expressed genes showed that the main metabolic differences between heat-sensitive and heat-tolerant cultivars were the carbohydrate metabolism and phenylpropanoid biosynthesis. The results of carbohydrate profiles and RT-qPCR also suggested that heat stress altered carbohydrate metabolism and associated changes in transcriptional level of genes involved in sugar transport and metabolic transition.

Conclusions

The prolonged heat stress resulted in a reduced antioxidant capacity while the role of antioxidant capacity in a prolonged thermotolerance of water spinach was not predominant. Transcriptome analysis and the measurement of carbohydrates as well as the gene expression evaluation indicated that the response of the metabolic pathway such as carbohydrate and phenylpropanoid biosynthesis to heat stress may be a key player in thermo resistance.

Exogenous phosphite application alleviates the adverse effects of heat stress and improves thermotolerance of potato (Solanum tuberosum L.) seedlings

Phosphite (Phi), an analog of phosphate (Pi) anion, is emerging as a potential biostimulator, fungicide and insecticide. Here, we reported that Phi also significantly enhanced thermotolerance in potatoes under heat stress. Potato plants with and without Phi pretreatment were exposed to heat stress and their heat tolerance was examined by assessing the morphological characteristics, photosynthetic pigment content, photosystem II (PS II) efficiency, levels of oxidative stress, and level of DNA damage. In addition, RNA-sequencing (RNA-Seq) was adopted to investigate the roles of Phi signals and the underlying heat resistance mechanism. RNA-Seq revealed that Phi orchestrated plant immune responses against heat stress by reprograming global gene expressions. Results from physiological data combined with RNA-Seq suggested that the supply of Phi not only was essential for the better plant performance, but also improved thermotolerance of the plants by alleviating oxidative stress and DNA damage, and improved biosynthesis of osmolytes and defense metabolites when exposed to unfavorable thermal conditions. This is the first study to explore the role of Phi in thermotolerance in plants, and the work can be applied to other crops under the challenging environment.

Comparative transcriptome analyses of genes involved in sulforaphane metabolism at different treatment in Chinese kale using full-length transcriptome sequencing

Background

Sulforaphane is a natural isothiocyanate available from cruciferous vegetables with multiple characteristics including antioxidant, antitumor and anti-inflammatory effect. Single-molecule real-time (SMRT) sequencing has been used for long-read de novo assembly of plant genome. Here, we investigated the molecular mechanism related to glucosinolates biosynthesis in Chinese kale using combined NGS and SMRT sequencing.

Results

SMRT sequencing produced 185,134 unigenes, higher than 129,325 in next-generation sequencing (NGS). NaCl (75 mM), methyl jasmonate (MeJA, 40 μM), selenate (Se, sodium selenite 100 μM), and brassinolide (BR, 1.5 μM) treatment induced 6893, 13,287, 13,659 and 11,041 differentially expressed genes (DEGs) in Chinese kale seedlings comparing with control. These genes were associated with pathways of glucosinolates biosynthesis, including phenylalanine, tyrosine and tryptophan biosynthesis, cysteine and methionine metabolism, and glucosinolate biosynthesis. We found NaCl decreased sulforaphane and glucosinolates (indolic and aliphatic) contents and downregulated expression of cytochrome P45083b1 (CYP83b1), S-alkyl-thiohydroximatelyase or carbon–sulfur lyase (SUR1) and UDP-glycosyltransferase 74B1 (UGT74b1). MeJA increased sulforaphane and glucosinolates contents and upregulated the expression of CYP83b1, SUR1 and UGT74b1; Se increased sulforaphane; BR increased expression of CYP83b1, SUR1 and UGT74b1, and increased glucosinolates contents. The desulfoglucosinolate sulfotransferases ST5a_b_c were decreased by all treatments.

Conclusions

We confirmed that NaCl inhibited the biosynthesis of both indolic and aliphatic glucosinolates, while MeJA and BR increased them. MeJA and BR treatments, conferred the biosynthesis of glucosinolates, and Se and MeJA contributed to sulforaphane in Chinese kale via regulating the expression of CYP83b1, SUR1 and UGT74b1.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5758-2) contains supplementary material, which is available to authorized users.

Comparative transcriptome analyses revealed different heat stress responses in high- and low-GS Brassica alboglabra sprouts

Background

Chinese kale (Brassica alboglabra) contains high nutritional elements and functional molecules, especially anticarcinogenic and antioxidant glucosinolates (GS), which was highly affected by environment temperature. To investigate the link of GS biosynthesis with heat stress response in Chinese kale, global transcription profiles of high-GS line (HG), low-GS line (LG), high-GS line under heat stress (HGT) and low-GS line under heat stress (LGT) were analyzed.

Results

Based on three biological replicates of each RNA sequencing data, 3901, 4062 and 2396 differentially expressed genes in HG vs HGT, LG vs LGT and HGT vs LGT were obtained, respectively. GO annotation, KEGG pathway analysis and a comprehensive analysis of DEGs showed a strong correlation between the GS biosynthesis and heat stress response. It was noticed that 11 differentially expressed genes tied to the GS biosynthesis were down-regulated, 23 heat shock transcription factors and 61 heat shock proteins were up-regulated upon the heat treatment. Another two Chinese kale varieties Cuibao and Shunbao with high- and low- GS content respectively, were used to validate the relationship of GS content and heat-response, and the results showed that high-GS content variety were more thermotolerant than the low-GS content one although GS significantly decreased in both varieties under heat stress. In addition, HSP100/ClpB, HSP90, HSP70 and sHSPs were differentially expressed in high- and low-GS varieties. Notably, HSP90 and sHSPs showed an obviously early response to heat stress than other related genes.

Conclusion

The higher heat resistance of high-GS Chinese kale and the sharp decrease of glucosinolate content under heat stress indicated a strong relationship of GS accumulation and heat stress response. Combined with the previous report on the low expression of HSP90 at elevated temperatures in GS-deficient mutant TU8 of Arabidopsis, the differential expression pattern of HSP90 in high- and low- GS varieties and its early heat response implied it might be a key regulator in GS metabolism and heat-resistance in Chinese kale.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5652-y) contains supplementary material, which is available to authorized users.

Comparative Transcriptome Analyses Reveal Potential Mechanisms of Enhanced Drought Tolerance in Transgenic Salvia Miltiorrhiza Plants Expressing AtDREB1A from Arabidopsis

In our previous study, drought-resistant transgenic plants of Salvia miltiorrhiza were produced via overexpression of the transcription factor AtDREB1A. To unravel the molecular mechanisms underpinning elevated drought tolerance in transgenic plants, in the present study we compared the global transcriptional profiles of wild-type (WT) and AtDREB1A-expressing transgenic plants using RNA-sequencing (RNA-seq). Using cluster analysis, we identified 3904 differentially expressed genes (DEGs). Compared with WT plants, 423 unigenes were up-regulated in pRD29A::AtDREB1A-31 before drought treatment, while 936 were down-regulated and 1580 and 1313 unigenes were up- and down-regulated after six days of drought. COG analysis revealed that the 'signal transduction mechanisms' category was highly enriched among these DEGs both before and after drought stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation, DEGs associated with "ribosome", "plant hormone signal transduction", photosynthesis", "plant-pathogen interaction", "glycolysis/gluconeogenesis" and "carbon fixation" are hypothesized to perform major functions in drought resistance in AtDREB1A-expressing transgenic plants. Furthermore, the number of DEGs associated with different transcription factors increased significantly after drought stress, especially the AP2/ERF, bZIP and MYB protein families. Taken together, this study substantially expands the transcriptomic information for S. miltiorrhiza and provides valuable clues for elucidating the mechanism of AtDREB1A-mediated drought tolerance in transgenic plants.

Enhancement Of Glucosinolate and Isothiocyanate Profiles in Brassicaceae Crops: Addressing Challenges in Breeding for Cultivation, Storage, and Consumer-Related Traits

Glucosinolates (GSLs) and isothiocyanates (ITCs) produced by Brassicaceae plants are popular targets for analysis due to the health benefits associated with them. Breeders aim to increase the concentrations in commercial varieties; however, there are few examples of this. The most well-known is Beneforté broccoli, which has increased glucoraphanin/sulforaphane concentrations compared to those of conventional varieties. It was developed through traditional breeding methods with considerations for processing, consumption, and health made throughout this process. Many studies presented in the literature do not take a holistic approach, and key points about breeding, cultivation methods, postharvest storage, sensory attributes, and consumer preferences are not properly taken into account. In this review, we draw together data for multiple species and address how such factors can influence GSL profiles. We encourage researchers and institutions to engage with industry and consumers to produce research that can be utilized in the improvement of Brassicaceae crops.

Understanding of MYB Transcription Factors Involved in Glucosinolate Biosynthesis in Brassicaceae

Glucosinolates (GSLs) are widely known secondary metabolites that have anticarcinogenic and antioxidative activities in humans and defense roles in plants of the Brassicaceae family. Some R2R3-type MYB (myeloblastosis) transcription factors (TFs) control GSL biosynthesis in Arabidopsis. However, studies on the MYB TFs involved in GSL biosynthesis in Brassica species are limited because of the complexity of the genome, which includes an increased number of paralog genes as a result of genome duplication. The recent completion of the genome sequencing of the Brassica species permits the identification of MYB TFs involved in GSL biosynthesis by comparative genome analysis with A. thaliana. In this review, we describe various findings on the regulation of GSL biosynthesis in Brassicaceae. Furthermore, we identify 63 orthologous copies corresponding to five MYB TFs from Arabidopsis, except MYB76 in Brassica species. Fifty-five MYB TFs from the Brassica species possess a conserved amino acid sequence in their R2R3 MYB DNA-binding domain, and share close evolutionary relationships. Our analysis will provide useful information on the 55 MYB TFs involved in the regulation of GSL biosynthesis in Brassica species, which have a polyploid genome.