MYB34, MYB51, and MYB122 distinctly regulate indolic glucosinolate biosynthesis in Arabidopsis thaliana

MYB24, MYB144, and MYB168 positively regulate suberin biosynthesis at potato tuber wounds during healing

The essence of wound healing is the accumulation of suberin at wounds, which is formed by suberin polyphenolic (SPP) and suberin polyaliphatic (SPA). The biosynthesis of SPP and SPA monomers is catalyzed by several enzyme classes related to phenylpropanoid metabolism and fatty acid metabolism, respectively. However, how suberin biosynthesis is regulated at the transcriptional level during potato (Solanum tuberosum) tuber wound healing remains largely unknown. Here, 6 target genes and 15 transcription factors related to suberin biosynthesis in tuber wound healing were identified by RNA-seq technology and qRT-PCR. Dual luciferase and yeast one-hybrid assays showed that StMYB168 activated the target genes StPAL, StOMT, and St4CL in phenylpropanoid metabolism. Meanwhile, StMYB24 and StMYB144 activated the target genes StLTP, StLACS, and StCYP in fatty acid metabolism, and StFHT involved in the assembly of SPP and SPA domains in both native and wound periderms. More importantly, virus-induced gene silencing in S. tuberosum and transient overexpression in Nicotiana benthamiana assays confirmed that StMYB168 regulates the biosynthesis of free phenolic acids, such as ferulic acid. Furthermore, StMYB24/144 regulated the accumulation of suberin monomers, such as ferulates, α, ω-diacids, and ω-hydroxy acids. In conclusion, StMYB24, StMYB144, and StMYB168 have an elaborate division of labor in regulating the synthesis of suberin during tuber wound healing.

Gene regulatory networks underlying sulfate deficiency responses in plants

Sulfur (S) is an essential macronutrient for plants and its availability in soils is an important determinant for growth and development. Current regulatory policies aimed at reducing industrial S emissions together with changes in agronomical practices have led to a decline in S contents in soils worldwide. Deficiency of sulfate-the primary form of S accessible to plants in soil-has adverse effects on both crop yield and nutritional quality. Hence, recent research has increasingly focused on unraveling the molecular mechanisms through which plants detect and adapt to a limiting supply of sulfate. A significant part of these studies involves the use of omics technologies and has generated comprehensive catalogs of sulfate deficiency-responsive genes and processes, principally in Arabidopsis together with a few studies centering on crop species such as wheat, rice, or members of the Brassica genus. Although we know that sulfate deficiency elicits an important reprogramming of the transcriptome, the transcriptional regulators orchestrating this response are not yet well understood. In this review, we summarize our current knowledge of gene expression responses to sulfate deficiency and recent efforts towards the identification of the transcription factors that are involved in controlling these responses. We further compare the transcriptional response and putative regulators between Arabidopsis and two important crop species, rice and tomato, to gain insights into common mechanisms of the response to sulfate deficiency.

The RNA-Binding Protein BoRHON1 Positively Regulates the Accumulation of Aliphatic Glucosinolates in Cabbage

Aliphatic glucosinolates are an abundant group of plant secondary metabolites in Brassica vegetables, with some of their degradation products demonstrating significant anti-cancer effects. The transcription factors MYB28 and MYB29 play key roles in the transcriptional regulation of aliphatic glucosinolates biosynthesis, but little is known about whether BoMYB28 and BoMYB29 are also modulated by upstream regulators or how, nor their gene regulatory networks. In this study, we first explored the hierarchical transcriptional regulatory networks of MYB28 and MYB29 in a model plant, then systemically screened the regulators of the three BoMYB28 homologs in cabbage using a yeast one-hybrid. Furthermore, we selected a novel RNA binding protein, BoRHON1, to functionally validate its roles in modulating aliphatic glucosinolates biosynthesis. Importantly, BoRHON1 induced the accumulation of all detectable aliphatic and indolic glucosinolates, and the net photosynthetic rates of BoRHON1 overexpression lines were significantly increased. Interestingly, the growth and biomass of these overexpression lines of BoRHON1 remained the same as those of the control plants. BoRHON1 was shown to be a novel, potent, positive regulator of glucosinolates biosynthesis, as well as a novel regulator of normal plant growth and development, while significantly increasing plants' defense costs.

Functional studies of plant transcription factors and their relevance in the plant root-knot nematode interaction

Root-knot nematodes are polyphagous parasitic nematodes that cause severe losses in the agriculture worldwide. They enter the root in the elongation zone and subtly migrate to the root meristem where they reach the vascular cylinder and establish a feeding site called gall. Inside the galls they induce a group of transfer cells that serve to nurture them along their parasitic stage, the giant cells. Galls and giant cells develop through a process of post-embryogenic organogenesis that involves manipulating different genetic regulatory networks within the cells, some of them through hijacking some molecular transducers of established plant developmental processes, such as lateral root formation or root regeneration. Galls/giant cells formation involves different mechanisms orchestrated by the nematode´s effectors that generate diverse plant responses in different plant tissues, some of them include sophisticated mechanisms to overcome plant defenses. Yet, the plant-nematode interaction is normally accompanied to dramatic transcriptomic changes within the galls and giant cells. It is therefore expected a key regulatory role of plant-transcription factors, coordinating both, the new organogenesis process induced by the RKNs and the plant response against the nematode. Knowing the role of plant-transcription factors participating in this process becomes essential for a clear understanding of the plant-RKNs interaction and provides an opportunity for the future development and design of directed control strategies. In this review, we present the existing knowledge of the TFs with a functional role in the plant-RKN interaction through a comprehensive analysis of current scientific literature and available transcriptomic data.

Genome-Wide Analysis of MYB Gene Family in Chrysanthemum ×morifolium Provides Insights into Flower Color Regulation

MYBs constitute the second largest transcription factor (TF) superfamily in flowering plants with substantial structural and functional diversity, which have been brought into focus because they affect flower colors by regulating anthocyanin biosynthesis. Up to now, the genomic data of several Chrysanthemum species have been released, which provides us with abundant genomic resources for revealing the evolution of the MYB gene family in Chrysanthemum species. In the present study, comparative analyses of the MYB gene family in six representative species, including C. lavandulifolium, C. seticuspe, C. ×morifolium, Helianthus annuus, Lactuca sativa, and Arabidopsis thaliana, were performed. A total of 1104 MYBs, which were classified into four subfamilies and 35 lineages, were identified in the three Chrysanthemum species (C. lavandulifolium, C. seticuspe, and C. ×morifolium). We found that whole-genome duplication and tandem duplication are the main duplication mechanisms that drove the occurrence of duplicates in CmMYBs (particularly in the R2R3-MYB subfamily) during the evolution of the cultivated chrysanthemums. Sequence structure and selective pressure analyses of the MYB gene family revealed that some of R2R3-MYBs were subjected to positive selection, which are mostly located on the distal telomere segments of the chromosomes and contain motifs 7 and 8. In addition, the gene expression analysis of CmMYBs in different organs and at various capitulum developmental stages of C. ×morifolium indicated that CmMYBS2, CmMYB96, and CmMYB109 might be the negative regulators for anthocyanin biosynthesis. Our results provide the phylogenetic context for research on the genetic and functional evolution of the MYB gene family in Chrysanthemum species and deepen our understanding of the regulatory mechanism of MYB TFs on the flower color of C. ×morifolium.

Sulfate Availability and Hormonal Signaling in the Coordination of Plant Growth and Development

Sulfur (S), one of the crucial macronutrients, plays a pivotal role in fundamental plant processes and the regulation of diverse metabolic pathways. Additionally, it has a major function in plant protection against adverse conditions by enhancing tolerance, often interacting with other molecules to counteract stresses. Despite its significance, a thorough comprehension of how plants regulate S nutrition and particularly the involvement of phytohormones in this process remains elusive. Phytohormone signaling pathways crosstalk to modulate growth and developmental programs in a multifactorial manner. Additionally, S availability regulates the growth and development of plants through molecular mechanisms intertwined with phytohormone signaling pathways. Conversely, many phytohormones influence or alter S metabolism within interconnected pathways. S metabolism is closely associated with phytohormones such as abscisic acid (ABA), auxin (AUX), brassinosteroids (BR), cytokinins (CK), ethylene (ET), gibberellic acid (GA), jasmonic acid (JA), salicylic acid (SA), and strigolactones (SL). This review provides a summary of the research concerning the impact of phytohormones on S metabolism and, conversely, how S availability affects hormonal signaling. Although numerous molecular details are yet to be fully understood, several core signaling components have been identified at the crossroads of S and major phytohormonal pathways.

Analyzing the Diversity of MYB Family Response Strategies to Drought Stress in Different Flax Varieties Based on Transcriptome Data

The MYB transcription factor family has numerous members, and is involved in biological activities, such as ABA signaling, which plays an important role in a plant's resistance to abiotic stresses such as drought. However, the diversity of MYB members that respond to drought stress and their regulatory mechanisms in different flax varieties were unclear. In this study, we obtained 855.69 Gb of clean data from 120 flax root samples from 20 flax (Linum usitatissimum L.) varieties, assembled 92,861 transcripts, and identified 434 MYB family members in each variety. The expression profiles of the MYB transcription factor family from 20 flax varieties under drought stress were analyzed. The results indicated that there are four strategies by which the MYB family responds to drought stress in these 20 flax varieties, each of which has its own specific processes, such as development, reproduction, and localization processes. The four strategies also include common biological processes, such as stimulus responses, metabolic processes, and biological regulation. The WGCNA method was subsequently employed to identify key members of the MYB family involved in response strategies to drought stress. The results demonstrated that a 1R-MYB subfamily gene co-expression network is significantly related to the gibberellin response and cytokinin-activated signaling pathway processes in the 'Strategy 4' for MYB family response to drought, identifying core genes such as Lus.scaffold70.240. Our results showed a diversity of MYB family responses to drought stress within flax varieties, and these results contribute to deciphering the mechanisms of the MYB family regulation of drought resistance. This will promote the more accurate breeding development of flax to adapt to agricultural production under drought conditions.

Interplay between secondary metabolites and plant hormones in silver nitrate-elicited Arabidopsis thaliana plants

Plants produce a myriad of specialized compounds in response to threats such as pathogens or pests and different abiotic factors. The stress-related induction of specialized metabolites can be mimicked using silver nitrate (AgNO3) as an elicitor, which application in conservation agriculture has gained interest. In Arabidopsis thaliana, AgNO3 triggers the accumulation of indole glucosinolates (IGs) and the phytoalexin camalexin as well as pheylpropanoid-derived defensive metabolites such as coumaroylagmatins and scopoletin through a yet unknown mechanism. In this work, the role of jasmonic (JA) and salicylic acid (SA) signaling in the AgNO3-triggered specialized metabolite production was investigated. To attain this objective, AgNO3, MeJA and SA were applied to A. thaliana lines impaired in JA or SA signaling, or affected in the endogenous levels of IGs and AGs. Metabolomics data indicated that AgNO3 elicitation required an intact JA and SA signaling to elicit the metabolic response, although mutants impaired in hormone signaling retained certain capacity to induce specialized metabolites. In turn, plants overproducing or abolishing IGs production had also an altered hormonal signaling response, both in the accumulation of signaling molecules and the molecular response mechanisms (ORA59, PDF1.2, VSP2 and PR1 gene expression), which pointed out to a crosstalk between defense hormones and specialized metabolites. The present work provides evidence of a crosstalk mechanism between JA and SA underlying AgNO3 defense metabolite elicitation in A. thaliana. In this mechanism, IGs would act as retrograde feedback signals dampening the hormonal response; hence, expanding the signaling molecule concept.

MicroRNAs constitute an additional layer in plant response to simultaneous bio- and abiotic stresses as exemplified by UV-B radiation and flg22-treatment on Arabidopsis thaliana

Plants are confronted with various environmental stresses and develop sophisticated adaptive mechanisms. Our previous work demonstrated that the crosstalk of flg22 and ultraviolet (UV)-B-induced signalling cascades reprograms the expression of flavonol pathway genes (FPGs), benefiting plant defence responses. Although several transcription factors have been identified to be involved in this crosstalk, the underlying mechanism is largely unclear. Here, we analyzed microRNAs (miRNAs) and identified 126, 129 and 113 miRNAs with altered abundances compared to untreated control in flg22-, UV-B- and flg22/UV-B-treated seedlings, respectively. Two distinct modules were identified: The first consists of 10 miRNAs repressed by UV-B but up-regulated by flg22, and the second with five miRNAs repressed by flg22 but up-regulated by UV-B. In Arabidopsis, the knockdown of miR858a, a representative of module I, increased the abundance of CHS (a marker gene for FPGs), whereas its overexpression reduced CHS. Conversely, knockout of miR164b from module II decreased CHS and its overexpression increased CHS transcript levels. These data suggest a decisive role of miRNAs in the crosstalk. In the next, we described the interaction between miR858a and its target MYB111 (a positive regulator of FPGs) from module I in detail. We showed that MYB111 was profoundly post-transcriptionally regulated by miR858a during the crosstalk, whose expression was specifically but antagonistically controlled by UVR8- and FLS2-mediated signallings. Moreover, transcriptional monitoring using the GUS reporter gene demonstrates that miRNA-mediated posttranscriptional regulation is the main driving force in reprogramming the expression of FPGs and regulates plant adaptation to multiple concurrent environmental stresses.

AtRAC7/ROP9 Small GTPase Regulates A. thaliana Immune Systems in Response to B. cinerea Infection

Botrytis cinerea is a necrotrophic fungus that can cause gray mold in over 1400 plant species. Once it is detected by Arabidopsis thaliana, several defense responses are activated against this fungus. The proper activation of these defenses determines plant susceptibility or resistance. It has been proposed that the RAC/ROP small GTPases might serve as a molecular link in this process. In this study, we investigate the potential role of the Arabidopsis RAC7 gene during infection with B. cinerea. For that, we evaluated A. thaliana RAC7-OX lines, characterized by the overexpression of the RAC7 gene. Our results reveal that these RAC7-OX lines displayed increased susceptibility to B. cinerea infection, with enhanced fungal colonization and earlier lesion development. Additionally, they exhibited heightened sensitivity to bacterial infections caused by Pseudomonas syringae and Pectobacterium brasiliense. By characterizing plant canonical defense mechanisms and performing transcriptomic profiling, we determined that RAC7-OX lines impaired the plant transcriptomic response before and during B. cinerea infection. Global pathway analysis of differentially expressed genes suggested that RAC7 influences pathogen perception, cell wall homeostasis, signal transduction, and biosynthesis and response to hormones and antimicrobial compounds through actin filament modulation. Herein, we pointed out, for first time, the negative role of RAC7 small GTPase during A. thaliana-B. cinerea interaction.

ER body-resident myrosinases and tryptophan specialized metabolism modulate root microbiota assembly

Endoplasmic reticulum (ER) bodies are ER-derived structures that contain a large amount of PYK10 myrosinase, which hydrolyzes tryptophan (Trp)-derived indole glucosinolates (IGs). Given the well-described role of IGs in root-microbe interactions, we hypothesized that ER bodies in roots are important for interaction with soil-borne microbes at the root-soil interface. We used mutants impaired in ER bodies (nai1), ER body-resident myrosinases (pyk10bglu21), IG biosynthesis (myb34/51/122), and Trp specialized metabolism (cyp79b2b3) to profile their root microbiota community in natural soil, evaluate the impact of axenically collected root exudates on soil or synthetic microbial communities, and test their response to fungal endophytes in a mono-association setup. Tested mutants exhibited altered bacterial and fungal communities in rhizoplane and endosphere, respectively. Natural soils and bacterial synthetic communities treated with mutant root exudates exhibited distinctive microbial profiles from those treated with wild-type (WT) exudates. Most tested endophytes severely restricted the growth of cyp79b2b3, a part of which also impaired the growth of pyk10bglu21. Our results suggest that root ER bodies and their resident myrosinases modulate the profile of root-secreted metabolites and thereby influence root-microbiota interactions.

Large-scale identification of novel transcriptional regulators of the aliphatic glucosinolate pathway in Arabidopsis

Aliphatic glucosinolates are a large group of plant secondary metabolites characteristic of Brassicaceae, including the model plant Arabidopsis. The diverse and complex degradation products of aliphatic glucosinolates contribute to plant responses to herbivory, pathogen attack, and environmental stresses. Most of the biosynthesis genes in the aliphatic glucosinolate pathway have been cloned in Arabidopsis, and the research focus has recently shifted to the regulatory mechanisms controlling aliphatic glucosinolate accumulation. Up till now, more than 40 transcriptional regulators have been identified as regulating the aliphatic glucosinolate pathway, but many more novel regulators likely remain to be discovered based on research evidence over the past decade. In the current study, we took a systemic approach to functionally test 155 candidate transcription factors in Arabidopsis identified by yeast one-hybrid assay, and successfully validated at least 30 novel regulators that could significantly influence the accumulation of aliphatic glucosinolates in our experimental set-up. We also showed that the regulators of the aliphatic glucosinolate pathway have balanced positive and negative effects, and glucosinolate metabolism and plant development can be coordinated. Our work is the largest scale effort so far to validate transcriptional regulators of a plant secondary metabolism pathway, and provides new insights into how the highly diverse plant secondary metabolism is regulated at the transcriptional level.

Glucosinolate O-methyltransferase mediated callus formation and affected ROS homeostasis in Arabidopsis thaliana

Auxin-induced callus formation was largely dependent on the function of Lateral Organ Boundaries Domain (LBD) family transcription factors. We previously revealed that two IGMT (Indole glucosinolate oxy-methyl transferase) genes, IGMT2 and IGMT3, may be involved in the callus formation process as potential target genes of LBD29. Overexpression of the IGMT genes induces spontaneous callus formation. However, the details of the IGMT involvement in callus formation process were not well studied. IGMT1-4, but not IGMT5, are targeted and induced by LBD29 during the early stage of callus formation. Cell membrane and nucleus localized IGMT3 was mainly expressed in the elongation and maturation zones tissues of the primary root and lateral root, which could be further accumulated after CIM treatment. The igmts quadruple mutant, which obtained by CRISPR/Cas9 technology, exhibits a phenotype of attenuated callus formation. Enhanced indole glucosinolate anabolic pathway caused by IGMT1-4 overexpression promotes callus formation. In addition, the IGMT genes were involved in the reactive oxygen species homeostasis, which could be responsible for its role on callus formation. This study provides novel insights into the role of IGMTs gene-mediated callus formation. Activation of the Indole glucosinolate anabolic pathway is an inducing factor for plant callus initiation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01409-2.

Transcriptome Dynamics of Brassica juncea Leaves in Response to Omnivorous Beet Armyworm (Spodoptera exigua, Hübner)

Cruciferous plants manufacture glucosinolates (GSLs) as special and important defense compounds against insects. However, how insect feeding induces glucosinolates in Brassica to mediate insect resistance, and how plants regulate the strength of anti-insect defense response during insect feeding, remains unclear. Here, mustard (Brassica juncea), a widely cultivated Brassica plant, and beet armyworm (Spodoptera exigua), an economically important polyphagous pest of many crops, were used to analyze the changes in GSLs and transcriptome of Brassica during insect feeding, thereby revealing the plant-insect interaction in Brassica plants. The results showed that the content of GSLs began to significantly increase after 48 h of herbivory by S. exigua, with sinigrin as the main component. Transcriptome analysis showed that a total of 8940 DEGs were identified in mustard challenged with beet armyworm larvae. The functional enrichment results revealed that the pathways related to the biosynthesis of glucosinolate and jasmonic acid were significantly enriched by upregulated DEGs, suggesting that mustard might provide a defense against herbivory by inducing JA biosynthesis and then promoting GSL accumulation. Surprisingly, genes regulating JA catabolism and inactivation were also activated, and both JA signaling repressors (JAZs and JAMs) and activators (MYCs and NACs) were upregulated during herbivory. Taken together, our results indicate that the accumulation of GSLs regulated by JA signaling, and the regulation of active and inactive JA compound conversion, as well as the activation of JA signaling repressors and activators, collectively control the anti-insect defense response and avoid over-stunted growth in mustard during insect feeding.

Light regulation of the biosynthesis of phenolics, terpenoids, and alkaloids in plants

Biosynthesis of specialized metabolites (SM), including phenolics, terpenoids, and alkaloids, is stimulated by many environmental factors including light. In recent years, significant progress has been made in understanding the regulatory mechanisms involved in light-stimulated SM biosynthesis at the transcriptional, posttranscriptional, and posttranslational levels of regulation. While several excellent recent reviews have primarily focused on the impacts of general environmental factors, including light, on biosynthesis of an individual class of SM, here we highlight the regulation of three major SM biosynthesis pathways by light-responsive gene expression, microRNA regulation, and posttranslational modification of regulatory proteins. In addition, we present our future perspectives on this topic.

Cell-type-specific responses to fungal infection in plants revealed by single-cell transcriptomics

Pathogen infection is a dynamic process. Here, we employ single-cell transcriptomics to investigate plant response heterogeneity. By generating an Arabidopsis thaliana leaf atlas encompassing 95,040 cells during infection by a fungal pathogen, Colletotrichum higginsianum, we unveil cell-type-specific gene expression, notably an enrichment of intracellular immune receptors in vasculature cells. Trajectory inference identifies cells that had different interactions with the invading fungus. This analysis divulges transcriptional reprogramming of abscisic acid signaling specifically occurring in guard cells, which is consistent with a stomatal closure dependent on direct contact with the fungus. Furthermore, we investigate the transcriptional plasticity of genes involved in glucosinolate biosynthesis in cells at the fungal infection sites, emphasizing the contribution of the epidermis-expressed MYB122 to disease resistance. This work underscores spatially dynamic, cell-type-specific plant responses to a fungal pathogen and provides a valuable resource that supports in-depth investigations of plant-pathogen interactions.

Diversification of JAZ-MYC signaling function in immune metabolism

Jasmonate (JA) re-programs metabolism to confer resistance to diverse environmental threats. Jasmonate stimulates the degradation of JASMONATE ZIM-DOMAIN (JAZ) proteins that repress the activity of MYC transcription factors. In Arabidopsis thaliana, MYC and JAZ are encoded by 4 and 13 genes, respectively. The extent to which expansion of the MYC and JAZ families has contributed to functional diversification of JA responses is not well understood. Here, we investigated the role of MYC and JAZ paralogs in controlling the production of defense compounds derived from aromatic amino acids (AAAs). Analysis of loss-of-function and dominant myc mutations identified MYC3 and MYC4 as the major regulators of JA-induced tryptophan metabolism. We developed a JAZ family-based, forward genetics approach to screen randomized jaz polymutants for allelic combinations that enhance tryptophan biosynthetic capacity. We found that mutants defective in all members (JAZ1/2/5/6) of JAZ group I over-accumulate AAA-derived defense compounds, constitutively express marker genes for the JA-ethylene branch of immunity and are more resistant to necrotrophic pathogens but not insect herbivores. In defining JAZ and MYC paralogs that regulate the production of amino-acid-derived defense compounds, our results provide insight into the specificity of JA signaling in immunity.

Blue Light Enhances Health-Promoting Sulforaphane Accumulation in Broccoli (Brassica oleracea var. italica) Sprouts through Inhibiting Salicylic Acid Synthesis

As a vegetable with high nutritional value, broccoli (Brassica oleracea var. italica) is rich in vitamins, antioxidants and anti-cancer compounds. Glucosinolates (GLs) are one of the important functional components widely found in cruciferous vegetables, and their hydrolysate sulforaphane (SFN) plays a key function in the anti-cancer process. Herein, we revealed that blue light significantly induced the SFN content in broccoli sprouts, and salicylic acid (SA) was involved in this process. We investigated the molecular mechanisms of SFN accumulation with blue light treatment in broccoli sprouts and the relationship between SFN and SA. The results showed that the SFN accumulation in broccoli sprouts was significantly increased under blue light illumination, and the expression of SFN synthesis-related genes was particularly up-regulated by SA under blue light. Moreover, blue light considerably decreased the SA content compared with white light, and this decrease was more suppressed by paclobutrazol (Pac, an inhibitor of SA synthesis). In addition, the transcript level of SFN synthesis-related genes and the activity of myrosinase (MYR) paralleled the trend of SFN accumulation under blue light treatment. Overall, we concluded that SA participates in the SFN accumulation in broccoli sprouts under blue light.

LED Lights Influenced Phytochemical Contents and Biological Activities in Kale (Brassica oleracea L. var. acephala) Microgreens

Light-emitting diodes (LEDs) are regarded as an effective artificial light source for producing sprouts, microgreens, and baby leaves. Thus, this study aimed to investigate the influence of different LED lights (white, red, and blue) on the biosynthesis of secondary metabolites (glucosinolates, carotenoids, and phenolics) and the biological effects on kale microgreens. Microgreens irradiated with white LEDs showed higher levels of carotenoids, including lutein, 13-cis-β-carotene, α-carotene, β-carotene, and 9-cis-β-carotene, than those irradiated with red or blue LEDs. These findings were consistent with higher expression levels of carotenoid biosynthetic genes (BoPDS and BoZDS) in white-irradiated kale microgreens. Similarly, microgreens irradiated with white and blue LEDs showed slightly higher levels of glucosinolates, including glucoiberin, progoitrin, sinigrin, and glucobrassicanapin, than those irradiated with red LEDs. These results agree with the high expression levels of BoMYB28-2, BoMYB28-3, and BoMYB29 in white- and blue-irradiated kale microgreens. In contrast, kale microgreens irradiated with blue LEDs contained higher levels of phenolic compounds (gallic acid, catechin, ferulic acid, sinapic acid, and quercetin). According to the total phenolic content (TPC) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) inhibition assays, the extracts of kale microgreens irradiated with blue LEDs had slightly higher antioxidant activities, and the DPPH inhibition percentage had a positive correlation with TPC in the microgreens. Furthermore, the extracts of kale microgreens irradiated with blue LEDs exhibited stronger antibacterial properties against normal pathogens and multidrug-resistant pathogens than those irradiated with white and red LEDs. These results indicate that white-LED lights are suitable for carotenoid production, whereas blue-LED lights are efficient in increasing the accumulation of phenolics and their biological activities in kale microgreens.

New insights into the regulation of plant metabolism by O-acetylserine: sulfate and beyond

Under conditions of sulfur deprivation, O-acetylserine (OAS) accumulates, which leads to the induction of a common set of six genes, called OAS cluster genes. These genes are induced not only under sulfur deprivation, but also under other conditions where OAS accumulates, such as shift to darkness and stress conditions leading to reactive oxygen species (ROS) or methyl-jasmonate accumulation. Using the OAS cluster genes as a query in ATTED-II, a co-expression network is derived stably spanning several hundred conditions. This allowed us not only to describe the downstream function of the OAS cluster genes but also to score for functions of the members of the co-regulated co-expression network and hence the effects of the OAS signal on the sulfate assimilation pathway and co-regulated pathways. Further, we summarized existing knowledge on the regulation of the OAS cluster and the co-expressed genes. We revealed that the known sulfate deprivation-related transcription factor EIL3/SLIM1 exhibits a prominent role, as most genes are subject to regulation by this transcription factor. The role of other transcription factors in response to OAS awaits further investigation.

The good, the bad, and the phosphate: regulation of beneficial and detrimental plant-microbe interactions by the plant phosphate status

Phosphate (P_i ) is indispensable for life on this planet. However, for sessile land plants it is poorly accessible. Therefore, plants have developed a variety of strategies for enhanced acquisition and recycling of P_i . The mechanisms to cope with P_i limitation as well as direct uptake of P_i from the substrate via the root epidermis are regulated by a conserved P_i starvation response (PSR) system based on a family of key transcription factors (TFs) and their inhibitors. Furthermore, plants obtain P_i indirectly through symbiosis with mycorrhiza fungi, which employ their extensive hyphal network to drastically increase the soil volume that can be explored by plants for P_i . Besides mycorrhizal symbiosis, there is also a variety of other interactions with epiphytic, endophytic, and rhizospheric microbes that can indirectly or directly influence plant P_i uptake. It was recently discovered that the PSR pathway is involved in the regulation of genes that promote formation and maintenance of AM symbiosis. Furthermore, the PSR system influences plant immunity and can also be a target of microbial manipulation. It is known for decades that the nutritional status of plants influences the outcome of plant-microbe interactions. The first molecular explanations for these observations are now emerging.

Brassinosteroids fine-tune secondary and primary sulfur metabolism through BZR1-mediated transcriptional regulation

For adaptation to ever-changing environments, plants have evolved elaborate metabolic systems coupled to a regulatory network for optimal growth and defense. Regulation of plant secondary metabolic pathways such as glucosinolates (GSLs) by defense phytohormones in response to different stresses and nutrient deficiency has been intensively investigated, while how growth-promoting hormone balances plant secondary and primary metabolism has been largely unexplored. Here, we found that growth-promoting hormone brassinosteroid (BR) inhibits GSLs accumulation while enhancing biosynthesis of primary sulfur metabolites, including cysteine (Cys) and glutathione (GSH) both in Arabidopsis and Brassica crops, fine-tuning secondary and primary sulfur metabolism to promote plant growth. Furthermore, we demonstrate that of BRASSINAZOLE RESISTANT 1 (BZR1), the central component of BR signaling, exerts distinct transcriptional inhibition regulation on indolic and aliphatic GSL via direct MYB51 dependent repression of indolic GSL biosynthesis, while exerting partial MYB29 dependent repression of aliphatic GSL biosynthesis. Additionally, BZR1 directly activates the transcription of APR1 and APR2 which encodes rate-limiting enzyme adenosine 5'-phosphosulfate reductases in the primary sulfur metabolic pathway. In summary, our findings indicate that BR inhibits the biosynthesis of GSLs to prioritize sulfur usage for primary metabolites under normal growth conditions. These findings expand our understanding of BR promoting plant growth from a metabolism perspective.

Epigenetic Changes Occurring in Plant Inbreeding

Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.

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.

Genome-wide analysis of MYB family in Nicotiana benthamiana and the functional role of the key members in resistance to Bemisia tabaci

MYB transcription factors (TFs) play a key role in plant resistance to abiotic and biotical stresses. However, little is currently known about their involvement in the plant defense to piercing-sucking insects. Here, we studied the MYB TFs that responded to and resisted Bemisia tabaci whitefly in the model plant Nicotiana benthamiana. Firstly, a total of 453 NbMYB TFs in N. benthamiana genome were identified and 182 R2R3-MYB TFs were analyzed for molecular characteristics, phylogenetic analysis, genetic structure, motif composition, and cis-elements. Then, six stress-related NbMYB genes were selected for further study. The expression pattern shows they were highly expressed in mature leaves and intensively induced upon whitefly attack. Combined with bioinformatic analysis, overexpression, β-Glucuronidase (GUS) assay, and virus-induced silencing tests, we determined the transcriptional regulation of these NbMYBs on the genes in lignin biosynthesis and SA-signaling pathways. Meanwhile, we tested the performance of whitefly on plants with increased or silenced NbMYB genes expression and found that NbMYB42, NbMYB107, NbMYB163, and NbMYB423 were resistant to whitefly. Our results contribute to a comprehensive understanding of the MYB TFs in N. benthamiana. Furthermore, our findings will facilitate further studies on the role of MYB TFs in the interaction between plants and piercing-sucking insects.

AtBBX29 integrates photomorphogenesis and defense responses in Arabidopsis

Light is an environmental signal that modulates plant defenses against attackers. Recent research has focused on the effects of light on defense hormone signaling; however, the connections between light signaling pathways and the biosynthesis of specialized metabolites involved in plant defense have been relatively unexplored. Here, we show that Arabidopsis BBX29, a protein that belongs to the B-Box transcription factor (TF) family, integrates photomorphogenic signaling with defense responses by promoting flavonoid, sinapate and glucosinolate accumulation in Arabidopsis leaves. AtBBX29 transcript levels were up regulated by light, through photoreceptor signaling pathways. Genetic evidence indicated that AtBBX29 up-regulates MYB12 gene expression, a TF known to induce genes related to flavonoid biosynthesis in a light-dependent manner, and MYB34 and MYB51, which encode TFs involved in the regulation of glucosinolate biosynthesis. Thus, bbx29 knockout mutants displayed low expression levels of key genes of the flavonoid biosynthetic pathway, and the opposite was true in BBX29 overexpression lines. In agreement with the transcriptomic data, bbx29 mutant plants accumulated lower levels of kaempferol glucosides, sinapoyl malate, indol-3-ylmethyl glucosinolate (I3M), 4-methylsulfinylbutyl glucosinolate (4MSOB) and 3-methylthiopropyl glucosinolate (3MSP) in rosette leaves compared to the wild-type, and showed increased susceptibility to the necrotrophic fungus Botrytis cinerea and to the herbivore Spodoptera frugiperda. In contrast, BBX29 overexpressing plants displayed increased resistance to both attackers. In addition, we found that AtBBX29 plays an important role in mediating the effects of ultraviolet-B (UV-B) radiation on plant defense against B. cinerea. Taken together, these results suggest that AtBBX29 orchestrates the accumulation of specific light-induced metabolites and regulates Arabidopsis resistance against pathogens and herbivores.

Loss of MYB34 Transcription Factor Supports the Backward Evolution of Indole Glucosinolate Biosynthesis in a Subclade of the Camelineae Tribe and Releases the Feedback Loop in This Pathway in Arabidopsis

Glucosinolates are specialized defensive metabolites characteristic of the Brassicales order. Among them, aliphatic and indolic glucosinolates (IGs) are usually highly abundant in species from the Brassicaceae family. The exceptions this trend are species representing a subclade of the Camelineae tribe, including Capsella and Camelina genera, which have reduced capacity to produce and metabolize IGs. Our study addresses the contribution of specific glucosinolate-related myeloblastosis (MYB) transcription factors to this unprecedented backward evolution of IG biosynthesis. To this end, we performed phylogenomic and functional studies of respective MYB proteins. The obtained results revealed weakened conservation of glucosinolate-related MYB transcription factors, including loss of functional MYB34 protein, in the investigated species. We showed that the introduction of functional MYB34 from Arabidopsis thaliana partially restores IG biosynthesis in Capsella rubella, indicating that the loss of this transcription factor contributes to the backward evolution of this metabolic pathway. Finally, we performed an analysis of the impact of particular myb mutations on the feedback loop in IG biosynthesis, which drives auxin overproduction, metabolic dysregulation and strong growth retardation caused by mutations in IG biosynthetic genes. This uncovered the unique function of MYB34 among IG-related MYBs in this feedback regulation and consequently in IG conservation in Brassicaceae plants.

Genome-Wide Association Study of Glucosinolate Metabolites (mGWAS) in Brassica napus L

Glucosinolates (GSLs) are secondary plant metabolites that are enriched in rapeseed and related Brassica species, and they play important roles in defense due to their anti-nutritive and toxic properties. Here, we conducted a genome-wide association study of six glucosinolate metabolites (mGWAS) in rapeseed, including three aliphatic glucosinolates (m145 gluconapin, m150 glucobrassicanapin and m151 progoitrin), one aromatic glucosinolate (m157 gluconasturtiin) and two indole glucosinolates (m165 indolylmethyl glucosinolate and m172 4-hydroxyglucobrassicin), respectively. We identified 113 candidate intervals significantly associated with these six glucosinolate metabolites. In the genomic regions linked to the mGWAS peaks, 187 candidate genes involved in glucosinolate biosynthesis (e.g., BnaMAM1, BnaGGP1, BnaSUR1 and BnaMYB51) and novel genes (e.g., BnaMYB44, BnaERF025, BnaE2FC, BnaNAC102 and BnaDREB1D) were predicted based on the mGWAS, combined with analysis of differentially expressed genes. Our results provide insight into the genetic basis of glucosinolate biosynthesis in rapeseed and should facilitate marker-based breeding for improved seed quality in Brassica species.

Natural variation and artificial selection at the BnaC2.MYB28 locus modulate Brassica napus seed glucosinolate

The degradation products of glucosinolates (GSLs) greatly lower the nutritional value of rapeseed (Brassica napus) meal; thus, reduction of seed GSL content (SGC) has become an important objective of rapeseed breeding. In our previous study, we finely mapped a major QTL (qGSL-C2) for SGC to a 49-kb collinear region on B. rapa chromosome A2. Here, we experimentally validated that BnaC2.MYB28, encoding an R2R3-MYB transcription factor, is the causal gene of qGSL-C2. BnaC2.MYB28 is a nucleus-localized protein mainly expressed in vegetative tissues. Knockout of BnaC2.MYB28 in the high-SGC parent G120 reduced SGC to a value lower than that in the low-SGC parent ZY50, while overexpression of BnaC2.MYB28 in both parental lines (G120 and ZY50) led to extremely high SGC, indicating that BnaC2.MYB28 acts as a positive regulator of SGC in both parents. Molecular characterization revealed that BnaC2.MYB28 forms a homodimer and specifically interacts with BnaMYC3. Moreover, BnaC2.MYB28 can directly activate the expression of GSL biosynthesis genes. Differential expression abundance resulting from the polymorphic promoter sequences, in combination with the different capability in activating downstream genes involved in aliphatic GSL biosynthesis, caused the functional divergence of BnaC2.MYB28 in SGC regulation between the parents. Natural variation of BnaC2.MYB28 was highly associated with SGC in natural germplasm and has undergone artificial selection in modern low-GSL breeding. This study provides important insights into the core function of BnaC2.MYB28 in regulating SGC and a promising strategy for manipulating SGC in rapeseed.

Ablation of glucosinolate accumulation in the oil crop Camelina sativa by targeted mutagenesis of genes encoding the transporters GTR1 and GTR2 and regulators of biosynthesis MYB28 and MYB29

Camelina sativa is an oil crop with low input costs and resistance to abiotic and biotic stresses. The presence of glucosinolates, plant metabolites with adverse health effects, restricts the use of camelina for human and animal nutrition. Cas9 endonuclease-based targeted mutagenesis of the three homeologs of each of the glucosinolate transporters CsGTR1 and CsGTR2 caused a strong decrease in glucosinolate amounts, highlighting the power of this approach for inactivating multiple genes in a hexaploid crop. Mutagenesis of the three homeologs of each of the transcription factors CsMYB28 and CsMYB29 resulted in the complete loss of glucosinolates, representing the first glucosinolate-free Brassicaceae crop. The oil and protein contents and the fatty acid composition of the csgtr1csgtr2 and csmyb28csmyb29 mutant seeds were not affected. The decrease and elimination of glucosinolates improves the quality of the oil and press cake of camelina, which thus complies with international standards regulating glucosinolate levels for human consumption and animal feeding.

The calcium sensor CBL7 is required for Serendipita indica-induced growth stimulation in Arabidopsis thaliana, controlling defense against the endophyte and K+ homoeostasis in the symbiosis

Calcium is an important second messenger in plants. The activation of Ca²⁺ signalling cascades is critical in the activation of adaptive processes in response to environmental stimuli. Root colonization by the growth promoting endophyte Serendipita indica involves the increase of cytosolic Ca²⁺ levels in Arabidopsis thaliana. Here, we investigated transcriptional changes in Arabidopsis roots during symbiosis with S. indica. RNA-seq profiling disclosed the induction of Calcineurin B-like 7 (CBL7) during early and later phases of the interaction. Consistently, reverse genetic evidence highlighted the functional relevance of CBL7 and tested the involvement of a CBL7-CBL-interacting protein kinase 13 signalling pathway. The loss-of-function of CBL7 abolished the growth promoting effect and affected root colonization. The transcriptomics analysis of cbl7 revealed the involvement of this Ca²⁺ sensor in activating plant defense responses. Furthermore, we report on the contribution of CBL7 to potassium transport in Arabidopsis. We analysed K⁺ contents in wild-type and cbl7 plants and observed a significant increase of K⁺ in roots of cbl7 plants, while shoot tissues demonstrated K⁺ depletion. Taken together, our work associates CBL7 with an important role in the mutual interaction between Arabidopsis and S. indica and links CBL7 to K⁺ transport.

Acoustic radiation force on a long cylinder, and potential sound transduction by tomato trichomes

Acoustic transduction by plants has been proposed as a mechanism to enable just-in-time up-regulation of metabolically expensive defensive compounds. Although the mechanisms by which this "hearing" occurs are unknown, mechanosensation by elongated plant hair cells known as trichomes is suspected. To evaluate this possibility, we developed a theoretical model to evaluate the acoustic radiation force that an elongated cylinder can receive in response to sounds emitted by animals, including insect herbivores, and applied it to the long, cylindrical stem trichomes of the tomato plant Solanum lycopersicum. Based on perturbation theory and validated by finite element simulations, the model quantifies the effects of viscosity and frequency on this acoustic radiation force. Results suggest that acoustic emissions from certain animals, including insect herbivores, may produce acoustic radiation force sufficient to trigger stretch-activated ion channels.

Jasmonate regulates plant resistance to Pectobacterium brasiliense by inducing indole glucosinolate biosynthesis

Pectobacterium brasiliense (P. brasiliense) is a necrotrophic bacterium that causes the soft rot disease in Brassica rapa. However, the mechanisms underlying plant immune responses against necrotrophic bacterial pathogens with a broad host range are still not well understood. Using a flg22-triggered seedling growth inhibition (SGI) assay with 455 Brassica rapa inbred lines, we selected six B. rapa flagellin-insensitive lines (Brfin2-7) and three B. rapa flagellin-sensitive lines (Brfs1-3). Brfin lines showed compromised flg22-induced immune responses (oxidative burst, mitogen-activated protein kinase (MAPK) activation, and seedling growth inhibition) compared to the control line R-o-18; nevertheless, they were resistant to P. brasiliense. To explain this, we analyzed the phytohormone content and found that most Brfin lines had higher P. brasiliense-induced jasmonic acid (JA) than Brfs lines. Moreover, MeJA pretreatment enhanced the resistance of B. rapa to P. brasiliense. To explain the correlation between the resistance of Brfin lines to P. brasiliense and activated JA signaling, we analyzed pathogen-induced glucosinolate (GS) content in B. rapa. Notably, in Brfin7, the neoglucobrassicin (NGBS) content among indole glucosinolates (IGS) was significantly higher than that in Brfs2 following P. brasiliense inoculation, and genes involved in IGSs biosynthesis were also highly expressed. Furthermore, almost all Brfin lines with high JA levels and resistance to P. brasiliense had higher P. brasiliense-induced NGBS levels than Brfs lines. Thus, our results show that activated JA-mediated signaling attenuates flg22-triggered immunity but enhances resistance to P. brasiliense by inducing indole glucosinolate biosynthesis in Brassica rapa. This study provides novel insights into the role of JA-mediated defense against necrotrophic bacterial pathogens within a broad host range.

Production of benzylglucosinolate in genetically engineered carrot suspension cultures

Glucosinolates, a group of sulfur-containing specialized metabolites of the Brassicales, have attracted a lot of interest in nutrition, medicine and agriculture due to their positive health effects and their involvement in plant defense. Their biological activities and the extensive knowledge of their biosynthesis have inspired research into development of crops with enhanced glucosinolate contents as well as their biotechnological production in homologous and heterologous systems. Here, we provide proof-of-concept for transgenic suspension cultures of carrot (Daucus carota, Apiacae) as a scalable production platform for plant specialized metabolites using benzylglucosinolate as a model. Two T-DNAs carrying in total six genes of the benzylglucosinolate biosynthesis pathway from Arabidopsis thaliana as well as NPTII and BAR as selectable markers were transferred to carrot cells by Agrobacterium tumefaciens-mediated transformation. Putative transformants selected based on their kanamycin and BASTA resistances were subjected to HPLC-MS analysis. Of 79 putative transformants, 17 produced benzylglucosinolate. T-DNA-integration was confirmed for the five best producers. Callus from these transformants was used to establish suspension cultures for quantitative analysis. When grown in 60-ml-cultures, the best transformants produced roughly 2.5 nmol (g fw)^-1 benzylglucosinolate, together with up to 10 nmol (g fw)^-1 desulfobenzylglucosinolate. Only one transformant produced more benzylglucosinolate than desulfobenzylglucosinolate. The concentration of sulfate in the medium was not a major limiting factor. High production seemed to be associated with poor growth and vice versa. Therefore, future research should try to optimize medium and cultivation process and to separate growth and production phase by using an inducible promoter.

MYB transcription factors and their role in Medicinal plants

Transcription factors are multi-domain proteins that regulate gene expression in eukaryotic organisms. They are one of the largest families of proteins, which are structurally and functionally diverse. While there are transcription factors that are plant-specific, such as AP2/ERF, B3, NAC, SBP and WRKY, some transcription factors are present in both plants as well as other eukaryotic organisms. MYB transcription factors are widely distributed among all eukaryotes. In plants, the MYB transcription factors are involved in the regulation of numerous functions such as gene regulation in different metabolic pathways especially secondary metabolic pathways, regulation of different signalling pathways of plant hormones, regulation of genes involved in various developmental and morphological processes etc. Out of the thousands of MYB TFs that have been studied in plants, the majority of them have been studied in the model plants like Arabidopsis thaliana, Oryza sativa etc. The study of MYBs in other plants, especially medicinal plants, has been comparatively limited. But the increasing demand for medicinal plants for the production of biopharmaceuticals and important bioactive compounds has also increased the need to explore more number of these multifaceted transcription factors which play a significant role in the regulation of secondary metabolic pathways. These studies will ultimately contribute to medicinal plants' research and increased production of secondary metabolites, either through transgenic plants or through synthetic biology approaches. This review compiles studies on MYB transcription factors that are involved in the regulation of diverse functions in medicinal plants.

Glucosinolates and Biotic Stress Tolerance in Brassicaceae with Emphasis on Cabbage: A Review

Glucosinolates (GSLs) and GSL-associated genes are receiving increasing attention from molecular biologists due to their multifunctional properties. GSLs are secondary metabolites considered to be highly active in most Brassica species. Their importance has motivated the discovery and functional analysis of the GSLs and GSL hydrolysis products involved in disease development in brassicas and other plants. Comprehensive knowledge of the GSL content of Brassica species and the molecular details of GSL-related genes will help elucidate the molecular control of this plant defense system. This report provides an overview of the current status of knowledge on GSLs, GSL biosynthesis, as well as hydrolysis related genes, and GSL hydrolysis products that regulate fungal, bacterial, and insect resistance in cabbage and other brassicas.

Further insight into decreases in seed glucosinolate content based on QTL mapping and RNA-seq in Brassica napus L

The QTL hotspots determining seed glucosinolate content instead of only four HAG1 loci and elucidation of a potential regulatory model for rapeseed SGC variation. Glucosinolates (GSLs) are amino acid-derived, sulfur-rich secondary metabolites that function as biopesticides and flavor compounds, but the high seed glucosinolate content (SGC) reduces seed quality for rapeseed meal. To dissect the genetic mechanism and further reduce SGC in rapeseed, QTL mapping was performed using an updated high-density genetic map based on a doubled haploid (DH) population derived from two parents that showed significant differences in SGC. In 15 environments, a total of 162 significant QTLs were identified for SGC and then integrated into 59 consensus QTLs, of which 32 were novel QTLs. Four QTL hotspot regions (QTL-HRs) for SGC variation were discovered on chromosomes A09, C02, C07 and C09, including seven major QTLs that have previously been reported and four novel major QTLs in addition to HAG1 loci. SGC was largely determined by superimposition of advantage allele in the four QTL-HRs. Important candidate genes directly related to GSL pathways were identified underlying the four QTL-HRs, including BnaC09.MYB28, BnaA09.APK1, BnaC09.SUR1 and BnaC02.GTR2a. Related differentially expressed candidates identified in the minor but environment stable QTLs indicated that sulfur assimilation plays an important rather than dominant role in SGC variation. A potential regulatory model for rapeseed SGC variation constructed by combining candidate GSL gene identification and differentially expressed gene analysis based on RNA-seq contributed to a better understanding of the GSL accumulation mechanism. This study provides insights to further understand the genetic regulatory mechanism of GSLs, as well as the potential loci and a new route to further diminish the SGC in rapeseed.

Genetic disruption of Arabidopsis secondary metabolite synthesis leads to microbiome-mediated modulation of nematode invasion

In-depth understanding of metabolite-mediated plant-nematode interactions can guide us towards novel nematode management strategies. To improve our understanding of the effects of secondary metabolites on soil nematode communities, we grew Arabidopsis thaliana genetically altered in glucosinolate, camalexin, or flavonoid synthesis pathways, and analyzed their root-associated nematode communities using metabarcoding. To test for any modulating effects of the associated microbiota on the nematode responses, we characterized the bacterial and fungal communities. Finally, as a proxy of microbiome-modulating effects on nematode invasion, we isolated the root-associated microbiomes from the mutants and tested their effect on the ability of the plant parasitic nematode Meloidogyne incognita to penetrate tomato roots. Most mutants had altered relative abundances of several nematode taxa with stronger effects on the plant parasitic Meloidogyne hapla than on other root feeding taxa. This probably reflects that M. hapla invades and remains embedded within root tissues and is thus intimately associated with the host. When transferred to tomato, microbiomes from the flavonoid over-producing pap1-D enhanced M. incognita root-invasion, whereas microbiomes from flavonoid-deficient mutants reduced invasion. This suggests microbiome-mediated effect of flavonoids on Meloidogyne infectivity plausibly mediated by the alteration of the abundances of specific microbial taxa in the transferred microbiomes, although we could not conclusively pinpoint such causative microbial taxa.

Structural insights into partner selection for MYB and bHLH transcription factor complexes

MYB and basic helix-loop-helix (bHLH) transcription factors form complexes to regulate diverse metabolic and developmental processes in plants. However, the molecular mechanisms responsible for MYB-bHLH interaction and partner selection remain unclear. Here, we report the crystal structures of three MYB-bHLH complexes (WER-EGL3, CPC-EGL3 and MYB29-MYC3), uncovering two MYB-bHLH interaction modes. WER and CPC are R2R3- and R3-type MYBs, respectively, but interact with EGL3 through their N-terminal R3 domain in a similar mode. A single amino acid of CPC, Met49, is crucial for competition with WER to interact with EGL3. MYB29, a R2R3-type MYB transcription factor, interacts with MYC3 by its C-terminal MYC-interaction motif. The WER-EGL3 and MYB29-MYC3 binding modes are widely applied among MYB-bHLH complexes in Arabidopsis and evolve independently in plants.

BcWRKY33A Enhances Resistance to Botrytis cinerea via Activating BcMYB51-3 in Non-Heading Chinese Cabbage

The transcription factor WRKY33 is a vital regulator of the biological process of the necrotrophic fungus Botrytis cinerea (B. cinerea). However, its specific regulatory mechanism remains to be further investigated. In non-heading Chinese cabbage (NHCC, Brassica campestris (syn. Brassica rapa) ssp. Chinensis), our previous study showed that BcWRKY33A is induced not only by salt stress, but also by B. cinerea infection. Here, we noticed that BcWRKY33A is expressed in trichomes and confer plant defense resistance. Disease symptoms and qRT-PCR analyses revealed that BcWRKY33A-overexpressing and -silencing lines were less and more severely impaired, respectively, than wild type upon B. cinerea treatment. Meanwhile, the transcripts’ abundance of indolic glucosinolates’ (IGSs) biosynthetic genes is consistent with plants’ B. cinerea tolerance. Identification and expression pattern analysis of BcMYB51s showed that BcMYB51-3 has a similar trend to BcWRKY33A upon B. cinerea infection. Moreover, BcWRKY33A directly binds to the BcMYB51-3 promoter, which was jointly confirmed by Y1H, dual-LUC, and EMSA assays. The importance of MYB51, the homolog of BcMYB51-3, in the BcWRKY33A-mediated B. cinerea resistance was also verified using the TRV-based VIGS system. Overall, our data concludes that BcWRKY33A directly activates the expression of BcMYB51-3 and downstream IGSs’ biosynthetic genes, thereby improving the B. cinerea tolerance of NHCC plants.

PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave

Immune responses triggered by pathogen-associated molecular patterns (PAMPs) are key to pathogen defense, but drivers and stabilizers of the growth-to-defense genetic reprogramming remain incompletely understood in plants. Here, we report a time-course study of the establishment of PAMP-triggered immunity (PTI) using cap analysis of gene expression. We show that around 15% of all transcription start sites (TSSs) rapidly induced during PTI define alternative transcription initiation events. From these, we identify clear examples of regulatory TSS change via alternative inclusion of target peptides or domains in encoded proteins, or of upstream open reading frames in mRNA leader sequences. We also find that 60% of PAMP response genes respond earlier than previously thought. In particular, a cluster of rapidly and transiently PAMP-induced genes is enriched in transcription factors (TFs) whose functions, previously associated with biological processes as diverse as abiotic stress adaptation and stem cell activity, appear to converge on growth restriction. Furthermore, examples of known potentiators of PTI, in one case under direct mitogen-activated protein kinase control, support the notion that the rapidly induced TFs could constitute direct links to PTI signaling pathways and drive gene expression changes underlying establishment of the immune state.

Mapping‑by‑Sequencing Reveals Genomic Regions Associated with Seed Quality Parameters in Brassica napus

Rapeseed (Brassica napus L.) is an important oil crop and has the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has high nutritional value for humans. Seed protein content (SPC) and seed oil content (SOC) are two complex quantitative and polygenic traits which are negatively correlated and assumed to be controlled by additive and epistatic effects. A reduction in seed glucosinolate (GSL) content is desired as GSLs cause a stringent and bitter taste. The goal here was the identification of genomic intervals relevant for seed GSL content and SPC/SOC. Mapping by sequencing (MBS) revealed 30 and 15 new and known genomic intervals associated with seed GSL content and SPC/SOC, respectively. Within these intervals, we identified known but also so far unknown putatively causal genes and sequence variants. A 4 bp insertion in the MYB28 homolog on C09 shows a significant association with a reduction in seed GSL content. This study provides insights into the genetic architecture and potential mechanisms underlying seed quality traits, which will enhance future breeding approaches in B. napus.

Comprehensive analysis of 1R- and 2R-MYBs reveals novel genic and protein features, complex organisation, selective expansion and insights into evolutionary tendencies

Myeloblastosis (MYB) family, the largest plant transcription factor family, has been subcategorised based on the number and type of repeats in the MYB domain. In spite of several reports, evolution of MYB genes and repeats remains enigmatic. Brassicaceae members are endowed with complex genomes, including dysploidy because of its unique history with multiple rounds of polyploidisation, genomic fractionations and rearrangements. The present study is an attempt to gain insights into the complexities of MYB family diversity, understand impacts of genome evolution on gene families and develop an evolutionary framework to understand the origin of various subcategories of MYB gene family. We identified and analysed 1129 MYBs that included 1R-, 2R-, 3R- and atypical-MYBs across sixteen species representing protists, fungi, animals and plants and exclude MYB identified from Brassicaceae except Arabidopsis thaliana; in addition, a total of 1137 2R-MYB genes from six Brassicaceae species were also analysed. Comparative analysis revealed predominance of 1R-MYBs in protists, fungi, animals and lower plants. Phylogenetic reconstruction and analysis of selection pressure suggested ancestral nature of R1-type repeat containing 1R-MYBs that might have undergone intragenic duplication to form multi-repeat MYBs. Distinct differences in gene structure between 1R-MYB and 2R-MYBs were observed regarding intron number, the ratio of gene length to coding DNA sequence (CDS) length and the length of exons encoding the MYB domain. Conserved as well as novel and lineage-specific intron phases were identified. Analyses of physicochemical properties revealed drastic differences indicating functional diversification in MYBs. Phylogenetic reconstruction of 1R- and 2R-MYB genes revealed a shared structure-function relationship in clades which was supported when transcriptome data was analysed in silico. Comparative genomics to study distribution pattern and mapping of 2R-MYBs revealed congruency and greater degree of synteny and collinearity among closely related species. Micro-synteny analysis of genomic segments revealed high conservation of genes that are immediately flanking the surrounding tandemly organised 2R-MYBs along with instances of local duplication, reorganisations and genome fractionation. In summary, polyploidy, dysploidy, reshuffling and genome fractionation were found to cause loss or gain of 2R-MYB genes. The findings need to be supported with functional validation to understand gene structure-function relationship along the evolutionary lineage and adaptive strategies based on comparative functional genomics in plants.

Genome-Wide Association Study of Phenylalanine Derived Glucosinolates in Brassica rapa

Glucosinolates (GSLs) are sulfur-containing bioactive compounds usually present in Brassicaceae plants and are usually responsible for a pungent flavor and reduction of the nutritional values of seeds. Therefore, breeding rapeseed varieties with low GSL levels is an important breeding objective. Most GSLs in Brassica rapa are derived from methionine or tryptophan, but two are derived from phenylalanine, one directly (benzylGSL) and one after a round of chain elongation (phenethylGSL). In the present study, two phenylalanine (Phe)-derived GSLs (benzylGSL and phenethylGSL) were identified and quantified in seeds by liquid chromatography and mass spectrometry (LC-MS) analysis. Levels of benzylGSL were low but differed among investigated low and high GSL genotypes. Levels of phenethylGSL (also known as 2-phenylethylGSL) were high but did not differ among GSL genotypes. Subsequently, a genome-wide association study (GWAS) was conducted using 159 B. rapa accessions to demarcate candidate regions underlying 43 and 59 QTNs associated with benzylGSL and phenethylGSL that were distributed on 10 chromosomes and 9 scaffolds, explaining 0.56% to 70.86% of phenotypic variations, respectively. Furthermore, we find that 15 and 18 known or novel candidate genes were identified for the biosynthesis of benzylGSL and phenethylGSL, including known regulators of GSL biosynthesis, such as BrMYB34, BrMYB51, BrMYB28, BrMYB29 and BrMYB122, and novel regulators or structural genes, such as BrMYB44/BrMYB77 and BrMYB60 for benzylGSL and BrCYP79B2 for phenethylGSL. Finally, we investigate the expression profiles of the biosynthetic genes for two Phe-derived GSLs by transcriptomic analysis. Our findings provide new insight into the complex machinery of Phe-derived GSLs in seeds of B. rapa and help to improve the quality of Brassicaceae plant breeding.

Camalexin accumulation as a component of plant immunity during interactions with pathogens and beneficial microbes

This review provides an overview on the role of camalexin in plant immunity taking into account various plant-pathogen and beneficial microbe interactions, regulation mechanisms and the contribution in basal and induced plant resistance. In a hostile environment, plants evolve complex and sophisticated defense mechanisms to counteract invading pathogens and herbivores. Several lines of evidence support the assumption that secondary metabolites like phytoalexins which are synthesized de novo, play an important role in plant defenses and contribute to pathogens' resistance in a wide variety of plant species. Phytoalexins are synthesized and accumulated in plants upon pathogen challenge, root colonization by beneficial microbes, following treatment with chemical elicitors or in response to abiotic stresses. Their protective properties against pathogens have been reported in various plant species as well as their contribution to human health. Phytoalexins are synthesized through activation of particular sets of genes encoding specific pathways. Camalexin (3'-thiazol-2'-yl-indole) is the primary phytoalexin produced by Arabidopsis thaliana after microbial infection or abiotic elicitation and an iconic representative of the indole phytoalexin family. The synthesis of camalexin is an integral part of cruciferous plant defense mechanisms. Although the pathway leading to camalexin has been largely elucidated, the regulatory networks that control the induction of its biosynthetic steps by pathogens with different lifestyles or by beneficial microbes remain mostly unknown. This review thus presents current knowledge regarding camalexin biosynthesis induction during plant-pathogen and beneficial microbe interactions as well as in response to microbial compounds and provides an overview on its regulation and interplay with signaling pathways. The contribution of camalexin to basal and induced plant resistance and its detoxification by some pathogens to overcome host resistance are also discussed.

Diverse roles of MYB transcription factors in regulating secondary metabolite biosynthesis, shoot development, and stress responses in tea plants (Camellia sinensis)

Tea (Camellia sinensis) is concocted from tea plant shoot tips that produce catechins, caffeine, theanine, and terpenoids, which collectively determine the rich flavors and health benefits of the infusion. However, little is known about the integrated regulation of shoot tip development and characteristic secondary metabolite biosynthesis in tea plants. Here, we demonstrate that MYB transcription factors (TFs) play key and yet diverse roles in regulating leaf and stem development, secondary metabolite biosynthesis, and environmental stress responses in tea plants. By integrating transcriptomic and metabolic profiling data in different tissues at a series of developmental stages or under various stress conditions, alongside biochemical and genetic analyses, we predicted the MYB TFs involved in regulating shoot development (CsMYB2, 98, 107, and 221), epidermal cell initiation (CsMYB184, 41, 139, and 219), stomatal initiation (CsMYB113 and 153), and the biosynthesis of flavonoids (including catechins, anthocyanins, and flavonols; CsMYB8 and 99), caffeine (CsMYB85 and 86), theanine (CsMYB9 and 49), carotenoids (CsMYB110), mono-/sesquiterpenoid volatiles (CsMYB68, 147, 148, and 193), lignin (CsMYB164 and 192), and indolic compounds (CsMYB139, 162, and 198), as well as the MYB TFs that are likely involved in hormone signaling-mediated environmental stress and defense responses. We characterized the functions of some key MYBs in regulating flavonoid and carotenoid biosynthesis for tea quality and flavor. This study provides a cross-family analysis of MYBs in tea alongside new insights into the coordinated regulation of tea plant shoot development and secondary metabolism, paving the way towards understanding of tea quality trait formation and genetic improvement of quality tea plants.

WRKY33-mediated indolic glucosinolate metabolic pathway confers resistance against Alternaria brassicicola in Arabidopsis and Brassica crops

The tryptophan (Trp)-derived plant secondary metabolites, including camalexin, 4-hydroxy-indole-3-carbonylnitrile, and indolic glucosinolate (IGS), show broad-spectrum antifungal activity. However, the distinct regulations of these metabolic pathways among different plant species in response to fungus infection are rarely studied. In this study, our results revealed that WRKY33 directly regulates IGS biosynthesis, notably the production of 4-methoxyindole-3-ylmethyl glucosinolate (4MI3G), conferring resistance to Alternaria brassicicola, an important pathogen which causes black spot in Brassica crops. WRKY33 directly activates the expression of CYP81F2, IGMT1, and IGMT2 to drive side-chain modification of indole-3-ylmethyl glucosinolate (I3G) to 4MI3G, in both Arabidopsis and Chinese kale (Brassica oleracea var. alboglabra Bailey). However, Chinese kale showed a more severe symptom than Arabidopsis when infected by Alternaria brassicicola. Comparative analyses of the origin and evolution of Trp metabolism indicate that the loss of camalexin biosynthesis in Brassica crops during evolution might attenuate the resistance of crops to Alternaria brassicicola. As a result, the IGS metabolic pathway mediated by WRKY33 becomes essential for Chinese kale to deter Alternaria brassicicola. Our results highlight the differential regulation of Trp-derived camalexin and IGS biosynthetic pathways in plant immunity between Arabidopsis and Brassica crops.

IQD1 Involvement in Hormonal Signaling and General Defense Responses Against Botrytis cinerea

IQ Domain 1 (IQD1) is a novel Arabidopsis thaliana calmodulin-binding protein, which was found to be a positive regulator of glucosinolate (GS) accumulation and plant defense responses against insects. We demonstrate here that the IQD1 overexpressing line (IQD1 ^OXP ) was also more resistant also to the necrotrophic fungus Botrytis cinerea, whereas an IQD1 knockout line (iqd1-1) was much more sensitive. Furthermore, we showed that IQD1 is up-regulated by jasmonic acid (JA) and downregulated by salicylic acid (SA). A comparison of whole transcriptome expression between iqd1-1 and wild type plants revealed a substantial downregulation of genes involved in plant defense and hormone regulation. Further examination revealed a marked reduction of SA and increases in the levels of ethylene, JA and abscisic acid response genes in the iqd1-1 line. Moreover, quantification of SA, JA, and abscisic acids in IQD1 ^OXP and iqd1-1 lines relative to the wild type, showed a significant reduction in endogenous JA levels in the knockout line, simultaneously with increased SA levels. Relations between IQD1 ^OXP and mutants defective in plant-hormone response indicated that IQD1 cannot rescue the absence of NPR1 or impaired SA accumulation in the NahG line. IQD1 cannot rescue ein2 or eto1 mutations connected to the ethylene pathway involved in both defense responses against B. cinerea and in regulating GS accumulation. Furthermore, IQD1cannot rescue the aos, coi1 or jar1mutations, all involved in the defense response against B. cinerea and it depends on JAR1 to control indole glucosinolate accumulation. We also found that in the B. cinerea, which infected the iqd1-1 mutant, the most abundant upregulated group of proteins is involved in the degradation of complex carbohydrates, as correlated with the sensitivity of this mutant. In summary, our results suggest that IQD1 is an important A. thaliana defensive protein against B. cinerea that is integrated into several important pathways, such as those involved in plant defense and hormone responses.

Exogenous Selenium Treatment Promotes Glucosinolate and Glucoraphanin Accumulation in Broccoli by Activating Their Biosynthesis and Transport Pathways

Supplementation using selenium (Se) on plants is an effective and widely used approach. It can not only be converted to more Se rich compounds but promote the accumulation of glucosinolates (GSLs) with anti-carcinogenic properties. However, the molecular mechanism of Se in regulating GSLs synthesis remains unclear. In the present study, we analyzed the effects of Se treatment (50 μM sodium selenite) on GSLs, glucoraphanin (4MSOB), and sulforaphane compounds in broccoli tissues. The transcript levels of genes involved in sulfur absorption and transport, GSLs biosynthesis, translocation, and degradation pathways were also evaluated. The study showed that Se treatment remarkably promoted the accumulation of total sulfur and total Se contents and increased Trp-derived GSLs levels in roots by 2 times. The 4MSOB concentration and sulforaphane content in fresh leaves was increased by 67% and 30% after Se treatment, respectively. For genes expressions, some genes involved in sulfate uptake and transporters, GSLs biosynthesis, and transporters were induced strongly upon Se exposure. Results revealed that exogenous Se treatment promotes the overaccumulation of GSLs and 4MSOB content in broccoli by activating the transcript levels of genes involved in sulfur absorption, GSLs biosynthesis, and translocation pathways.

A plant balancing act: Meshing new and existing metabolic pathways towards an optimized system

Specialized metabolic pathways evolve from existing pathways, creating new functionality potentially boosting fitness. However, how these pathways are integrated into a pre-existing working and well-balanced metabolic system is unclear. They could be integrated to the system as a functional appendage, or they could be fully embedded into primary metabolism by establishing new biochemical and regulatory connections. A full integration into the primary metabolic system requires substantial system re-wiring and because of this complexity, the latter is often not experimentally pursued. New studies provide evidence that some specialized metabolic pathways are fully embedded in primary metabolism with extensive new regulatory and biochemical connections. This suggests, that we should consider whether other specialized metabolic pathways could be fully integrated rather than being simple appendages. In this mini review, we survey compelling evidence supporting that some specialized metabolic pathways are fully integrated and ask if these metabolites now act as de-facto primary metabolites?