Single-cell proteomic analysis of glucosinolate-rich S-cells in Arabidopsis thaliana

Acidification and tissue disruption affect glucosinolate and S-methyl-l-cysteine sulfoxide hydrolysis and formation of amines, isothiocyanates and other organosulfur compounds in red cabbage (Brassica oleracea var. capitata f. rubra)

Cabbages are rich in sulfur-containing metabolites like glucosinolates (GLSs) and S-methyl-l-cysteine sulfoxide (SMCSO). Tissue disruption initiates hydrolysis of these compounds and bioactive volatile hydrolysis products such as isothiocyanates (ITCs), sulfides, and thiosulfinates are formed. However, nitriles, epithionitriles, or amines can also result from GLSs. Here, the influence of hydrolysis time, extent of tissue disruption (chopping vs. homogenization), and addition of lemon juice or vinegar on the outcome of enzymatic hydrolysis of GLSs and SMCSO was investigated in red cabbage. Chopping led to partial hydrolysis of GLSs, whereas homogenization completely degraded GLSs but only had a small effect on SMCSO. Homogenization increased amine formation from alkenyl and methylthioalkyl ITCs, but not from methylsulfinylalkyl ITCs. Acidification inhibited formation of products from SMCSO. Further, it reduced nitrile and epithionitrile formation and stopped amine formation, thereby increasing ITC levels. Therefore, acidification is a valuable mean to enhance ITC levels in fresh Brassica foods.

Impact of refrigerated storage on (bio)chemical conversions of health-related compounds in pretreated, pasteurized Brussels sprouts and leek

Vegetable processing often consists of multiple processing steps. Research mostly focused on the impact of individual processing steps on individual health-related compounds. However, there is a need for more holistic approaches to understand the overall impact of the processing chain on the health potential of vegetables. Therefore, this work studied the impact of pretreatment (relatively intact versus pureed vegetable systems), pasteurization and subsequent refrigerated storage (kinetic evaluation) on multiple health-related compounds (vitamin C, vitamin K1, carotenoids, glucosinolates and S-alk(en)yl-L-cysteine sulfoxides (ACSOs)) in Brussels sprouts and leek. It could be shown that differences introduced by different types of pretreatment were not nullified during pasteurization and refrigerated storage. Clearly, enzymatic conversions controlled during pretreatment resulted in different health-related compound profiles still observable after pasteurization. Moreover, about -42% and -100% relative concentration differences of ACSOs and dehydroascorbic acid, respectively, were detected immediately after pasteurization, while glucosinolates concentrations decreased by about 47% during refrigerated storage. All other compounds were stable during pasteurization and refrigerated storage.

Application of single-cell multi-omics approaches in horticulture research

Cell heterogeneity shapes the morphology and function of various tissues and organs in multicellular organisms. Elucidation of the differences among cells and the mechanism of intercellular regulation is essential for an in-depth understanding of the developmental process. In recent years, the rapid development of high-throughput single-cell transcriptome sequencing technologies has influenced the study of plant developmental biology. Additionally, the accuracy and sensitivity of tools used to study the epigenome and metabolome have significantly increased, thus enabling multi-omics analysis at single-cell resolution. Here, we summarize the currently available single-cell multi-omics approaches and their recent applications in plant research, review the single-cell based studies in fruit, vegetable, and ornamental crops, and discuss the potential of such approaches in future horticulture research.

Occurrence, Function, and Biosynthesis of the Natural Auxin Phenylacetic Acid (PAA) in Plants

Auxins are a class of plant hormones playing crucial roles in a plant's growth, development, and stress responses. Phenylacetic acid (PAA) is a phenylalanine-derived natural auxin found widely in plants. Although the auxin activity of PAA in plants was identified several decades ago, PAA homeostasis and its function remain poorly understood, whereas indole-3-acetic acid (IAA), the most potent auxin, has been used for most auxin studies. Recent studies have revealed unique features of PAA distinctive from IAA, and the enzymes and intermediates of the PAA biosynthesis pathway have been identified. Here, we summarize the occurrence and function of PAA in plants and highlight the recent progress made in PAA homeostasis, emphasizing PAA biosynthesis and crosstalk between IAA and PAA homeostasis.

The Impact of Nitrile-Specifier Proteins on Indolic Carbinol and Nitrile Formation in Homogenates of Arabidopsis thaliana

Glucosinolates, specialized metabolites of the Brassicales including Brassica crops and Arabidopsis thaliana, have attracted considerable interest as chemical defenses and health-promoting compounds. Their biological activities are mostly due to breakdown products formed upon mixing with co-occurring myrosinases and specifier proteins, which can result in multiple products with differing properties, even from a single glucosinolate. Whereas product profiles of aliphatic glucosinolates have frequently been reported, indole glucosinolate breakdown may result in complex mixtures, the analysis of which challenging. The aim of this study was to assess the breakdown of indole glucosinolates in A. thaliana root and rosette homogenates and to test the impact of nitrile-specifier proteins (NSPs) on product profiles. To develop a GC-MS-method for quantification of carbinols and nitriles derived from three prominent indole glucosinolates, we synthesized standards, established derivatization conditions, determined relative response factors and evaluated applicability of the method to plant homogenates. We show that carbinols are more dominant among the detected products in rosette than in root homogenates of wild-type and NSP1- or NSP3-deficient mutants. NSP1 is solely responsible for nitrile formation in rosette homogenates and is the major NSP for indolic nitrile formation in root homogenates, with no contribution from NSP3. These results will contribute to the understanding of the roles of NSPs in plants.

Identification of Potential Genes Encoding Protein Transporters in Arabidopsis thaliana Glucosinolate (GSL) Metabolism

Several species in Brassicaceae produce glucosinolates (GSLs) to protect themselves against pests. As demonstrated in A. thaliana, the reallocation of defence compounds, of which GSLs are a major part, is highly dependent on transport processes and serves to protect high-value tissues such as reproductive tissues. This study aimed to identify potential GSL-transporter proteins (TPs) using a network-biology approach. The known A. thaliana GSL genes were retrieved from the literature and pathway databases and searched against several co-expression databases to generate a gene network consisting of 1267 nodes and 14,308 edges. In addition, 1151 co-expressed genes were annotated, integrated, and visualised using relevant bioinformatic tools. Based on three criteria, 21 potential GSL genes encoding TPs were selected. The AST68 and ABCG40 potential GSL TPs were chosen for further investigation because their subcellular localisation is similar to that of known GSL TPs (SULTR1;1 and SULTR1;2) and ABCG36, respectively. However, AST68 was selected for a molecular-docking analysis using AutoDOCK Vina and AutoDOCK 4.2 with the generated 3D model, showing that both domains were well superimposed on the homologs. Both molecular-docking tools calculated good binding-energy values between the sulphate ion and Ser419 and Val172, with the formation of hydrogen bonds and van der Waals interactions, respectively, suggesting that AST68 was one of the sulphate transporters involved in GSL biosynthesis. This finding illustrates the ability to use computational analysis on gene co-expression data to screen and characterise plant TPs on a large scale to comprehensively elucidate GSL metabolism in A. thaliana. Most importantly, newly identified potential GSL transporters can serve as molecular tools in improving the nutritional value of crops.

iTRAQ-based proteomic and physiological analyses of broccoli sprouts in response to exogenous melatonin with ZnSO4 stress

Exogenous melatonin (10 μM) enhances ZnSO4 (4 mM) stress tolerance and regulates the isothiocyanate content of broccoli sprouts. Nevertheless, the molecular mechanism underlying the role of melatonin in isothiocyanate metabolism under ZnSO4 stress is unclear. The effects of exogenous melatonin on growth and isothiocyanate metabolism in broccoli sprouts under ZnSO4 stress during germination were investigated by physio-biochemical methods, quantification of relative gene expression levels, and the isobaric tags for the relative and absolute quantitation (iTRAQ) labelling technique. Compared with sprouts under ZnSO4 stress alone, sprout length, fresh weight and free calcium content increased significantly in sprouts under ZnSO4 stress plus melatonin treatment while electrolyte leakage and malonaldehyde content decreased. The glucosinolate content and myrosinase activity also significantly increased in sprouts under ZnSO4 stress plus melatonin treatment compared with the control, and thus the isothiocyanate and sulforaphane content increased markedly. Meanwhile, the expression of glucoraphanin biosynthesis genes, such as MYB28, CYP83A1, AOP2, BoSAT1, and BoHMT1 was significantly induced by melatonin in sprouts under ZnSO4 stress. Furthermore, compared with sprouts under ZnSO4 stress alone, a total of 145 proteins in broccoli sprouts under ZnSO4 stress plus melatonin treatment showed differential relative abundances. These proteins were divided into 13 functional classes and revealed that pathways for sulfur metabolism, glucosinolate biosynthesis, selenocompound metabolism, biosynthesis of secondary metabolites and peroxisome were significantly enriched. The present study indicates that exogenous melatonin alleviates the adverse effects of ZnSO4 stress on sprout growth and promotes glucoraphanin biosynthesis and the hydrolysis of glucoraphanin to form isothiocyanates in broccoli sprouts.

The Versatile Roles of Sulfur-Containing Biomolecules in Plant Defense-A Road to Disease Resistance

Sulfur (S) is an essential plant macronutrient and the pivotal role of sulfur compounds in plant disease resistance has become obvious in recent decades. This review attempts to recapitulate results on the various functions of sulfur-containing defense compounds (SDCs) in plant defense responses to pathogens. These compounds include sulfur containing amino acids such as cysteine and methionine, the tripeptide glutathione, thionins and defensins, glucosinolates and phytoalexins and, last but not least, reactive sulfur species and hydrogen sulfide. SDCs play versatile roles both in pathogen perception and initiating signal transduction pathways that are interconnected with various defense processes regulated by plant hormones (salicylic acid, jasmonic acid and ethylene) and reactive oxygen species (ROS). Importantly, ROS-mediated reversible oxidation of cysteine residues on plant proteins have profound effects on protein functions like signal transduction of plant defense responses during pathogen infections. Indeed, the multifaceted plant defense responses initiated by SDCs should provide novel tools for plant breeding to endow crops with efficient defense responses to invading pathogens.

Seasonal Variation of Glucosinolate Hydrolysis Products in Commercial White and Red Cabbages (Brassica oleracea var. capitata)

Brassica vegetables contain glucosinolates, which are well-known for their potential to form health-promoting isothiocyanates. Among those crucifers, white and red cabbage are commonly consumed vegetables, exhibiting different glucosinolate and hydrolysis profiles thereof. Regarding the health beneficial effects from these vegetables, more information, especially concerning the seasonal variation of glucosinolate profiles and the formation of their bioactive hydrolysis products in commercial cabbages, is needed. In this study, glucosinolates and glucosinolate hydrolysis product profiles in red and white cabbages from three different food retailers were monitored over six different sampling dates across the selling season in autumn. For the first time, it was shown that, while glucosinolate profiles were similar in each cabbage variety, glucosinolate hydrolysis product profiles and hydrolysis behavior varied considerably over the season. The highest total isothiocyanate concentrations were observed in conventional red (1.66 μmol/g FW) and organic white (0.93 μmol/g FW) cabbages purchased at the first sampling date in September. Here, red cabbage was with up to 1.06 μmol/g FW of 4-(methylsulfinyl)butyl isothiocyanate (sulforaphane), an excellent source for this health-promoting isothiocyanate. Cabbages purchased 11 weeks later in autumn released lower levels of isothiocyanates, but mainly nitriles and epithionitriles. The results indicate that commercial cabbages purchased in early autumn could be healthier options than those purchased later in the year.

A Comprehensive Gene Inventory for Glucosinolate Biosynthetic Pathway in Arabidopsis thaliana

Glucosinolates (GSLs) are plant secondary metabolites comprising sulfur and nitrogen mainly found in plants from the order of Brassicales, such as broccoli, cabbage, and Arabidopsis thaliana. The activated forms of GSL play important roles in fighting against pathogens and have health benefits to humans. The increasing amount of data on A. thaliana generated from various omics technologies can be investigated more deeply in search of new genes or compounds involved in GSL biosynthesis and metabolism. This review describes a comprehensive inventory of A. thaliana GSLs identified from published literature and databases such as KNApSAcK, KEGG, and AraCyc. A total of 113 GSL genes encoding for 23 transcription components, 85 enzymes, and five protein transporters were experimentally characterized in the past two decades. Continuous efforts are still on going to identify all molecules related to the production of GSLs. A manually curated database known as SuCCombase (http://plant-scc.org) was developed to serve as a comprehensive GSL inventory. Realizing lack of information on the regulation of GSL biosynthesis and degradation mechanisms, this review also includes relevant information and their connections with crosstalk among various factors, such as light, sulfur metabolism, and nitrogen metabolism, not only in A. thaliana but also in other crucifers.

Involvement of BGLU30 in Glucosinolate Catabolism in the Arabidopsis Leaf under Dark Conditions

Glucosinolates (GSLs) are secondary metabolites that play important roles in plant defense and are suggested to act as storage compounds. Despite their important roles, metabolic dynamics of GSLs under various growth conditions remain poorly understood. To determine how light conditions influence the levels of different GSLs and their distribution in Arabidopsis leaves, we visualized the GSLs under different light conditions using matrix-assisted laser desorption/ionization mass spectrometry imaging. We observed the unique distribution patterns of each GSL in the inner regions of leaves and marked decreases under darkness, indicating light conditions influenced GSL metabolism. GSLs are hydrolyzed by a group of ß-glucosidase (BGLU) called myrosinase. Previous transcriptome data for GSL metabolism under light and dark conditions have revealed the highly induced expression of BGLU30, one of the putative myrosinases, which is also annotated as Dark INducible2, under darkness. Impairment of the darkness-induced GSL decrease in the disruption mutants of BGLU30, bglu30, indicated that BGLU30 mediated GSL hydrolysis under darkness. Based on the GSL profiles in the wild-type and bglu30 leaves under both conditions, short-chain GSLs were potentially preferable substrates for BGLU30. Our findings provide an effective way of visualizing GSL distribution in plants and highlighted the carbon storage GSL function.

Sulfur Deficiency-Induced Glucosinolate Catabolism Attributed to Two β-Glucosidases, BGLU28 and BGLU30, is Required for Plant Growth Maintenance under Sulfur Deficiency

Sulfur (S) is an essential element for plants, and S deficiency causes severe growth retardation. Although the catabolic process of glucosinolates (GSLs), the major S-containing metabolites specific to Brassicales including Arabidopsis, has been recognized as one of the S deficiency (-S) responses in plants, the physiological function of this metabolic process is not clear. Two β-glucosidases (BGLUs), BGLU28 and BGLU30, are assumed to be responsible for this catabolic process as their transcript levels were highly upregulated by -S. To clarify the physiological function of BGLU28 and BGLU30 and their roles in GSL catabolism, we analyzed the accumulation of GSLs and other S-containing compounds in the single and double mutant lines of BGLU28 and BGLU30 and in wild-type plants under different S conditions. GSL levels were highly increased, while the levels of sulfate, cysteine, glutathione and protein were decreased in the double mutant line of BGLU28 and BGLU30 (bglu28/30) under -S. Furthermore, transcript level of Sulfate Transporter1;2, the main contributor of sulfate uptake from the environment, was increased in bglu28/30 mutants under -S. With these metabolic and transcriptional changes, bglu28/30 mutants displayed obvious growth retardation under -S. Overall, our results indicate that BGLU28 and BGLU30 are required for -S-induced GSL catabolism and contribute to sustained plant growth under -S by recycling sulfate to primary S metabolism.

Arabidopsis glucosinolate storage cells transform into phloem fibres at late stages of development

The phloem cap of Arabidopsis thaliana accumulates glucosinolates that yield toxic catabolites upon damage-induced hydrolysis. These defence compounds are stored in high concentrations in millimetre long S-cells. At early stages of development, S-cells initiate a process indicative of programmed cell death. How these cells are maintained in a highly turgescent state following this process is currently unknown. Here, we show that S-cells undergo substantial morphological changes during early differentiation. Vacuolar collapse and rapid clearance of the cytoplasm did not occur until senescence. Instead, smooth endoplasmic reticulum, Golgi bodies, vacuoles, and undifferentiated plastids were observed. Lack of chloroplasts indicates that S-cells depend on metabolite supply from neighbouring cells. Interestingly, TEM revealed numerous plasmodesmata between S-cells and neighbouring cells. Photoactivation of a symplasmic tracer showed coupling with neighbouring cells that are involved in glucosinolate synthesis. Hence, symplasmic transport might contribute to glucosinolate storage in S-cells. To investigate the fate of S-cells, we traced them in flower stalks from the earliest detectable stages to senescence. At late stages, S-cells were shown to deposit thick secondary cell walls and transform into phloem fibres. Thus, phloem fibres in the herbaceous plant Arabidopsis pass a pronounced phase of chemical defence during early stages of development.

[Biosynthesis of indole glucosinolates and ecological role of secondary modification pathways]

Indole glucosinolates are plant secondary metabolites derived from the amino acid tryptophan. They are part of a large group of sulfur-containing molecules almost exclusively found among Brassicales, which include the mustard family (Brassicaceae) with many edible plant species of major nutritional importance. These compounds mediate numerous interactions between these plants and their natural enemies and are therefore of major biological and economical interest. This literature review aims at taking stock of recent advances of our knowledge about the biosynthetic pathways of indole glucosinolates, but also about the defense strategies and ecological processes involving these metabolites.

Chemodiversity of the Glucosinolate-Myrosinase System at the Single Cell Type Resolution

Glucosinolates (GLSs) are a well-defined group of specialized metabolites, and like any other plant specialized metabolites, their presence does not directly affect the plant survival in terms of growth and development. However, specialized metabolites are essential to combat environmental stresses, such as pathogens and herbivores. GLSs naturally occur in many pungent plants in the order of Brassicales. To date, more than 200 different GLS structures have been characterized and their distribution differs from species to species. GLSs co-exist with classical and atypical myrosinases, which can hydrolyze GLS into an unstable aglycone thiohydroximate-O-sulfonate, which rearranges to produce different degradation products. GLSs, myrosinases, myrosinase interacting proteins, and GLS degradation products constitute the GLS-myrosinase (GM) system ("mustard oil bomb"). This review discusses the cellular and subcellular organization of the GM system, its chemodiversity, and functions in different cell types. Although there are many studies on the functions of GLSs and/or myrosinases at the tissue and whole plant levels, very few studies have focused on different single cell types. Single cell type studies will help to reveal specific functions that are missed at the tissue and organismal level. This review aims to highlight (1) recent progress in cellular and subcellular compartmentation of GLSs, myrosinases, and myrosinase interacting proteins; (2) molecular and biochemical diversity of GLSs and myrosinases; and (3) myrosinase interaction with its interacting proteins, and how it regulates the degradation of GLSs and thus the biological functions (e.g., plant defense against pathogens). Future prospects may include targeted approaches for engineering/breeding of plants and crops in the cell type-specific manner toward enhanced plant defense and nutrition.

Atypical Myrosinase as a Mediator of Glucosinolate Functions in Plants

Glucosinolates (GLSs) are a well-known class of specialized plant metabolites, distributed mostly in the order Brassicales. A vast research field in basic and applied sciences has grown up around GLSs owing to their presence in important agricultural crops and the model plant Arabidopsis thaliana, and their broad range of bioactivities beneficial to human health. The major purpose of GLSs in plants has been considered their function as a chemical defense against predators. GLSs are physically separated from a specialized class of beta-thioglucosidases called myrosinases, at the tissue level or at the single-cell level. They are brought together as a consequence of tissue damage, primarily triggered by herbivores, and their interaction results in the release of toxic volatile chemicals including isothiocyanates. In addition, recent studies have suggested that plants may adopt other strategies independent of tissue disruption for initiating GLS breakdown to cope with certain biotic/abiotic stresses. This hypothesis has been further supported by the discovery of an atypical class of GLS-hydrolyzing enzymes possessing features that are distinct from those of the classical myrosinases. Nevertheless, there is only little information on the physiological importance of atypical myrosinases. In this review, we focus on the broad diversity of the beta-glucosidase subclasses containing known atypical myrosinases in A. thaliana to discuss the hypothesis that numerous members of these subclasses can hydrolyze GLSs to regulate their diverse functions in plants. Also, the increasingly broadening functional repertoires of known atypical/classical myrosinases are described with reference to recent findings. Assessment of independent insights gained from A. thaliana with respect to (1) the phenotype of mutants lacking genes in the GLS metabolic/breakdown pathways, (2) fluctuation in GLS contents/metabolism under specific conditions, and (3) the response of plants to exogenous GLSs or their hydrolytic products, will enable us to reconsider the physiological importance of GLS breakdown in particular situations, which is likely to be regulated by specific beta-glucosidases.

Isothiocyanates from Brassica Vegetables-Effects of Processing, Cooking, Mastication, and Digestion

The formation of health-beneficial isothiocyanates (ITCs) from glucosinolates depends on a wide variety of plant-intrinsic factors (e.g., concentration of glucosinolates, activity of myrosinase, and specifier proteins) and on a multitude of extrinsic postharvest factors such as the conditions used during industrial processing, domestic preparation, mastication, and digestion. All of these factors contribute to a large variability in the formation of ITCs (and other breakdown products), as well as their intake and absorption upon consumption of Brassica vegetables. This uncertainty in ITC intake and absorption is a barrier for the determination of an optimal Brassica vegetable consumption pattern. In this review, the intrinsic and extrinsic factors that affect the formation, intake, and absorption of ITCs are described according to the most recent findings. The focus of this review includes the hydrolysis reaction mechanisms, the elucidation of the primary factors that play a role in the hydrolysis reaction, the influence of processing and cooking conditions, the effect of chewing, and the roles of the gastric and upper intestinal phases, including the effect of the meal composition (e.g., the effect of other meal compounds present during digestion) on the potential formation of ITCs.

Targeting detoxification genes by phloem-mediated RNAi: A new approach for controlling phloem-feeding insect pests

Many phloem-feeding insects are considered severe pests of agriculture and are controlled mainly by chemical insecticides. Continued extensive use of these inputs is environmentally undesirable, and also leads to the development of insecticide resistance. Here, we used a plant-mediated RNA interference (RNAi) approach, to develop a new control strategy for phloem-feeding insects. The approach aims to silence "key" detoxification genes, involved in the insect's ability to neutralize defensive and toxic plant chemistry. We targeted a glutathione S-transferase (GST) gene, BtGSTs5, in the phloem-feeding whitefly Bemisia tabaci, a devastating global agricultural pest. We report three major findings. First, significant down regulation of the BtGSTs5 gene was obtained in the gut of B. tabaci when the insects were fed on Arabidopsis thaliana transgenic plants expressing dsRNA against BtGSTs5 under a phloem-specific promoter. This brings evidence that phloem-feeding insects can be efficiently targeted by plant-mediated RNAi. Second, in-silico and in-vitro analyses indicated that the BtGSTs5 enzyme can accept as substrates, hydrolyzed aliphatic- and indolic-glucosinolates, and produce their corresponding detoxified conjugates. Third, performance assays suggested that the BtGSTs5 gene silencing prolongs the developmental period of B. tabaci nymphs. Taken together, these findings suggest that BtGSTs5 is likely to play an important role in enabling B. tabaci to successfully feed on glucosinolate-producing plants. Targeting the gene by RNAi in Brassicaceae cropping systems, will likely not eliminate the pest populations from the fields but will significantly reduce their success over the growing season, support prominent activity of natural enemies, eventually allowing the establishment of stable and sustainable agroecosystem.

Spatially Resolved Proteome Profiling of <200 Cells from Tomato Fruit Pericarp by Integrating Laser-Capture Microdissection with Nanodroplet Sample Preparation

Due to sensitivity limitations, global proteome measurements generally require large amounts of biological starting material, which masks heterogeneity within the samples and differential protein expression among constituent cell types. Methods for spatially resolved proteomics are being developed to resolve protein expression for distinct cell types among highly heterogeneous tissues, but have primarily been applied to mammalian systems. Here we evaluate the performance of cell-type-specific proteome analysis of tomato fruit pericarp tissues by a platform integrating laser-capture microdissection (LCM) and a recently developed automated sample preparation system (nanoPOTS, nanodroplet processing in one pot for trace samples). Tomato fruits were cryosectioned prior to LCM and tissues were dissected and captured directly into nanoPOTS chips for processing. Following processing, samples were analyzed by nanoLC-MS/MS. Approximately 1900 unique peptides and 422 proteins were identified on average from ∼0.04 mm² tissues comprising ∼8-15 parenchyma cells. Spatially resolved proteome analyses were performed using cells of outer epidermis, collenchyma, and parenchyma. Using ≤200 cells, a total of 1,870 protein groups were identified and the various tissues were easily resolved. The results provide spatial and tissue-specific insights into key enzymes and pathways involved in carbohydrate transport and source-sink relationships in tomato fruit. Of note, at the time of fruit ripening studied here, we identified differentially abundant proteins throughout the pericarp related to chlorophyll biogenesis, photosynthesis, and especially transport.

Extended darkness induces internal turnover of glucosinolates in Arabidopsis thaliana leaves

Prolonged darkness leads to carbohydrate starvation, and as a consequence plants degrade proteins and lipids to oxidize amino acids and fatty acids as alternative substrates for mitochondrial ATP production. We investigated, whether the internal breakdown of glucosinolates, a major class of sulfur-containing secondary metabolites, might be an additional component of the carbohydrate starvation response in Arabidopsis thaliana (A. thaliana). The glucosinolate content of A. thaliana leaves was strongly reduced after seven days of darkness. We also detected a significant increase in the activity of myrosinase, the enzyme catalyzing the initial step in glucosinolate breakdown, coinciding with a strong induction of the main leaf myrosinase isoforms TGG1 and TGG2. In addition, nitrilase activity was increased suggesting a turnover via nitriles and carboxylic acids. Internal degradation of glucosinolates might also be involved in diurnal or developmental adaptations of the glucosinolate profile. We observed a diurnal rhythm for myrosinase activity in two-week-old plants. Furthermore, leaf myrosinase activity and protein abundance of TGG2 varied during plant development, whereas leaf protein abundance of TGG1 remained stable indicating regulation at the transcriptional as well as post-translational level.

Localization of the glucosinolate biosynthetic enzymes reveals distinct spatial patterns for the biosynthesis of indole and aliphatic glucosinolates

Glucosinolates constitute the primary defense metabolites in Arabidopsis thaliana (Arabidopsis). Indole and aliphatic glucosinolates, biosynthesized from tryptophan and methionine, respectively, are known to serve distinct biological functions. Although all genes in the biosynthetic pathways are identified, and it is known where glucosinolates are stored, it has remained elusive where glucosinolates are produced at the cellular and tissue level. To understand how the spatial organization of the different glucosinolate biosynthetic pathways contributes to their distinct biological functions, we investigated the localization of enzymes of the pathways under constitutive conditions and, for indole glucosinolates, also under induced conditions, by analyzing the spatial distribution of several fluorophore-tagged enzymes at the whole plant and the cellular level. We show that key steps in the biosynthesis of the different types of glucosinolates are localized in distinct cells in separate as well as overlapping vascular tissues. The presence of glucosinolate biosynthetic enzymes in parenchyma cells of the vasculature may assign new defense-related functions to these cell types. The knowledge gained in this study is an important prerequisite for understanding the orchestration of chemical defenses from site of synthesis to site of storage and potential (re)mobilization upon attack.

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.

How does a plant orchestrate defense in time and space? Using glucosinolates in Arabidopsis as case study

The sessile nature of plants has caused plants to develop means to defend themselves against attacking organisms. Multiple strategies range from physical barriers to chemical warfare including pre-formed anticipins as well as phytoalexins produced only upon attack. While phytoalexins require rapid induction, constitutive defenses can impose ecological costs if they deter pollinators or attract specialized herbivores. In the model Arabidopsis thaliana, the well-characterized glucosinolate anticipins are categorized into different classes, aliphatic and indole glucosinolates, depending on their amino acid precursor. Using glucosinolates in Arabidopsis as case study, we will discuss how plants orchestrate synthesis, storage and activation of pre-formed defense compounds spatially and temporally.

PP2A-B'γ modulates foliar trans-methylation capacity and the formation of 4-methoxy-indol-3-yl-methyl glucosinolate in Arabidopsis leaves

Glucosinolates (GSL) of cruciferous plants comprise a major group of structurally diverse secondary compounds which act as deterrents against aphids and microbial pathogens and have large commercial and ecological impacts. While the transcriptional regulation governing the biosynthesis and modification of GSL is now relatively well understood, post-translational regulatory components that specifically determine the structural variation of indole glucosinolates have not been reported. We show that the cytoplasmic protein phosphatase 2A regulatory subunit B'γ (PP2A-B'γ) physically interacts with indole glucosinolate methyltransferases and controls the methoxylation of indole glucosinolates and the formation of 4-methoxy-indol-3-yl-methyl glucosinolate in Arabidopsis leaves. By taking advantage of proteomic approaches and metabolic analysis we further demonstrate that PP2A-B'γ is required to control the abundance of oligomeric protein complexes functionally linked with the activated methyl cycle and the trans-methylation capacity of leaf cells. These findings highlight the key regulatory role of PP2A-B'γ in methionine metabolism and provide a previously unrecognized perspective for metabolic engineering of glucosinolate metabolism in cruciferous plants.

Fire and Brimstone: Molecular Interactions between Sulfur and Glucosinolate Biosynthesis in Model and Crop Brassicaceae

Glucosinolates (GSLs) represent one of the most widely studied classes of plant secondary metabolite, and have a wide range of biological activities. Their unique properties also affect livestock and human health, and have been harnessed for food and other end-uses. Since GSLs are sulfur (S)-rich there are many lines of evidence suggesting that plant S status plays a key role in determining plant GSL content. However, there is still a need to establish a detailed knowledge of the distribution and remobilization of S and GSLs throughout the development of Brassica crops, and to represent this in terms of primary and secondary sources and sinks. The increased genome complexity, gene duplication and divergence within brassicas, together with their ontogenetic plasticity during crop development, appear to have a marked effect on the regulation of S and GSLs. Here, we review the current understanding of inorganic S (sulfate) assimilation into organic S forms, including GSLs and their precursors, the intracellular and inter-organ transport of inorganic and organic S forms, and the accumulation of GSLs in specific tissues. We present this in the context of overlapping sources and sinks, transport processes, signaling molecules and their associated molecular interactions. Our analysis builds on recent insights into the molecular regulation of sulfate uptake and transport by different transporters, transcription factors and miRNAs, and the role that these may play in GSL biosynthesis. We develop a provisional model describing the key processes that could be targeted in crop breeding programs focused on modifying GSL content.

Regulation of plant secondary metabolism and associated specialized cell development by MYBs and bHLHs

Plants are unrivaled in the natural world in both the number and complexity of secondary metabolites they produce, and the ubiquitous phenylpropanoids and the lineage-specific glucosinolates represent two such large and chemically diverse groups. Advances in genome-enabled biochemistry and metabolomic technologies have greatly increased the understanding of their metabolic networks in diverse plant species. There also has been some progress in elucidating the gene regulatory networks that are key to their synthesis, accumulation and function. This review highlights what is currently known about the gene regulatory networks and the stable sub-networks of transcription factors at their cores that regulate the production of these plant secondary metabolites and the differentiation of specialized cell types that are equally important to their defensive function. Remarkably, some of these core components are evolutionarily conserved between secondary metabolism and specialized cell development and across distantly related plant species. These findings suggest that the more ancient gene regulatory networks for the differentiation of fundamental cell types may have been recruited and remodeled for the generation of the vast majority of plant secondary metabolites and their specialized tissues.

Comparative proteomics of cucurbit phloem indicates both unique and shared sets of proteins

Cucurbits are well-studied models for phloem biology but unusually possess both fascicular phloem (FP) within vascular bundles and additional extrafascicular phloem (EFP). Although the functional differences between the two systems are not yet clear, sugar analysis and limited protein profiling have established that FP and EFP have divergent compositions. Here we report a detailed comparative proteomics study of FP and EFP in two cucurbits, pumpkin and cucumber. We re-examined the sites of exudation by video microscopy, and confirmed that in both species, the spontaneous exudate following tissue cutting derives almost exclusively from EFP. Comparative gel electrophoresis and mass spectrometry-based proteomics of exudates, sieve element contents and microdissected stem tissues established that EFP and FP profiles are highly dissimilar, and that there are also species differences. Searches against cucurbit databases enabled identification of more than 300 FP proteins from each species. Few of the detected proteins (about 10%) were shared between the sieve element contents of FP and EFP, and enriched Gene Ontology categories also differed. To explore quantitative differences in the proteomes, we developed multiple reaction monitoring methods for cucumber proteins that are representative markers for FP or EFP and assessed exudate composition at different times after tissue cutting. Based on failure to detect FP markers in exudate samples, we conclude that FP is blocked very rapidly and therefore makes a minimal contribution to the exudates. Overall, the highly divergent contents of FP and EFP indicate that they are substantially independent vascular compartments.

Meselect - A Rapid and Effective Method for the Separation of the Main Leaf Tissue Types

Individual tissues of complex eukaryotic organisms have specific gene expression programs that control their functions. Therefore, tissue-specific molecular information is required to increase our understanding of tissue-specific processes. Established methods in plants to obtain specific tissues or cell types from their organ or tissue context typically require the enzymatic degradation of cell walls followed by fluorescence-activated cell sorting (FACS) using plants engineered for localized expression of green fluorescent protein. This has facilitated the acquisition of valuable data, mainly on root cell type-specific transcript and protein expression. However, FACS of different leaf cell types is difficult because of chlorophyll autofluorescence that interferes with the sorting process. Furthermore, the cell wall composition is different in each cell type. This results in long incubation times for refractory cell types, and cell sorting itself can take several hours. To overcome these limitations, we developed Meselect (mechanical separation of leaf compound tissues), a rapid and effective method for the separation of leaf epidermal, vascular and mesophyll tissues. Meselect is a novel combination of mechanical separation and rapid protoplasting, which benefits from the unique cell wall composition of the different tissue types. Meselect has several advantages over cell sorting: it does not require expensive equipment such as a cell sorter and does not depend on specific fluorescent reporter lines, the use of blenders as well as the inherent mixing of different cell types and of intact and damaged cells can be avoided, and the time between wounding of the leaf and freezing of the sample is short. The efficacy and specificity of the method to enrich the different leaf tissue types has been confirmed using Arabidopsis leaves, but it has also been successfully used for leaves of other plants such as tomato or cassava. The method is therefore useful for plant scientists investigating leaf development or responses to stimuli at the tissue-specific level.

Transport of defense compounds from source to sink: lessons learned from glucosinolates

Plants synthesize a plethora of defense compounds crucial for their survival in a challenging and changing environment. Transport processes are important for shaping the distribution pattern of defense compounds, albeit focus hitherto has been mostly on their biosynthetic pathways. A recent identification of two glucosinolate transporters represents a breakthrough in our understanding of glucosinolate transport in Arabidopsis and has advanced knowledge in transport of defense compounds. In this review, we discuss the role of the glucosinolate transporters in establishing dynamic glucosinolate distribution patterns and source-sink relations. We focus on lessons learned from glucosinolate transport that may apply to transport of other defense compounds and discuss future avenues in the emerging field of defense compound transport.

Proteasome targeting of proteins in Arabidopsis leaf mesophyll, epidermal and vascular tissues

Protein and transcript levels are partly decoupled as a function of translation efficiency and protein degradation. Selective protein degradation via the Ubiquitin-26S proteasome system (UPS) ensures protein homeostasis and facilitates adjustment of protein abundance during changing environmental conditions. Since individual leaf tissues have specialized functions, their protein composition is different and hence also protein level regulation is expected to differ. To understand UPS function in a tissue-specific context we developed a method termed Meselect to effectively and rapidly separate Arabidopsis thaliana leaf epidermal, vascular and mesophyll tissues. Epidermal and vascular tissue cells are separated mechanically, while mesophyll cells are obtained after rapid protoplasting. The high yield of proteins was sufficient for tissue-specific proteome analyses after inhibition of the proteasome with the specific inhibitor Syringolin A (SylA) and affinity enrichment of ubiquitylated proteins. SylA treatment of leaves resulted in the accumulation of 225 proteins and identification of 519 ubiquitylated proteins. Proteins that were exclusively identified in the three different tissue types are consistent with specific cellular functions. Mesophyll cell proteins were enriched for plastid membrane translocation complexes as targets of the UPS. Epidermis enzymes of the TCA cycle and cell wall biosynthesis specifically accumulated after proteasome inhibition, and in the vascular tissue several enzymes involved in glucosinolate biosynthesis were found to be ubiquitylated. Our results demonstrate that protein level changes and UPS protein targets are characteristic of the individual leaf tissues and that the proteasome is relevant for tissue-specific functions.

Diversified glucosinolate metabolism: biosynthesis of hydrogen cyanide and of the hydroxynitrile glucoside alliarinoside in relation to sinigrin metabolism in Alliaria petiolata

Alliaria petiolata (garlic mustard, Brassicaceae) contains the glucosinolate sinigrin as well as alliarinoside, a γ-hydroxynitrile glucoside structurally related to cyanogenic glucosides. Sinigrin may defend this plant against a broad range of enemies, while alliarinoside confers resistance to specialized (glucosinolate-adapted) herbivores. Hydroxynitrile glucosides and glucosinolates are two classes of specialized metabolites, which generally do not occur in the same plant species. Administration of [UL-(14)C]-methionine to excised leaves of A. petiolata showed that both alliarinoside and sinigrin were biosynthesized from methionine. The biosynthesis of alliarinoside was shown not to bifurcate from sinigrin biosynthesis at the oxime level in contrast to the general scheme for hydroxynitrile glucoside biosynthesis. Instead, the aglucon of alliarinoside was formed from metabolism of sinigrin in experiments with crude extracts, suggesting a possible biosynthetic pathway in intact cells. Hence, the alliarinoside pathway may represent a route to hydroxynitrile glucoside biosynthesis resulting from convergent evolution. Metabolite profiling by LC-MS showed no evidence of the presence of cyanogenic glucosides in A. petiolata. However, we detected hydrogen cyanide (HCN) release from sinigrin and added thiocyanate ion and benzyl thiocyanate in A. petiolata indicating an enzymatic pathway from glucosinolates via allyl thiocyanate and indole glucosinolate derived thiocyanate ion to HCN. Alliarinoside biosynthesis and HCN release from glucosinolate-derived metabolites expand the range of glucosinolate-related defenses and can be viewed as a third line of defense, with glucosinolates and thiocyanate forming protein being the first and second lines, respectively.

Myrosin idioblast cell fate and development are regulated by the Arabidopsis transcription factor FAMA, the auxin pathway, and vesicular trafficking

Crucifer shoots harbor a glucosinolate-myrosinase system that defends against insect predation. Arabidopsis thaliana myrosinase (thioglucoside glucohydrolase [TGG]) accumulates in stomata and in myrosin idioblasts (MIs). This work reports that the basic helix-loop-helix transcription factor FAMA that is key to stomatal development is also expressed in MIs. The loss of FAMA function abolishes MI fate as well as the expression of the myrosinase genes TGG1 and TGG2. MI cells have previously been reported to be located in the phloem. Instead, we found that MIs arise from the ground meristem rather than provascular tissues and thus are not homologous with phloem. Moreover, MI patterning and morphogenesis are abnormal when the function of the ARF-GEF gene GNOM is lost as well as when auxin efflux and vesicular trafficking are chemically disrupted. Stomata and MI cells constitute part of a wider system that reduces plant predation, the so-called "mustard oil bomb," in which vacuole breakage in cells harboring myrosinase and glucosinolate yields a brew toxic to many animals, especially insects. This identification of the gene that confers the fate of MIs, as well as stomata, might facilitate the development of strategies for engineering crops to mitigate predation.

The broccoli (Brassica oleracea) phloem tissue proteome

BACKGROUND

The transport of sugars, hormones, amino acids, proteins, sugar alcohols, and other organic compounds from the sites of synthesis to the sites of use or storage occurs through the conducting cells of the phloem. To better understand these processes a comprehensive understanding of the proteins involved is required. While a considerable amount of data has been obtained from proteomic analyses of phloem sap, this has mainly served to identify the soluble proteins that are translocated through the phloem network.

RESULTS

In order to obtain more comprehensive proteomic data from phloem tissue we developed a simple dissection procedure to isolate phloem tissue from Brassica oleracea. The presence of a high density of phloem sieve elements was confirmed using light microscopy and fluorescently labeled sieve element-specific antibodies. To increase the depth of the proteomic analysis for membrane bound and associated proteins, soluble proteins were extracted first and subsequent extractions were carried out using two different detergents (SDS and CHAPSO). Across all three extractions almost four hundred proteins were identified and each extraction method added to the analysis demonstrating the utility of an approach combining several extraction protocols.

CONCLUSIONS

The phloem was found to be enriched in proteins associated with biotic and abiotic stress responses and structural proteins. Subsequent expression analysis identified a number of genes that appear to be expressed exclusively or at very high levels in phloem tissue, including genes that are known to express specifically in the phloem as well as novel phloem genes.

Arabidopsis thaliana plants with different levels of aliphatic- and indolyl-glucosinolates affect host selection and performance of Bemisia tabaci

Generalist insects show reduced selectivity when subjected to similar, but not identical, host plant chemical signatures. Here, we produced transgenic Arabidopsis thaliana plants that over-express genes regulating the aliphatic- and indolyl- glucosinolates biosynthetic pathways with either a constitutive (CaMV 35S) or a phloem-specific promoter (AtSUC2). This allowed us to examine how exposure to high levels of aliphatic- or indolyl-glucosinolates in homogenous habitats (leaf cage apparatus containing two wild-type or two transgenic leaves) and heterogeneous habitats (leaf cage apparatus containing one wild-type and one transgenic leaf) affects host selection and performance of Bemsia tabaci, a generalist phloem-feeding insect. Data from homogenous habitats indicated that exposure to A. thaliana plants accumulating high levels of aliphatic- or indolyl-glucosinolates negatively affected the performance of both adult females and nymphs of B. tabaci. Data from heterogeneous habitats indicated that B. tabaci adult females selected for oviposition plants on which their offspring perform better (preference-performance relationship). However, the combinations of wild-type and transgenic plants in heterogeneous habitats increased the period of time until the first choice was made and led to increased movement rate on transgenic plants, and reduced fecundity on wild-type plants. Overall, our findings are consistent with the view that both performance and selectivity of B. tabaci decrease in heterogeneous habitats that contain plants with closely-related chemical signatures.

Integration of biosynthesis and long-distance transport establish organ-specific glucosinolate profiles in vegetative Arabidopsis

Although it is essential for plant survival to synthesize and transport defense compounds, little is known about the coordination of these processes. Here, we investigate the above- and belowground source-sink relationship of the defense compounds glucosinolates in vegetative Arabidopsis thaliana. In vivo feeding experiments demonstrate that the glucosinolate transporters1 and 2 (GTR1 and GTR2), which are essential for accumulation of glucosinolates in seeds, are likely to also be involved in bidirectional distribution of glucosinolates between the roots and rosettes, indicating phloem and xylem as their transport pathways. Grafting of wild-type, biosynthetic, and transport mutants show that both the rosette and roots are able to synthesize aliphatic and indole glucosinolates. While rosettes constitute the major source and storage site for short-chained aliphatic glucosinolates, long-chained aliphatic glucosinolates are synthesized both in roots and rosettes with roots as the major storage site. Our grafting experiments thus indicate that in vegetative Arabidopsis, GTR1 and GTR2 are involved in bidirectional long-distance transport of aliphatic but not indole glucosinolates. Our data further suggest that the distinct rosette and root glucosinolate profiles in Arabidopsis are shaped by long-distance transport and spatially separated biosynthesis, suggesting that integration of these processes is critical for plant fitness in complex natural environments.

ZIC-cHILIC as a fractionation method for sensitive and powerful shotgun proteomics

Multidimensional liquid chromatography (LC) combined with mass spectrometry (MS) has become a standard technique in proteomics to reduce sample complexity and to tackle the dynamic range in protein abundance. Fractionation is necessary to obtain a comprehensive analysis of complex biological samples such as tissue and mammalian cell lines. However, extensive fractionation comes at the expense of sample loss, presenting a bottleneck in the analysis of limited amounts of material. In this protocol, we describe a two-dimensional chromatographic strategy based on a combination of hydrophilic interaction liquid chromatography (HILIC; with a zwitterionic packing material, ZIC-cHILIC) and reversed-phase chromatography, which allows proteomic analyses with minimal sample loss. Experimental aspects related to obtaining maximum recovery are discussed, including how to optimally prepare samples for this system. Examples involving protein lysates originating from cultured cell lines and cells sorted by flow cytometry are used to show the power, sensitivity and versatility of the technique. Once the ZIC-cHILIC fractionation system has been optimized and standardized, this protocol requires ∼5-6 d, including sample preparation and fraction analysis.

Quantitative biology of single neurons

The building blocks of complex biological systems are single cells. Fundamental insights gained from single-cell analysis promise to provide the framework for understanding normal biological systems development as well as the limits on systems/cellular ability to respond to disease. The interplay of cells to create functional systems is not well understood. Until recently, the study of single cells has concentrated primarily on morphological and physiological characterization. With the application of new highly sensitive molecular and genomic technologies, the quantitative biochemistry of single cells is now accessible.

Mass spectrometry imaging of glucosinolates in Arabidopsis flowers and siliques

Glucosinolates are multi-functional plant secondary metabolites which play a vital role in plant defence and are, as dietary compounds, important to human health and livestock well-being. Knowledge of the tissue-specific regulation of their biosynthesis and accumulation is essential for plant breeding programs. Here, we report that in Arabidopsis thaliana, glucosinolates are accumulated differentially in specific cells of reproductive organs. Using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI), distribution patterns of three selected compounds, 4-methylsulfinylbutyl (glucoraphanin), indol-3-ylmethyl (glucobrassicin), and 4-benzoyloxybutyl glucosinolates, were mapped in the tissues of whole flower buds, sepals and siliques. The results show that tissue localization patterns of aliphatic glucosinolate glucoraphanin and 4-benzoyloxybutyl glucosinolate were similar, but indole glucosinolate glucobrassicin had different localisation, indicating a possible difference in function. The high resolution images obtained by a complementary approach, cryo-SEM Energy Dispersive X-ray analysis (cryo-SEM-EDX), confirmed increased concentration of sulphur in areas with elevated amounts of glucosinolates, and allowed identifying the cell types implicated in accumulation of glucosinolates. High concentration of sulphur was found in S-cells adjacent to the phloem in pedicels and siliques, indicating the presence of glucosinolates. Moreover, both MALDI MSI and cryo-SEM-EDX analyses indicated accumulation of glucosinolates in cells on the outer surface of the sepals, suggesting that a layer of glucosinolate-accumulating epidermal cells protects the whole of the developing flower, in addition to the S-cells, which protect the phloem. This research demonstrates the high potential of MALDI MSI for understanding the cell-specific compartmentation of plant metabolites and its regulation.