The plastidic bile acid transporter 5 is required for the biosynthesis of methionine-derived glucosinolates in Arabidopsis thaliana

Improved pokeweed genome assembly and early gene expression changes in response to jasmonic acid

BACKGROUND

Jasmonic acid (JA) is a phytohormone involved in regulating responses to biotic and abiotic stress. Although the JA pathway is well characterized in model plants such as Arabidopsis thaliana, less is known about many non-model plants. Phytolacca americana (pokeweed) is native to eastern North Americana and is resilient to environmental stress. The goal of this study was to produce a publicly available pokeweed genome assembly and annotations and use this resource to determine how early response to JA changes gene expression, with particular focus on genes involved in defense.

RESULTS

We assembled the pokeweed genome de novo from approximately 30 Gb of PacBio Hifi long reads and achieved an NG50 of ~ 13.2 Mb and a minimum 93.9% complete BUSCO score for gene annotations. With this reference, we investigated the early changes in pokeweed gene expression following JA treatment. Approximately 5,100 genes were differentially expressed during the 0-6 h time course with almost equal number of genes with increased and decreased transcript levels. Cluster and gene ontology analyses indicated the downregulation of genes associated with photosynthesis and upregulation of genes involved in hormone signaling and defense. We identified orthologues of key transcription factors and constructed the first JA gene response network integrated with our transcriptomic data from orthologues of Arabidopsis genes. We discovered that pokeweed did not use leaf senescence as a means of reallocating resources during stress; rather, most secondary metabolite synthesis genes were constitutively expressed, suggesting that pokeweed directs its resources for survival over the long term. In addition, pokeweed synthesizes several RNA N-glycosylases hypothesized to function in defense, each with unique expression profiles in response to JA.

CONCLUSIONS

Our investigation of the early response of pokeweed to JA illustrates patterns of gene expression involved in defence and stress tolerance. Pokeweed provides insight into the defense mechanisms of plants beyond those observed in research models and crops, and further study may yield novel approaches to improving the resilience of plants to environmental changes. Our assembled pokeweed genome is the first within the taxonomic family Phytolaccaceae to be publicly available for continued research.

Chloroplast-localized PvBASS2 regulates salt tolerance in the C4 plant seashore paspalum

BILE ACID

SODIUM SYMPORTER FAMILY PROTEIN 2 (BASS2) is localized within chloroplast membranes, facilitating the translocation of pyruvate and Na+ from the cytosol to the plastid, where pyruvate supports isopentenyl diphosphate (IPP) synthesis via the methylerythritol phosphate pathway in C3 plants. Nevertheless, the biological function of BASS2 in C4 plants has not been well defined. This study unveils a previously unidentified role of PvBASS2 in Na+ and pyruvate transport in seashore paspalum (Paspalum vaginatum), a halophytic C4 grass, indicating a specific cellular function within this plant species. Data showed that overexpression of PvBASS2 in seashore paspalum attenuated salt tolerance, whereas its RNAi lines exhibited enhanced salt resistance compared to wild-type plants, suggesting a negative regulatory role of PvBASS2 in seashore paspalum salt tolerance. The constitutive overexpression of PvBASS2 was also found to reduce salt tolerance in Arabidopsis. Further study revealed that PvBASS2 negatively regulates seashore paspalum salt tolerance, possibly due to elevated Na+/K+ ratio, disrupted chloroplast structure, and reduced photosynthetic efficiency following exposure to salinity. Importantly, our subsequent investigations revealed that modulation of PvBASS2 expression in seashore paspalum influenced carbon dioxide assimilation, intermediary metabolites of the tricarboxylic acid cycle, and enzymatic activities under salinity treatment, which in turn led to alterations in free amino acid concentrations. Thus, this study reveals a role for BASS2 in the C4 plant seashore paspalum and enhances our comprehension of salt stress responses in C4 plants.

Genome-Wide Identification and Expression Analysis of BrBASS Genes in Brassica rapa Reveals Their Potential Roles in Abiotic Stress Tolerance

The bile acid sodium symporter (BASS) family plays an important role in transporting substances and coordinating plants' salt tolerance. However, the function of BASS in Brassica rapa has not yet been elucidated. In this study, eight BrBASS genes distributed on five chromosomes were identified that belonged to four subfamilies. Expression profile analysis showed that BrBASS7 was highly expressed in roots, whereas BrBASS4 was highly expressed in flowers. The promoter element analysis also identified several typical homeopathic elements involved in abiotic stress tolerance and stress-related hormonal responses. Notably, under salt stress, the expression of BrBASS2 was significantly upregulated; under osmotic stress, that of BrBASS4 increased and then decreased; and under cold stress, that of BrBASS7 generally declined. The protein-protein interaction analysis revealed that the BrBASS2 homologous gene AtBASS2 interacted with Nhd1 (N-mediated heading date-1) to alleviate salt stress in plants, while the BrBASS4 homologous gene AtBASS3 interacted with BLOS1 (biogenesis of lysosome-related organelles complex 1 subunit 1) via co-regulation with SNX1 (sorting nexin 1) to mitigate an unfavorable growing environment for roots. Further, Bra-miR396 (Bra-microRNA396) targeting BrBASS4 and BrBASS7 played a role in the plant response to osmotic and cold stress conditions, respectively. This research demonstrates that BrBASS2, BrBASS4, and BrBASS7 harbor great potential for regulating abiotic stresses. The findings will help advance the study of the functions of the BrBASS gene family.

AtMYB41 acts as a dual-function transcription factor that regulates the formation of lipids in an organ- and development-dependent manner

The plant cuticle controls non-stomatal water loss and can serve as a barrier against biotic agents, whereas the heteropolymer suberin and its associated waxes are deposited constitutively at specific cell wall locations. While several transcription factors controlling cuticle formation have been identified, those involved in the transcriptional regulation of suberin biosynthesis remain poorly characterized. The major goal of this study was to further analyse the function of the R2R3-Myeloblastosis (MYB) transcription factor AtMYB41 in formation of the cuticle, suberin, and suberin-associated waxes throughout plant development. For functional analysis, the organ-specific expression pattern of AtMYB41 was analysed and Atmyb41ge alleles were generated using the CRISPR/Cas9 system. These were investigated for root growth and water permeability upon stress. In addition, the fatty acid, wax, cutin, and suberin monomer composition of different organs was evaluated by gas chromatography. The characterization of Atmyb41ge mutants revealed that AtMYB41 negatively regulates the production of cuticular lipids and fatty acid biosynthesis in leaves and seeds, respectively. Remarkably, biochemical analyses indicate that AtMYB41 also positively regulates the formation of cuticular waxes in stems of Arabidopsis thaliana. Overall, these results suggest that the AtMYB41 acts as a negative regulator of cuticle and fatty acid biosynthesis in leaves and seeds, respectively, but also as a positive regulator of wax production in A. thaliana stems.

Subcellular compartmentalization in the biosynthesis and engineering of plant natural products

Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.

Mechanism of substrate binding and transport in BASS transporters

The bile acid sodium symporter (BASS) family transports a wide array of molecules across membranes, including bile acids in humans, and small metabolites in plants. These transporters, many of which are sodium-coupled, have been shown to use an elevator mechanism of transport, but exactly how substrate binding is coupled to sodium ion binding and transport is not clear. Here, we solve the crystal structure at 2.3 Å of a transporter from Neisseria meningitidis (ASBTNM) in complex with pantoate, a potential substrate of ASBTNM. The BASS family is characterised by two helices that cross-over in the centre of the protein in an arrangement that is intricately held together by two sodium ions. We observe that the pantoate binds, specifically, between the N-termini of two of the opposing helices in this cross-over region. During molecular dynamics simulations the pantoate remains in this position when sodium ions are present but is more mobile in their absence. Comparison of structures in the presence and absence of pantoate demonstrates that pantoate elicits a conformational change in one of the cross-over helices. This modifies the interface between the two domains that move relative to one another to elicit the elevator mechanism. These results have implications, not only for ASBTNM but for the BASS family as a whole and indeed other transporters that work through the elevator mechanism.

Mechanism of substrate binding and transport in BASS transporters

The Bile Acid Sodium Symporter (BASS) family transports a wide array of molecules across membranes, including bile acids in humans, and small metabolites in plants. These transporters, many of which are sodium-coupled, have been shown to use an elevator mechanism of transport, but exactly how substrate binding is coupled to sodium ion binding and transport is not clear. Here we solve the crystal structure at 2.3 Å of a transporter from Neisseria Meningitidis (ASBTNM) in complex with pantoate, a potential substrate of ASBTNM. The BASS family is characterised by two helices that cross-over in the centre of the protein in an arrangement that is intricately held together by two sodium ions. We observe that the pantoate binds, specifically, between the N-termini of two of the opposing helices in this cross-over region. During molecular dynamics simulations the pantoate remains in this position when sodium ions are present but is more mobile in their absence. Comparison of structures in the presence and absence of pantoate demonstrates that pantoate elicits a conformational change in one of the cross-over helices. This modifies the interface between the two domains that move relative to one another to elicit the elevator mechanism. These results have implications, not only for ASBTNM but for the BASS family as a whole and indeed other transporters that work through the elevator mechanism.

Identification of new potential downstream transcriptional targets of the strigolactone pathway including glucosinolate biosynthesis

Strigolactones regulate shoot branching and many aspects of plant growth, development, and allelopathy. Strigolactones are often discussed alongside auxin because they work together to inhibit shoot branching. However, the roles and mechanisms of strigolactones and how they act independently of auxin are still elusive. Additionally, there is still much in general to be discovered about the network of molecular regulators and their interactions in response to strigolactones. Here, we conducted an experiment in Arabidopsis with physiological treatments and strigolactone mutants to determine transcriptional pathways associated with strigolactones. The three physiological treatments included shoot tip removal with and without auxin treatment and treatment of intact plants with the auxin transport inhibitor, N-1-naphthylphthalamic acid (NPA). We identified the glucosinolate biosynthesis pathway as being upregulated across strigolactone mutants indicating strigolactone-glucosinolate crosstalk. Additionally, strigolactone application cannot restore the highly branched phenotype observed in glucosinolate biosynthesis mutants, placing glucosinolate biosynthesis downstream of strigolactone biosynthesis. Oxidative stress genes were enriched across the experiment suggesting that this process is mediated through multiple hormones. Here, we also provide evidence supporting non-auxin-mediated, negative feedback on strigolactone biosynthesis. Increases in strigolactone biosynthesis gene expression seen in strigolactone mutants could not be fully restored by auxin. By contrast, auxin could fully restore auxin-responsive gene expression increases, but not sugar signaling-related gene expression. Our data also point to alternative roles of the strigolactone biosynthesis genes and potential new signaling functions of strigolactone precursors. In this study, we identify a strigolactone-specific regulation of glucosinolate biosynthesis genes indicating that the two are linked and may work together in regulating stress and shoot ranching responses in Arabidopsis. Additionally, we provide evidence for non-auxinmediated feedback on strigolactone biosynthesis and discuss this in the context of sugar signaling.

Transcriptomic and epigenomic analyses revealed that polycomb repressive complex 2 regulates not only developmental but also stress responsive metabolism in Brassica rapa

Polycomb group proteins (PcG) play a crucial role in developmental programs in eukaryotic organisms, including plants. PcG-mediated gene repression is achieved by epigenetic histone modification on target chromatins. Loss of PcG components leads to severe developmental defects. CURLY LEAF (CLF), a PcG component in Arabidopsis, catalyzes the trimethylation of histone H3 on lysine 27 (H3K27me3), a repressive histone mark in numerous genes in Arabidopsis. In this study, we isolated a single homolog of Arabidopsis CLF, namely, BrCLF, in Brassica rapa ssp. trilocularis. Transcriptomic analysis revealed that BrCLF participated in B. rapa developmental processes, such as seed dormancy, leaf and flower organ development, and floral transition. BrCLF was also involved in stress signaling and stress-responsive metabolism, such as aliphatic and indolic glucosinolate metabolism in B. rapa. Epigenome analysis showed that H3K27me3 was substantially enriched in genes related to these developmental and stress-responsive processes. Thus, this study provided a basis for elucidating the molecular mechanism of the PcG-mediated regulation of development and stress responses in B. rapa.

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.

Genetic Improvement of Camelina sativa (L.) Crantz: Opportunities and Challenges

In recent years, a renewed interest in novel crops has been developing due to the environmental issues associated with the sustainability of agricultural practices. In particular, a cover crop, Camelina sativa (L.) Crantz, belonging to the Brassicaceae family, is attracting the scientific community's interest for several desirable features. It is related to the model species Arabidopsis thaliana, and its oil extracted from the seeds can be used either for food and feed, or for industrial uses such as biofuel production. From an agronomic point of view, it can grow in marginal lands with little or no inputs, and is practically resistant to the most important pathogens of Brassicaceae. Although cultivated in the past, particularly in northern Europe and Italy, in the last century, it was abandoned. For this reason, little breeding work has been conducted to improve this plant, also because of the low genetic variability present in this hexaploid species. In this review, we summarize the main works on this crop, focused on genetic improvement with three main objectives: yield, seed oil content and quality, and reduction in glucosinolates content in the seed, which are the main anti-nutritional substances present in camelina. We also report the latest advances in utilising classical plant breeding, transgenic approaches, and CRISPR-Cas9 genome-editing.

Optimization of Heterologous Glucoraphanin Production In Planta

Glucoraphanin is a plant specialized metabolite found in cruciferous vegetables that has long been a target for production in a heterologous host because it can subsequently be hydrolyzed to form the chemopreventive compound sulforaphane before and during consumption. However, previous studies have only been able to produce small amounts of glucoraphanin in heterologous plant and microbial systems compared to the levels found in glucoraphanin-producing plants, suggesting that there may be missing auxiliary genes that play a role in improving production in planta. In an effort to identify auxiliary genes required for high glucoraphanin production, we leveraged transient expression in Nicotiana benthamiana to screen a combination of previously uncharacterized coexpressed genes and rationally selected genes alongside the glucoraphanin biosynthetic pathway. This strategy alleviated metabolic bottlenecks, which improved glucoraphanin production by 4.74-fold. Our optimized glucoraphanin biosynthetic pathway provides a pathway amenable for high glucoraphanin production.

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.

A Comparative Transcriptome and Metabolome Combined Analysis Reveals the Key Genes and Their Regulatory Model Responsible for Glucoraphasatin Accumulation in Radish Fleshy Taproots

Radish (Raphanus sativus L.) is rich in specific glucosinolates (GSLs), which benefit human health and special flavor formation. Although the basic GSLs metabolic pathway in Brassicaceae plants is clear, the regulating mechanism for specific glucosinolates content in radish fleshy taproots is not well understood. In this study, we discovered that there was a significant difference in the GSLs profiles and the content of various GSLs components. Glucoraphasatin (GRH) is the most predominant GSL in radish taproots of different genotypes as assessed by HPLC analysis. Further, we compared the taproot transcriptomes of three radish genotypes with high and low GSLs content by employing RNA-seq. Totally, we identified forty-one differentially expressed genes related to GSLs metabolism. Among them, thirteen genes (RsBCAT4, RsIPMDH1, RsMAM1a, RsMAM1b, RsCYP79F1, RsGSTF9, RsGGP1, RsSUR1, RsUGT74C1, RsST5b, RsAPK1, RsGSL-OH, and RsMYB28) were significantly higher co-expressed in the high content genotypes than in low content genotype. Notably, correlation analysis indicated that the expression level of RsMYB28, as an R2R3 transcription factor directly regulating aliphatic glucosinolate biosynthesis, was positively correlated with the GRH content. Co-expression network showed that RsMYB28 probably positively regulated the expression of the above genes, particularly RsSUR1, and consequently the synthesis of GRH. Moreover, the molecular mechanism of the accumulation of this 4-carbon (4C) GSL in radish taproots was explored. This study provides new perspectives on the GSLs accumulation mechanism and genetic improvements in radish taproots.

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.

Dissecting the Role of SAL1 in Metabolizing the Stress Signaling Molecule 3′-Phosphoadenosine 5′-Phosphate in Different Cell Compartments

Plants possess the most highly compartmentalized eukaryotic cells. To coordinate their intracellular functions, plastids and the mitochondria are dependent on the flow of information to and from the nuclei, known as retrograde and anterograde signals. One mobile retrograde signaling molecule is the monophosphate 3′-phosphoadenosine 5′-phosphate (PAP), which is mainly produced from 3′-phosphoadenosine 5′-phosphosulfate (PAPS) in the cytosol and regulates the expression of a set of nuclear genes that modulate plant growth in response to biotic and abiotic stresses. The adenosine bisphosphate phosphatase enzyme SAL1 dephosphorylates PAP to AMP in plastids and the mitochondria, but can also rescue sal1 Arabidopsis phenotypes (PAP accumulation, leaf morphology, growth, etc.) when expressed in the cytosol and the nucleus. To understand better the roles of the SAL1 protein in chloroplasts, the mitochondria, nuclei, and the cytosol, we have attempted to complement the sal1 mutant by specifically cargoing the transgenic SAL1 protein to these four cell compartments. Overexpression of SAL1 protein targeted to the nucleus or the mitochondria alone, or co-targeted to chloroplasts and the mitochondria, complemented most aspects of the sal1 phenotypes. Notably, targeting SAL1 to chloroplasts or the cytosol did not effectively rescue the sal1 phenotypes as these transgenic lines accumulated very low levels of SAL1 protein despite overexpressing SAL1 mRNA, suggesting a possibly lower stability of the SAL1 protein in these compartments. The diverse transgenic SAL1 lines exhibited a range of PAP levels. The latter needs to reach certain thresholds in the cell for its impacts on different processes such as leaf growth, regulation of rosette morphology, sulfate homeostasis, and glucosinolate biosynthesis. Collectively, these findings provide an initial platform for further dissection of the role of the SAL1–PAP pathway in different cellular processes under stress conditions.

Structural Studies of Aliphatic Glucosinolate Chain-Elongation Enzymes

Plants evolved specialized metabolic pathways through gene duplication and functional divergence of enzymes involved in primary metabolism. The results of this process are varied pathways that produce an array of natural products useful to both plants and humans. In plants, glucosinolates are a diverse class of natural products. Glucosinolate function stems from their hydrolysis products, which are responsible for the strong flavors of Brassicales plants, such as mustard, and serve as plant defense molecules by repelling insects, fighting fungal infections, and discouraging herbivory. Additionally, certain hydrolysis products such as isothiocyanates can potentially serve as cancer prevention agents in humans. The breadth of glucosinolate function is a result of its great structural diversity, which comes from the use of aliphatic, aromatic and indole amino acids as precursors and elongation of some side chains by up to nine carbons, which, after the formation of the core glucosinolate structure, can undergo further chemical modifications. Aliphatic methionine-derived glucosinolates are the most abundant form of these compounds. Although both elongation and chemical modification of amino acid side chains are important for aliphatic glucosinolate diversity, its elongation process has not been well described at the molecular level. Here, we summarize new insights on the iterative chain-elongation enzymes methylthioalkylmalate synthase (MAMS) and isopropylmalate dehydrogenase (IPMDH).

Influence of Genotype on High Glucosinolate Synthesis Lines of Brassica rapa

This study was conducted to investigate doubled haploid (DH) lines produced between high GSL (HGSL) Brassica rapa ssp. trilocularis (yellow sarson) and low GSL (LGSL) B. rapa ssp. chinensis (pak choi) parents. In total, 161 DH lines were generated. GSL content of HGSL DH lines ranged from 44.12 to 57.04 μmol·g⁻¹·dry weight (dw), which is within the level of high GSL B. rapa ssp. trilocularis (47.46 to 59.56 μmol g⁻¹ dw). We resequenced five of the HGSL DH lines and three of the LGSL DH lines. Recombination blocks were formed between the parental and DH lines with 108,328 single-nucleotide polymorphisms in all chromosomes. In the measured GSL, gluconapin occurred as the major substrate in HGSL DH lines. Among the HGSL DH lines, BrYSP_DH005 had glucoraphanin levels approximately 12-fold higher than those of the HGSL mother plant. The hydrolysis capacity of GSL was analyzed in HGSL DH lines with a Korean pak choi cultivar as a control. Bioactive compounds, such as 3-butenyl isothiocyanate, 4-pentenyl isothiocyanate, 2-phenethyl isothiocyanate, and sulforaphane, were present in the HGSL DH lines at 3-fold to 6.3-fold higher levels compared to the commercial cultivar. The selected HGSL DH lines, resequencing data, and SNP identification were utilized for genome-assisted selection to develop elite GSL-enriched cultivars and the industrial production of potential anti-cancerous metabolites such as gluconapin and glucoraphanin.

Genome-wide identification of the BASS gene family in four Gossypium species and functional characterization of GhBASSs against salt stress

Bile acid sodium symporter (BASS) family proteins encode a class of sodium/solute symporters. Even though the sodium transporting property of BASSs in mammals was well studied, their sodium transportability and functional roles in plant salt tolerance remained largely unknown. Here, BASS family members from 4 cotton species, as well as 30 other species were identified. Then, they were designated as members of BASS1 to BASS5 subfamilies according to their sequence similarity and phylogenetic relationships. There were 8, 11, 16 and 18 putative BASS genes in four cotton species. While whole-genome duplications (WGD) and segmental duplications rendered the expansion of the BASS gene family in cotton, BASS gene losses occurred in the tetraploid cotton during the evolution from diploids to allotetraploids. Concerning functional characterizations, the transcript profiling of GhBASSs revealed that they not only preferred tissue-specific expression but also were differently induced by various stressors and phytohormones. Gene silencing and overexpression experiments showed that GhBASS1 and GhBASS3 positively regulated, whereas GhBASS2, GhBASS4 and GhBASS5 negatively regulated plant salt tolerance. Taken together, BASS family genes have evolved before the divergence from the common ancestor of prokaryotes and eukaryotes, and GhBASSs are plastidial sodium-dependent metabolite co-transporters that can influence plant salt tolerance.

Comparative Transcriptome Analysis of Rutabaga (Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae

Clubroot, caused by Plasmodiophora brassicae Woronin, is an important soilborne disease of Brassica napus L. and other crucifers. To improve understanding of the mechanisms of resistance and pathogenesis in the clubroot pathosystem, the rutabaga (B. napus subsp. rapifera Metzg) cultivars ‘Wilhelmsburger’ (resistant) and ‘Laurentian’ (susceptible) were inoculated with P. brassicae pathotype 3A and their transcriptomes were analyzed at 7, 14, and 21 days after inoculation (dai) by RNA sequencing (RNA-seq). Thousands of transcripts with significant changes in expression were identified in each host at each time-point in inoculated vs. non-inoculated plants. Molecular responses at 7 and 14 dai supported clear differences in the clubroot response mechanisms of the two genotypes. Both the resistant and the susceptible cultivars activated receptor-like protein (RLP) genes, resistance (R) genes, and genes involved in salicylic acid (SA) signaling as clubroot defense mechanisms. In addition, genes related to calcium signaling and genes encoding leucine-rich repeat (LRR) receptor kinases, the respiratory burst oxidase homolog (RBOH) protein, and transcription factors such as WRKYs, ethylene responsive factors, and basic leucine zippers (bZIPs), appeared to be upregulated in ‘Wilhelmsburger’ to restrict P. brassicae development. Some of these genes are essential components of molecular defenses, including ethylene (ET) signaling and the oxidative burst. Our study highlights the importance of activation of genes associated with SA- and ET-mediated responses in the resistant cultivar. A set of candidate genes showing contrasting patterns of expression between the resistant and susceptible cultivars was identified and includes potential targets for further study and validation through approaches such as gene editing.

Effect of light on sensory quality, health-promoting phytochemicals and antioxidant capacity in post-harvest baby mustard

The effect of light exposure on sensory quality, health-promoting phytochemical contents, and antioxidant capacity in the lateral buds of baby mustard plants was investigated at ambient storage temperature (20 °C). The results showed that light exposure (36 μmol m^-2 s^-1) during post-harvest storage significantly prolonged shelf life (more than 1.75-fold), delayed the weight loss and the decrease of firmness. Light treatments also enhanced chlorophyll and carotenoid contents, and retarded declines in contents of soluble sugars, ascorbic acid, flavonoids and glucosinolates, as well as antioxidant capacity. The quality of baby mustard plants receiving 24 h daily light treatment was superior to those in plants receiving 12 h treatment and constant darkness at 20 °C. These findings indicate that light exposure, especially 24 h treatment, is an effective method of prolonging shelf life and maintaining sensory and nutritional qualities in baby mustard plants stored at ambient temperature.

Ectopic overexpression of a cotton plastidial Na+ transporter GhBASS5 impairs salt tolerance in Arabidopsis via increasing Na+ loading and accumulation

GhBASS5 is a member of the bile acid sodium symporter (BASS) gene family from cotton and a plastid-localized Na⁺ transporter that negatively regulates salt tolerance of plants. Soil salinization is a major constraint on global cotton production, and Na⁺ is the most dominant toxic ion in salinity stress. Hence, insights into the identities and properties of transporters that catalyze Na⁺ movement between different tissues and within the cell compartments are vital to understand the salt-tolerant mechanisms of plants. Here, we identified the GhBASS5 gene, a member of the bile acid sodium symporter (BASS) gene family from cotton, served as a plastidic Na⁺ transporter. GhBASS5 encodes a membrane protein localized in the plastid envelope. It was highly expressed in cotton roots and predominantly existed in the vascular cylinder. Heterogenous expression of GhBASS5 in Arabidopsis chloroplasts promoted Na⁺ uptake into chloroplasts, which contributed to an increased cytoplasmic Na⁺ concentration. And GhBASS5-overexpressed transgenic plants showed an increase in Na⁺ translocation from roots to shoots and an elevated Na⁺ content in both roots and shoots, but a dramatic decrease in the Na⁺ efflux from root tissues and the K⁺/Na⁺ ratio, especially under salt stress conditions. Furthermore, overexpressing GhBASS5 greatly damaged plastid functions and enhanced salt sensitivity in transgenic Arabidopsis when compared with wild-type plants under salt stress. Additionally, the salt-responsive transporter genes that regulate K⁺/Na⁺ homeostasis were dramatically expressed in GhBASS5-overexpressed lines, especially under salt stress conditions. Taken together, our results suggest that GhBASS5 is a plastid-localized Na⁺ transporter, and high expression of GhBASS5 impairs salt tolerance of plants via increasing Na⁺ transportation and accumulation at both cell and tissue levels.

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

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

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.

Characterization of glucosinolates in 80 broccoli genotypes and different organs using UHPLC-Triple-TOF-MS method

We aimed to characterize and quantify glucosinolate compounds and contents in broccoli, and a total of 80 genotypes and eight developmental organs were analyzed with UHPLC-Triple-TOF-MS. The method was validated in terms of performance, and the coefficients of determination (R²) were 0.97 and 0.99 for glucoraphanin and gluconapin, respectively. In 80 genotypes, twelve glucosinolates were found in broccoli florets ranging from 0.467 to 57.156 µmol/g DW, with the highest glucosinolate content being approximately 122-fold higher than the lowest value. The principal component of glucobrassicin, neoglucobrassicin and glucoraphanin explained 60.53% of the total variance. There were positive correlations among hydroxyglucobrassicin, methoxyglucobrassicin, glucobrassicin, glucoerucin, gluconasturtiin, glucoraphanin, and glucotropaeolin (P < 0.05). The root contained 43% of total glucosinolates in 80 genotypes, and glucoraphanin represented 29% of the total glucosinolate content in different organs. The mutant broccoli genotypes were found by analysis of gluconapin contents in different organs.

In Arabidopsis thaliana Substrate Recognition and Tissue- as Well as Plastid Type-Specific Expression Define the Roles of Distinct Small Subunits of Isopropylmalate Isomerase

In Arabidopsis thaliana, the heterodimeric isopropylmalate isomerase (IPMI) is composed of a single large (IPMI LSU1) and one of three different small subunits (IPMI SSU1 to 3). The function of IPMI is defined by the small subunits. IPMI SSU1 is required for Leu biosynthesis and has previously also been proposed to be involved in the first cycle of Met chain elongation, the first phase of the synthesis of Met-derived glucosinolates. IPMI SSU2 and IPMI SSU3 participate in the Met chain elongation pathway. Here, we investigate the role of the three IPMI SSUs through the analysis of the role of the substrate recognition region spanning five amino acids on the substrate specificity of IPMI SSU1. Furthermore, we analyze in detail the expression pattern of fluorophore-tagged IPMI SSUs throughout plant development. Our study shows that the substrate recognition region that differs between IPMI SSU1 and the other two IMPI SSUs determines the substrate preference of IPMI. Expression of IPMI SSU1 is spatially separated from the expression of IPMI SSU2 and IPMI SSU3, and IPMI SSU1 is found in small plastids, whereas IMPI SSU2 and SSU3 are found in chloroplasts. Our data show a distinct role for IMPI SSU1 in Leu biosynthesis and for IMPI SSU2 and SSU3 in the Met chain elongation pathway.

Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)

Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on co-expression, co-regulation, and diversification of these potentially redundant defenses across this genus. We sequenced and assembled the genome of E. cheiranthoides and foliar transcriptomes of 47 additional Erysimum species to construct a phylogeny from 9868 orthologous genes, revealing several geographic clades but also high levels of gene discordance. Concentrations, inducibility, and diversity of the two defenses varied independently among species, with no evidence for trade-offs. Closely related, geographically co-occurring species shared similar cardenolide traits, but not glucosinolate traits, likely as a result of specific selective pressures acting on each defense. Ancestral and novel chemical defenses in Erysimum thus appear to provide complementary rather than redundant functions.

The TIR-NB-LRR pair DSC1 and WRKY19 contributes to basal immunity of Arabidopsis to the root-knot nematode Meloidogyne incognita

BACKGROUND

Root-knot nematodes transform vascular host cells into permanent feeding structures to withdraw nutrients from the host plant. Ecotypes of Arabidopsis thaliana can display large quantitative variation in susceptibility to the root-knot nematode Meloidogyne incognita, which is thought to be independent of dominant major resistance genes. However, in an earlier genome-wide association study of the interaction between Arabidopsis and M. incognita we identified a quantitative trait locus harboring homologs of dominant resistance genes but with minor effect on susceptibility to the M. incognita population tested.

RESULTS

Here, we report on the characterization of two of these genes encoding the TIR-NB-LRR immune receptor DSC1 (DOMINANT SUPPRESSOR OF Camta 3 NUMBER 1) and the TIR-NB-LRR-WRKY-MAPx protein WRKY19 in nematode-infected Arabidopsis roots. Nematode infection studies and whole transcriptome analyses using the Arabidopsis mutants showed that DSC1 and WRKY19 co-regulate susceptibility of Arabidopsis to M. incognita.

CONCLUSION

Given the head-to-head orientation of DSC1 and WRKY19 in the Arabidopsis genome our data suggests that both genes may function as a TIR-NB-LRR immune receptor pair. Unlike other TIR-NB-LRR pairs involved in dominant disease resistance in plants, DSC1 and WRKY19 most likely regulate basal levels of immunity to root-knot nematodes.

Overexpression of the MYB29 transcription factor affects aliphatic glucosinolate synthesis in Brassica oleracea

KEY MESSAGE

Overexpression of BoMYB29 gene up-regulates the aliphatic glucosinolate pathway in Brassica oleracea plants increasing the production of the anti-cancer metabolite glucoraphanin, and the toxic and pungent sinigrin. Isothiocyanates, the bio-active hydrolysis products of glucosinolates, naturally produced by several Brassicaceae species, play an important role in human health and agriculture. This study aims at correlating the content of aliphatic glucosinolates to the expression of genes involved in their synthesis in Brassica oleracea, and perform functional analysis of BoMYB29 gene. To this purpose, three genotypes were used: a sprouting broccoli, a cabbage, and a wild genotype (Winspit), a high glucosinolate containing accession. Winspit showed the highest transcript level of BoMYB28, BoMYB29 and BoAOP2 genes, and BoAOP2 expression was positively correlated with that of the two MYB genes. Further analyses of the aliphatic glucosinolates also showed a positive correlation between the expression of BoAOP2 and the production of sinigrin and gluconapin in Winspit. The Winspit BoMYB29 CDS was cloned and overexpressed in Winspit and in the DH AG1012 line. Overexpressing Winspit plants produced higher quantities of alkenyl glucosinolates, such as sinigrin. Conversely, the DH AG1012 transformants showed a higher production of methylsulphinylalkyl glucosinolates, including glucoraphanin, and, despite an up-regulation of the aliphatic glucosinolate genes, no increase in alkenyl glucosinolates. The latter may be explained by the absence of a functional AOP2 gene in DH AG1012. Nevertheless, an extract of DH AG1012 lines overexpressing BoMYB29 provided a chemoprotective effect on human colon cells. This work exemplifies how the genetic diversity of B. oleracea may be used by breeders to select for higher expression of transcription factors for glucosinolate biosynthesis to improve its natural, health-promoting properties.

Enhancement of Glucosinolate Production in Watercress ( Nasturtium officinale) Hairy Roots by Overexpressing Cabbage Transcription Factors

Glucosinolates are secondary metabolites that play important roles in plant defense and human health, as their production in plants is enhanced by overexpressing transcription factors. Here, four cabbage transcription factors (IQD1-1, IQD1-2, MYB29-1, and MYB29-2) affecting genes in both aliphatic and indolic glucosinolates biosynthetic pathways and increasing glucosinolates accumulation were overexpressed in watercress. Five IQD1-1, six IQD1-2, five MYB29-1, six MYB29-2, and one GUS hairy root lines were created. The expression of all genes involved in glucosinolates biosynthesis was higher in transgenic lines than in the GUS hairy root line, in agreement with total glucosinolates contents, determined by high-performance liquid chromatography. In transgenic IQD1-1 (1), IQD1-2 (4), MYB29-1 (2), and MYB29-2 (1) hairy root lines, total glucosinolates were 3.39-, 3.04-, 2.58-, and 4.69-fold higher than those in the GUS hairy root lines, respectively. These results suggest a central regulatory function for IQD1-1, IQD1-2, MYB29-1, and MYB29-2 transcription factors in glucosinolates biosynthesis in watercress hairy roots.

Comparative transcriptome analysis reveals defense responses against soft rot in Chinese cabbage

Pectobacterium carotovorum ssp. carotovorum (Pcc) is a necrotrophic bacterial species that causes soft rot disease in Chinese cabbage. In this study, plants harboring the resistant mutant sr gene, which confers resistance against Pcc, were screened from an 800 M₂ population mutated by ethyl methane sulfonate (EMS) and scored in vitro and in vivo for lesion size. The transcript profiles showed ~512 differentially expressed genes (DEGs) between sr and WT plants occurring between 6 and 12 h postinoculation (hpi), which corresponded to the important defense regulation period (resistance) to Pcc in Chinese cabbage. The downstream defense genes (CPK, CML, RBOH MPK3, and MPK4) of pathogen pattern-triggered immunity (PTI) were strongly activated during infection at 12 hpi in resistant mutant sr; PTI appears to be central to plant defense against Pcc via recognition by three putative pattern recognition receptors (PRRs; BrLYM1-BrCERK1, BrBKK1/SERK4-PEPR1, BrWAKs). Pcc triggered the upregulation of the jasmonic acid (JA) and ethylene (ET) biosynthesis genes in mutant sr, but auxins and other hormones may have affected some negative signals. Endogenous hormones (auxins, JAs, and SA), as well as exogenous auxins (MEJA and BTH), were also verified as functioning in the immune system. Concurrently, the expression of glucosinolate and lignin biosynthesis genes was increased at 12 hpi in resistant mutant sr, and the accumulation of glucosinolate and lignin also indicated that these genes have a functional defensive role against Pcc. Our study provides valuable information and elucidates the resistance mechanism of Chinese cabbage against Pcc infection.

PAPST2 Plays Critical Roles in Removing the Stress Signaling Molecule 3'-Phosphoadenosine 5'-Phosphate from the Cytosol and Its Subsequent Degradation in Plastids and Mitochondria

The compartmentalization of PAPS (the sulfate donor 3'-phosphoadenosine 5'-phosphosulfate) synthesis (mainly in plastids), PAPS consumption (in the cytosol), and PAP (the stress signaling molecule 3'-phosphoadenosine 5'-phosphate) degradation (in plastids and mitochondria) requires organellar transport systems for both PAPS and PAP. The plastidial transporter PAPST1 (PAPS TRANSPORTER1) delivers newly synthesized PAPS from the stroma to the cytosol. We investigated the activity of PAPST2, the closest homolog of PAPST1, which unlike PAPST1 is targeted to both the plastids and mitochondria. Biochemical characterization in Arabidopsis thaliana revealed that PAPST2 mediates the antiport of PAP, PAPS, ATP, and ADP. Strongly increased cellular PAP levels negatively affect plant growth, as observed in the fry1 papst2 mutant, which lacks the PAP-catabolizing enzyme SALT TOLERANCE 1 and PAPST2. PAP levels were specifically elevated in the cytosol of papst2 and fiery1 papst2, but not in papst1 or fry1 papst1 PAPST1 failed to complement the papst2 mutant phenotype in mitochondria, because it likely removes PAPS from the cell, as demonstrated by the increased expression of phytosulfokine genes. Overexpression of SAL1 in mitochondria rescued the phenotype of fry1 but not fry1 papst2 Therefore, PAPST2 represents an important organellar importer of PAP, providing a piece of the puzzle in our understanding of the organelle-to-nucleus PAP retrograde signaling pathway.

The bHLH transcription factor ILR3 modulates multiple stress responses in Arabidopsis

ILR3 and PYE function in a regulatory network that modulates GLS accumulation under iron deficiency. The molecular processes involved in the cross talk between iron (Fe) homeostasis and other metabolic processes in plants are poorly understood. In Arabidopsis thaliana the transcription factor IAA-LEUCINE RESISTANT3 (ILR3) regulates iron deficiency response, aliphatic glucosinolate (GLS) biosynthesis and pathogen response. ILR3 is also known to interact with its homolog, POPEYE (PYE), which also plays a role in Fe response. However, little is known about how ILR3 regulates such diverse processes, particularly, via its interaction with PYE. Since GLS are produced as part of a defense mechanism against wounding pathogens, we examined pILR3::β-GLUCURONIDASE expression and found that Fe deficiency enhances the wound-induced expression of ILR3 in roots and that ILR3 is induced in response to the wounding pathogen, sugarbeet root cyst nematode (Heterodera schachtii). We also examined the expression pattern of genes involved in Fe homeostasis and aliphatic GLS biosynthesis in pye-1, ilr3-2 and pye-1xilr3-2 (pxi) mutants and found that ILR3 and PYE differentially regulate the expression of genes involved these processes under Fe deficiency. We measured GLS levels and sugarbeet root cyst nematode infection rates under varying Fe conditions, and found that long-chain GLS levels are elevated in ilr3-2 and pxi mutants. This increase in long-chain GLS accumulation is correlated with elevated nematode resistance in ilr3-2 and pxi mutants in the absence of Fe. Our findings suggest that ILR3 and PYE function in a regulatory network that controls wounding pathogen response in plant roots by modulating GLS accumulation under iron deficiency.

A plastidial pantoate transporter with a potential role in pantothenate synthesis

The pantothenate (vitamin B5) synthesis pathway in plants is not fully defined because the subcellular site of its ketopantoate → pantoate reduction step is unclear. However, the pathway is known to be split between cytosol, mitochondria, and potentially plastids, and inferred to involve mitochondrial or plastidial transport of ketopantoate or pantoate. No proteins that mediate these transport steps have been identified. Comparative genomic and transcriptomic analyses identified Arabidopsis thaliana BASS1 (At1g78560) and its maize (Zea mays) ortholog as candidates for such a transport role. BASS1 proteins belong to the bile acid : sodium symporter family and share similarity with the Salmonella enterica PanS pantoate/ketopantoate transporter and with predicted bacterial transporters whose genes cluster on the chromosome with pantothenate synthesis genes. Furthermore, Arabidopsis BASS1 is co-expressed with genes related to metabolism of coenzyme A, the cofactor derived from pantothenate. Expression of Arabidopsis or maize BASS1 promoted the growth of a S. enterica panB panS mutant strain when pantoate, but not ketopantoate, was supplied, and increased the rate of [3H]pantoate uptake. Subcellular localization of green fluorescent protein fusions in Nicotiana tabacum BY-2 cells demonstrated that Arabidopsis BASS1 is targeted solely to the plastid inner envelope. Two independent Arabidopsis BASS1 knockout mutants accumulated pantoate ∼10-fold in leaves and had smaller seeds. Taken together, these data indicate that BASS1 is a physiologically significant plastidial pantoate transporter and that the pantoate reduction step in pantothenate biosynthesis could be at least partly localized in plastids.

Trans-methylation reactions in plants: focus on the activated methyl cycle

Trans-methylation reactions are vital in basic metabolism, epigenetic regulation, RNA metabolism, and posttranslational control of protein function and therefore fundamental in determining the physiological processes in all living organisms. The plant kingdom is additionally characterized by the production of secondary metabolites that undergo specific hydroxylation, oxidation and methylation reactions to obtain a wide array of different chemical structures. Increasing research efforts have started to reveal the enzymatic pathways underlying the biosynthesis of complex metabolites in plants. Further engineering of these enzymatic machineries offers significant possibilities in the development of bio-based technologies, but necessitates deep understanding of their potential metabolic and regulatory interactions. Trans-methylation reactions are tightly coupled with the so-called activated methyl cycle (AMC), an essential metabolic circuit that maintains the trans-methylation capacity in all living cells. Tight regulation of the AMC is crucial in ensuring accurate trans-methylation reactions in different subcellular compartments, cell types, developmental stages and environmental conditions. This review addresses the organization and posttranslational regulation of the AMC and elaborates its critical role in determining metabolic regulation through modulation of methyl utilization in stress-exposed plants.

Genomic and Transcriptomic Compilation of Chloroplast Ionic Transporters of Physcomitrella patens. Study of NHAD Transporters in Na+ and K+ Homeostasis

K+ is widely used by plant cells, whereas Na+ can easily reach toxic levels during plant growth, which typically occurs in saline environments; however, the effects and functions in the chloroplast have been only roughly estimated. Traditionally, the occurrence of ionic fluxes across the chloroplast envelope or the thylakoid membranes has been mostly deduced from physiological measurements or from knowledge of chloroplast metabolism. However, many of the proteins involved in these fluxes have not yet been characterized. Based on genomic and RNA sequencing (RNA-seq) analyses, we present a comprehensive compilation of genes encoding putative ion transporters and channels expressed in the chloroplasts of the moss Physcomitrella patens, with a special emphasis on those related to Na+ and K+ fluxes. Based on the functional characterization of nhad mutants, we also discuss the putative role of NHAD transporters in Na+ homeostasis and osmoregulation of this organelle and the putative contribution of chloroplasts to salt tolerance in this moss. We demonstrate that NaCl does not affect the chloroplast functionality in Physcomitrella despite significantly modifying expression of ionic transporters and cellular morphology, specifically the chloroplast ultrastructure, revealing a high starch accumulation. Additionally, NHAD transporters apparently do not play any essential roles in salt tolerance.

Insights into the species-specific metabolic engineering of glucosinolates in radish (Raphanus sativus L.) based on comparative genomic analysis

Glucosinolates (GSLs) and their hydrolysis products present in Brassicales play important roles in plants against herbivores and pathogens as well as in the protection of human health. To elucidate the molecular mechanisms underlying the formation of species-specific GSLs and their hydrolysed products in Raphanus sativus L., we performed a comparative genomics analysis between R. sativus and Arabidopsis thaliana. In total, 144 GSL metabolism genes were identified, and most of these GSL genes have expanded through whole-genome and tandem duplication in R. sativus. Crucially, the differential expression of FMOGS-OX2 in the root and silique correlates with the differential distribution of major aliphatic GSL components in these organs. Moreover, MYB118 expression specifically in the silique suggests that aliphatic GSL accumulation occurs predominantly in seeds. Furthermore, the absence of the expression of a putative non-functional epithiospecifier (ESP) gene in any tissue and the nitrile-specifier (NSP) gene in roots facilitates the accumulation of distinctive beneficial isothiocyanates in R. sativus. Elucidating the evolution of the GSL metabolic pathway in R. sativus is important for fully understanding GSL metabolic engineering and the precise genetic improvement of GSL components and their catabolites in R. sativus and other Brassicaceae crops.

Advances in methods for identification and characterization of plant transporter function

Transport proteins are crucial for cellular function at all levels. Numerous importers and exporters facilitate transport of a diverse array of metabolites and ions intra- and intercellularly. Identification of transporter function is essential for understanding biological processes at both the cellular and organismal level. Assignment of a functional role to individual transporter proteins or to identify a transporter with a given substrate specificity has notoriously been challenging. Recently, major advances have been achieved in function-driven screens, phenotype-driven screens, and in silico-based approaches. In this review, we highlight examples that illustrate how new technology and tools have advanced identification and characterization of plant transporter functions.

RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes

Accumulated microarray data are used for assessing gene function by providing statistical values for co-expressed genes; however, only a limited number of Web tools are available for analyzing the co-expression of genes of Brassica rapa. We have developed a Web tool called RapaNet (http://bioinfo.mju.ac.kr/arraynet/brassica300k/query/), which is based on a data set of 143 B rapa microarrays compiled from various organs and at different developmental stages during exposure to biotic or abiotic stress. RapaNet visualizes correlated gene expression information via correlational networks and phylogenetic trees using Pearson correlation coefficient (r). In addition, RapaNet provides hierarchical clustering diagrams, scatterplots of log ratio intensities, related pathway maps, and cis-element lists of promoter regions. To ascertain the functionality of RapaNet, the correlated genes encoding ribosomal protein (L7Ae), photosystem II protein D1 (psbA), and cytochrome P450 monooxygenase in glucosinolate biosynthesis (CYP79F1) were retrieved from RapaNet and compared with their Arabidopsis homologues. An analysis of the co-expressed genes revealed their shared and unique features.

Identification and characterization of a solute carrier, CIA8, involved in inorganic carbon acclimation in Chlamydomonas reinhardtii

The supply of inorganic carbon (Ci) at the site of fixation by Rubisco is a key parameter for efficient CO2 fixation in aquatic organisms including the green alga, Chlamydomonas reinhardtii. Chlamydomonas reinhardtii cells, when grown on limiting CO2, have a CO2-concentrating mechanism (CCM) that functions to concentrate CO2 at the site of Rubisco. Proteins thought to be involved in inorganic carbon uptake have been identified and localized to the plasma membrane or chloroplast envelope. However, current CCM models suggest that additional molecular components are involved in Ci uptake. In this study, the gene Cia8 was identified in an insertional mutagenesis screen and characterized. The protein encoded by Cia8 belongs to the sodium bile acid symporter subfamily. Transcript levels for this gene were significantly up-regulated when the cells were grown on low CO2. The cia8 mutant exhibited reduced growth and reduced affinity for Ci when grown in limiting CO2 conditions. Prediction programs localize this protein to the chloroplast. Ci uptake and the photosynthetic rate, particularly at high external pH, were reduced in the mutant. The results are consistent with the model that CIA8 is involved in Ci uptake in C. reinhardtii.

De novo transcriptome analysis and glucosinolate profiling in watercress (Nasturtium officinale R. Br.)

Background

Watercress (Nasturtium officinale R. Br.) is an aquatic herb species that is a rich source of secondary metabolites such as glucosinolates. Among these glucosinolates, watercress contains high amounts of gluconasturtiin (2-phenethyl glucosinolate) and its hydrolysis product, 2-phennethyl isothiocyanate, which plays a role in suppressing tumor growth. However, the use of N. officinale as a source of herbal medicines is currently limited due to insufficient genomic and physiological information.

Results

To acquire precise information on glucosinolate biosynthesis in N. officinale, we performed a comprehensive analysis of the transcriptome and metabolome of different organs of N. officinale. Transcriptome analysis of N. officinale seedlings yielded 69,570,892 raw reads. These reads were assembled into 69,635 transcripts, 64,876 of which were annotated to transcripts in public databases. On the basis of the functional annotation of N. officinale, we identified 33 candidate genes encoding enzymes related to glucosinolate biosynthetic pathways and analyzed the expression of these genes in the leaves, stems, roots, flowers, and seeds of N. officinale. The expression of NoMYB28 and NoMYB29, the main regulators of aliphatic glucosinolate biosynthesis, was highest in the stems, whereas the key regulators of indolic glucosinolate biosynthesis, such as NoDof1.1, NoMYB34, NoMYB51, and NoMYB122, were strongly expressed in the roots. Most glucosinolate biosynthetic genes were highly expressed in the flowers. HPLC analysis enabled us to detect eight glucosinolates in the different organs of N. officinale. Among these glucosinolates, the level of gluconasturtiin was considerably higher than any other glucosinolate in individual organs, and the amount of total glucosinolates was highest in the flower.

Conclusions

This study has enhanced our understanding of functional genomics of N. officinale, including the glucosinolate biosynthetic pathways of this plant. Ultimately, our data will be helpful for further research on watercress bio-engineering and better strategies for exploiting its anti-carcinogenic properties.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3792-5) contains supplementary material, which is available to authorized users.

Multi-Omics of Tomato Glandular Trichomes Reveals Distinct Features of Central Carbon Metabolism Supporting High Productivity of Specialized Metabolites

Glandular trichomes are metabolic cell factories with the capacity to produce large quantities of secondary metabolites. Little is known about the connection between central carbon metabolism and metabolic productivity for secondary metabolites in glandular trichomes. To address this gap in our knowledge, we performed comparative metabolomics, transcriptomics, proteomics, and ¹³C-labeling of type VI glandular trichomes and leaves from a cultivated (Solanum lycopersicum LA4024) and a wild (Solanum habrochaites LA1777) tomato accession. Specific features of glandular trichomes that drive the formation of secondary metabolites could be identified. Tomato type VI trichomes are photosynthetic but acquire their carbon essentially from leaf sucrose. The energy and reducing power from photosynthesis are used to support the biosynthesis of secondary metabolites, while the comparatively reduced Calvin-Benson-Bassham cycle activity may be involved in recycling metabolic CO₂ Glandular trichomes cope with oxidative stress by producing high levels of polyunsaturated fatty acids, oxylipins, and glutathione. Finally, distinct mechanisms are present in glandular trichomes to increase the supply of precursors for the isoprenoid pathways. Particularly, the citrate-malate shuttle supplies cytosolic acetyl-CoA and plastidic glycolysis and malic enzyme support the formation of plastidic pyruvate. A model is proposed on how glandular trichomes achieve high metabolic productivity.

Bile Acid Sodium Symporter BASS6 Can Transport Glycolate and Is Involved in Photorespiratory Metabolism in Arabidopsis thaliana

Photorespiration is an energy-intensive process that recycles 2-phosphoglycolate, a toxic product of the Rubisco oxygenation reaction. The photorespiratory pathway is highly compartmentalized, involving the chloroplast, peroxisome, cytosol, and mitochondria. Though the soluble enzymes involved in photorespiration are well characterized, very few membrane transporters involved in photorespiration have been identified to date. In this work, Arabidopsis thaliana plants containing a T-DNA disruption of the bile acid sodium symporter BASS6 show decreased photosynthesis and slower growth under ambient, but not elevated CO2 Exogenous expression of BASS6 complemented this photorespiration mutant phenotype. In addition, metabolite analysis and genetic complementation of glycolate transport in yeast showed that BASS6 was capable of glycolate transport. This is consistent with its involvement in the photorespiratory export of glycolate from Arabidopsis chloroplasts. An Arabidopsis double knockout line of both BASS6 and the glycolate/glycerate transporter PLGG1 (bass6, plgg1) showed an additive growth defect, an increase in glycolate accumulation, and reductions in photosynthetic rates compared with either single mutant. Our data indicate that BASS6 and PLGG1 partner in glycolate export from the chloroplast, whereas PLGG1 alone accounts for the import of glycerate. BASS6 and PLGG1 therefore balance the export of two glycolate molecules with the import of one glycerate molecule during photorespiration.

Pan- and core- network analysis of co-expression genes in a model plant

Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. Some studies involved construction of coexpression networks, a popular technique used to identify groups of co-regulated genes, to infer unknown gene functions. One approach is to construct a single coexpression network by combining multiple expression datasets generated in different labs. We advocate a complementary approach in which we construct a large collection of 134 coexpression networks based on expression datasets reported in individual publications. To this end we reanalyzed public expression data. To describe this collection of networks we introduced concepts of 'pan-network' and 'core-network' representing union and intersection between a sizeable fractions of individual networks, respectively. We showed that these two types of networks are different both in terms of their topology and biological function of interacting genes. For example, the modules of the pan-network are enriched in regulatory and signaling functions, while the modules of the core-network tend to include components of large macromolecular complexes such as ribosomes and photosynthetic machinery. Our analysis is aimed to help the plant research community to better explore the information contained within the existing vast collection of gene expression data in Arabidopsis.

Glucosinolate biosynthesis in Eruca sativa

Glucosinolates (GSLs) are a highly important group of secondary metabolites in the Caparalles order, both due to their significance in plant-biome interactions and to their chemoprotective properties. This study identified genes involved in all steps of aliphatic and indolic GSL biosynthesis in Eruca sativa, a cultivated plant closely related to Arabidopsis thaliana with agronomic and nutritional value. The impact of nitrogen (N) and sulfur (S) availability on GSL biosynthetic pathways at a transcriptional level, and on the final GSL content of plant leaf and root tissues, was investigated. N and S supply had a significant and interactive effect on the GSL content of leaves, in a structure-specific and tissue-dependent manner; the metabolites levels were significantly correlated with the relative expression of the genes involved in their biosynthesis. A more complex effect was observed in roots, where aliphatic and indolic GSLs and related biosynthetic genes responded differently to the various nutritional treatments suggesting that nitrogen and sulfur availability are important factors that control plant GSL content at a transcriptional level. The biological activity of extracts derived from these plants grown under the specific nutritional schemes was examined. N and S availability were found to significantly affect the cytotoxicity of E. sativa extracts on human cancer cells, supporting the notion that carefully designed nutritional schemes can promote the accumulation of chemoprotective substances in edible 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.

Exogenous Methyl Jasmonate and Salicylic Acid Induce Subspecies-Specific Patterns of Glucosinolate Accumulation and Gene Expression in Brassica oleracea L

Glucosinolates have anti-carcinogenic properties. In the recent decades, the genetics of glucosinolate biosynthesis has been widely studied, however, the expression of specific genes involved in glucosinolate biosynthesis under exogenous phytohormone treatment has not been explored at the subspecies level in Brassica oleracea. Such data are vital for strategies aimed at selective exploitation of glucosinolate profiles. This study quantified the expression of 38 glucosinolate biosynthesis-related genes in three B. oleracea subspecies, namely cabbage, broccoli and kale, and catalogued associations between gene expression and increased contents of individual glucosinolates under methyl jasmonate (MeJA) and salicylic acid (SA) treatments. Glucosinolate accumulation and gene expression in response to phytohormone elicitation was subspecies specific. For instance, cabbage leaves showed enhanced accumulation of the aliphatic glucoiberin, progoitrin, sinigrin and indolic neoglucobrassicin under both MeJA and SA treatment. MeJA treatment induced strikingly higher accumulation of glucobrassicin (GBS) in cabbage and kale and of neoglucobrassicin (NGBS) in broccoli compared to controls. Notably higher expression of ST5a (Bol026200), CYP81F1 (Bol028913, Bol028914) and CYP81F4 genes was associated with significantly higher GBS accumulation under MeJA treatment compared to controls in all three subspecies. CYP81F4 genes, trans-activated by MYB34 genes, were expressed at remarkably high levels in all three subspecies under MeJA treatment, which also induced in higher indolic NGBS accumulation in all three subspecies. Remarkably higher expression of MYB28 (Bol036286), ST5b, ST5c, AOP2, FMOGS-OX5 (Bol031350) and GSL-OH (Bol033373) was associated with much higher contents of aliphatic glucosinolates in kale leaves compared to the other two subspecies. The genes expressed highly could be utilized in strategies to selectively increase glucosinolate compounds in B. oleracea subspecies. These results promote efforts to develop genotypes of B. oleracea and other species with enhanced levels of desired glucosinolates.

Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis

Movement of nitrogen to the plant tissues where it is needed for growth is an important contribution to nitrogen use efficiency. However, we have very limited knowledge about the mechanisms of nitrogen transport. Loading of nitrogen into the xylem and/or phloem by transporter proteins is likely important, but there are several families of genes that encode transporters of nitrogenous molecules (collectively referred to as N transporters here), each comprised of many gene members. In this study, we leveraged publicly available microarray data of Arabidopsis to investigate the gene networks of N transporters to elucidate their possible biological roles. First, we showed that tissue-specificity of nitrogen (N) transporters was well reflected among the public microarray data. Then, we built coexpression networks of N transporters, which showed relationships between N transporters and particular aspects of plant metabolism, such as phenylpropanoid biosynthesis and carbohydrate metabolism. Furthermore, genes associated with several biological pathways were found to be tightly coexpressed with N transporters in different tissues. Our coexpression networks provide information at the systems-level that will serve as a resource for future investigation of nitrogen transport systems in plants, including candidate gene clusters that may work together in related biological roles.