Sulfur deficiency-induced repressor proteins optimize glucosinolate biosynthesis in plants

The role of OsBZR4 as a brassinosteroid-signaling component in mediating atrazine and isoproturon degradation in rice

Development of a biotechnological system for rapid degradation of pesticides is important to mitigate the environmental, food security, and health risks that they pose. Degradation of atrazine (ATZ) and isoproturon (IPU) in rice crops promoted by the brassinosteroid (BR) signaling component BRASSINAZOLE RESISTANT4 (OsBZR4) is explored. OsBZR4 is localized in the plasma membrane and nucleus, and is strongly induced by ATZ and IPU exposure. Transgenic rice OsBZR4-overexpression (OE) significantly enhances resistance to ATZ and IPU toxicity, improving growth, and reducing ATZ and IPU accumulation (particularly in grains) in rice crops. Genetic destruction of OsBZR4 (CRISPR/Cas9) increases rice sensitivity and leads to increased accumulation of ATZ and IPU. OE plants promote phase I, II, and III metabolic reactions, and expression of corresponding pesticide degradation genes under ATZ and IPU stress. UPLC-Q-TOF-MS/MS analysis reveals increased relative contents of ATZ and IPU metabolites and conjugates in OE plants, suggesting an increased OsBZR4 expression and consequent detoxification of ATZ and IPU in rice and the environment. The role of OsBZR4 in pesticide degradation is revealed, and its potential application in enhancing plant resistance to pesticides, and facilitating the breakdown of pesticides in rice and the environment, is discussed.

Gene regulatory networks underlying sulfate deficiency responses in plants

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

Transcriptional and metabolic profiling of sulfur starvation response in two monocots

BACKGROUND

Sulfur (S) is a mineral nutrient essential for plant growth and development, which is incorporated into diverse molecules fundamental for primary and secondary metabolism, plant defense, signaling, and maintaining cellular homeostasis. Although, S starvation response is well documented in the dicot model Arabidopsis thaliana, it is not clear if the same transcriptional networks control the response also in the monocots.

RESULTS

We performed series of physiological, expression, and metabolite analyses in two model monocot species, one representing the C3 plants, Oryza sativa cv. kitaake, and second representing the C4 plants, Setaria viridis. Our comprehensive transcriptomic analysis revealed twice as many differentially expressed genes (DEGs) in S. viridis than in O. sativa under S-deficiency, consistent with a greater loss of sulfur and S-containing metabolites under these conditions. Surprisingly, most of the DEGs and enriched gene ontology terms were species-specific, with an intersect of only 58 common DEGs. The transcriptional networks were different in roots and shoots of both species, in particular no genes were down-regulated by S-deficiency in the roots of both species.

CONCLUSIONS

Our analysis shows that S-deficiency seems to have different physiological consequences in the two monocot species and their nutrient homeostasis might be under distinct control mechanisms.

Overexpression of SLIM1 transcription factor accelerates vegetative development in Arabidopsis thaliana

The transcription factor Sulfur Limitation 1 (SLIM1) belongs to the plant-specific Ethylene Insenstive3-Like transcription factor family and is known to coordinate gene expression in response to sulfur deficiency. However, the roles of SLIM1 in nutrient-sufficient conditions have not been characterized. Employing constitutive SLIM1 overexpression (35S::SLIM1) and CRISPR/Cas9 mutant plants (slim1-cr), we identified several distinct phenotypes in nutrient-sufficient conditions in Arabidopsis thaliana. Overexpression of SLIM1 results in plants with approximately twofold greater rosette area throughout vegetative development. 35S::SLIM1 plants also bolt earlier and exhibit earlier downregulation of photosynthesis-associated genes and earlier upregulation of senescence-associated genes than Col-0 and slim1-cr plants. This suggests that overexpression of SLIM1 accelerates development in A. thaliana. Genome-wide differential gene expression analysis relative to Col-0 at three time points with slim1-cr and two 35S::SLIM1 lines allowed us to identify 1,731 genes regulated directly or indirectly by SLIM1 in vivo.

Traits linked to natural variation of sulfur content in Arabidopsis thaliana

Sulfur (S) is an essential mineral nutrient for plant growth and development; it is important for primary and specialized plant metabolites that are crucial for biotic and abiotic interactions. Foliar S content varies up to 6-fold under a controlled environment, suggesting an adaptive value under certain natural environmental conditions. However, a major quantitative regulator of S content in Arabidopsis thaliana has not been identified yet, pointing to the existence of either additional genetic factors controlling sulfate/S content or of many minor quantitative regulators. Here, we use overlapping information of two separate ionomics studies to select groups of accessions with low, mid, and high foliar S content. We quantify series of metabolites, including anions (sulfate, phosphate, and nitrate), thiols (cysteine and glutathione), and seven glucosinolates, gene expression of 20 genes, sulfate uptake, and three biotic traits. Our results suggest that S content is tightly connected with sulfate uptake, the concentration of sulfate and phosphate anions, and glucosinolate and glutathione synthesis. Additionally, our results indicate that the growth of pathogenic bacteria is enhanced in the A. thaliana accessions containing higher S in their leaves, suggesting a complex regulation between S homeostasis, primary and secondary metabolism, and biotic pressures.

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

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

Glucosinolate Catabolism Maintains Glucosinolate Profiles and Transport in Sulfur-Starved Arabidopsis

Glucosinolates (GSLs) are sulfur (S)-rich specialized metabolites present in Brassicales order plants. Our previous study found that GSL can function as a S source in Arabidopsis seedlings via its catabolism catalyzed by two β-glucosidases (BGLUs), BGLU28 and BGLU30. However, as GSL profiles in plants vary among growth stages and organs, the potential contribution of BGLU28/30-dependent GSL catabolism at the reproductive growth stage needs verification. Thus, in this study, we assessed growth, metabolic and transcriptional phenotypes of mature bglu28/30 double mutants grown under different S conditions. Our results showed that compared to wild-type plants grown under -S, mature bglu28/30 mutants displayed impaired growth and accumulated increased levels of GSL in their reproductive organs and rosette leaves of before-bolting plants. In contrast, the levels of primary S-containing metabolites, glutathione and cysteine decreased in their mature seeds. Furthermore, the transport of GSL from rosette leaves to the reproductive organs was stimulated in the bglu28/30 mutants under -S. Transcriptome analysis revealed that genes related to other biological processes, such as ethylene response, defense response and plant response to heat, responded differentially to -S in the bglu28/30 mutants. Altogether, these findings broadened our understanding of the roles of BGLU28/30-dependent GSL catabolism in plant adaptation to nutrient stress.

Asymmetric distribution of mineral nutrients aggravates uneven fruit pigmentation driven by sunlight exposure in litchi

MAIN CONCLUSION

Sunlight boosts anthocyanin synthesis/accumulation in sunny pericarp of litchi fruit, directly leading to uneven pigmentation. Distribution discrepancy of mineral element aggravates uneven coloration by modulating synthesis/accumulation of anthocyanin and sugar. Uneven coloration, characterized by red pericarp on sunny side and green pericarp on shady side, impacts fruit quality of 'Feizixiao' (cv.) litchi. The mechanisms of this phenomenon were explored by investigating the distribution of chlorophyll, flavonoids, sugars, and mineral elements in both types of pericarp. Transcriptome analysis in pericarp was conducted as well. Sunny pericarp contained higher anthocyanins in an order of magnitude and higher fructose, glucose, co-pigments (flavanols, flavonols, ferulic acid), and mineral elements like Ca, Mg and Mn, along with lower N, P, K, S, Cu, Zn and B (P < 0.01), compared to shady pericarp. Sunlight regulated the expression of genes involved in synthesis/accumulation of flavonoids and sugars and genes functioning in nutrient uptake and transport, leading to asymmetric distribution of these substances. Anthocyanins conferred red color on sunny pericarp, sugars, Ca and Mg promoted synthesis/accumulation of anthocyanins, and co-pigments enhanced color display of anthocyanins. The insufficiencies of anthocyanins, sugars and co-pigments, and inhibition effect of excess K, S, N and P on synthesis/accumulation of anthocyanins and sugars, jointly contributed to green color of shady pericarp. These findings highlight the role of asymmetric distribution of substances, mineral elements in particular, on uneven pigmentation in litchi, and provide insights into coloration improvement via precise fertilization.

Is specialized metabolite regulation specialized?

Recent technical and theoretical advances have generated an explosion in the identification of specialized metabolite pathways. In comparison, our understanding of how these pathways are regulated is relatively lagging. This and the relatively young age of specialized metabolite pathways has partly contributed to a default and common paradigm whereby specialized metabolite regulation is theorized as relatively simple with a few key transcription factors and the compounds are non-regulatory end-products. In contrast, studies into model specialized metabolites, such as glucosinolates, are beginning to identify a new understanding whereby specialized metabolites are highly integrated into the plants' core metabolic, physiological, and developmental pathways. This model includes a greatly extended compendium of transcription factors controlling the pathway, key transcription factors that co-evolve with the pathway and simultaneously control core metabolic and developmental components, and finally the compounds themselves evolve regulatory connections to integrate into the plants signaling machinery. In this review, these concepts are illustrated using studies in the glucosinolate pathway within the Brassicales. This suggests that the broader community needs to reconsider how they do or do not integrate specialized metabolism into the regulatory network of their study species.

Regulatory mechanisms of sulfur metabolism affecting tolerance and accumulation of toxic trace metals and metalloids in plants

Soil contamination with trace metals and metalloids can cause toxicity to plants and threaten food safety and human health. Plants have evolved sophisticated mechanisms to cope with excess trace metals and metalloids in soils, including chelation and vacuolar sequestration. Sulfur-containing compounds, such as glutathione and phytochelatins, play a crucial role in their detoxification, and sulfur uptake and assimilation are regulated in response to the stress of toxic trace metals and metalloids. This review focuses on the multi-level connections between sulfur homeostasis in plants and responses to such stresses, especially those imposed by arsenic and cadmium. We consider recent progress in understanding the regulation of biosynthesis of glutathione and phytochelatins and of the sensing mechanism of sulfur homeostasis for tolerance of trace metals and metalloids in plants. We also discuss the roles of glutathione and phytochelatins in controlling the accumulation and distribution of arsenic and cadmium in plants, and possible strategies for manipulating sulfur metabolism to limit their accumulation in food crops.

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

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

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

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

Floret Biofortification of Broccoli Using Amino Acids Coupled with Selenium under Different Surfactants: A Case Study of Cultivating Functional Foods

Broccoli serves as a functional food because it can accumulate selenium (Se), well-known bioactive amino-acid-derived secondary metabolites, and polyphenols. The chemical and physical properties of Se are very similar to those of sulfur (S), and competition between sulfate and selenate for uptake and assimilation has been demonstrated. Towards an efficient agronomic fortification of broccoli florets, the working questions were whether we could overcome this competition by exogenously applying the S-containing amino acids cysteine (Cys) or/and methionine (Met), or/and the precursors of Glucosinolate (GSL) types along with Se application. Broccoli plants were cultivated in a greenhouse and at the beginning of floret growth, we exogenously applied sodium selenate in the concentration gradient of 0, 0.2, 1.5, and 3.0 mM to study the impact of increased Se concentration on the organic S (S_org) content of the floret. The Se concentration of 0.2 mM (Se0.2) was coupled with the application of Cys, Met, their combination, or a mixture of phenylalanine, tryptophane, and Met. The application took place through fertigation or foliar application (FA) by adding isodecyl alcohol ethoxylate (IAE) or a silicon ethoxylate (SiE) surfactant. Fresh biomass, dry mass, and Se accumulation in florets were evaluated, along with their contents of S_org, chlorophylls (Chl), carotenoids (Car), glucoraphanin (GlRa), glucobrassicin (GlBra), glucoiberin (GlIb), and polyphenols (PPs), for the biofortification efficiency of the three application modes. From the studied selenium concentration gradient, the foliar application of 0.2 mM Se using silicon ethoxylate (SiE) as a surfactant provided the lowest commercially acceptable Se content in florets (239 μg or 0.3 μmol g^-1 DM); it reduced S_org (-45%), GlIb (-31%), and GlBr (-27%); and it increased Car (21%) and GlRa (27%). Coupled with amino acids, 0.2 mM Se provided commercially acceptable Se contents per floret only via foliar application. From the studied combinations, that of Met,Se0.2/FA,IAE provided the lowest Se content per floret (183 μg or 0.2 μmol g^-1 DM) and increased S_org (35%), Car (45%), and total Chl (27%), with no effect on PPs or GSLs. Cys,Met,Se0.2/FA,IAE and amino acid mix,Se0.2/FA,IAE increased S_org content, too, by 36% and 16%, respectively. Thus, the foliar application with the IAE surfactant was able to increase S_org, and methionine was the amino acid in common in these treatments, with varying positive effects on carotenoids and chlorophylls. Only the Cys,Met,Se0.2 combination presented positive effects on GSLs, especially GlRa, but it reduced the fresh mass of the floret. The foliar application with SiE as a surfactant failed to positively affect the organic S content. However, in all studied combinations of Se 0.2 mM with amino acids, the Se content per floret was commercially acceptable, the yield was not affected, the content of GSLs was increased (especially that of GlRa and GlIb), and PPs were not affected. The content of GlBr decreased except for the treatment with methionine (Met,Se0.2/FA,SiE) where GlBr remained unaffected. Hence, the combination of Se with the used amino acids and surfactants can provide enhanced biofortification efficiency in broccoli by providing florets as functional foods with enhanced functional properties.

Insights into the loss of glucoraphanin in post-harvested broccoli--Possible involvement of the declined supply capacity of sulfur donor

The loss of characteristic nutrient glucoraphanin during the shelf life seriously affects the nutritional quality of broccoli. Here, we monitored the changes in the levels of sulfur donors (cysteine and glutathione) required for glucoraphanin biosynthesis. Similar to glucoraphanin, cysteine content decreased sharply. Continuous down-regulation of BoCysK1 and BoCysK2 genes encoding cysteine synthase might account for cysteine loss. Contrarily, glutathione content accumulated steadily, which might owe to the up-regulation of biosynthetic gene (BoEC1). Additionally, the change of malondialdehyde content was positively correlated with glutathione, implying that oxidative stress might stimulate glutathione accumulation. Nevertheless, the expression of BoGSTF11 gene encoding glutathione S-transferases was down-regulated, which blocked the supply of glutathione. The increase in the content of raphanusamic acid (degradation product) indicated that insufficient supply of sulfur donors not only could constrain the biosynthesis of glucoraphanin but also triggered its degradation.

Natural Variation in OASC Gene for Mitochondrial O-Acetylserine Thiollyase Affects Sulfate Levels in Arabidopsis

Sulfur plays a vital role in the primary and secondary metabolism of plants, and carries an important function in a large number of different compounds. Despite this importance, compared to other mineral nutrients, relatively little is known about sulfur sensing and signalling, as well as about the mechanisms controlling sulfur metabolism and homeostasis. Sulfur contents in plants vary largely not only among different species, but also among accessions of the same species. We previously used associative transcriptomics to identify several genes potentially controlling variation in sulfate content in the leaves of Brassica napus, including an OASC gene for mitochondrial O-acetylserine thiollyase (OAS-TL), an enzyme involved in cysteine synthesis. Here, we show that loss of OASC in Arabidopsis thaliana lowers not only sulfate, but also glutathione levels in the leaves. The reduced accumulation is caused by lower sulfate uptake and translocation to the shoots; however, the flux through the pathway is not affected. In addition, we identified a single nucleotide polymorphism in the OASC gene among A. thaliana accessions that is linked to variation in sulfate content. Both genetic and transgenic complementation confirmed that the exchange of arginine at position 81 for lysine in numerous accessions resulted in a less active OASC and a lower sulfate content in the leaves. The mitochondrial isoform of OAS-TL is, thus, after the ATPS1 isoform of sulfurylase and the APR2 form of APS reductase 2, the next metabolic enzyme with a role in regulation of sulfate content in Arabidopsis.

Cytokinin modulates the metabolic network of sulfur and glutathione

The phytohormone cytokinin is implicated in a range of growth, developmental, and defense processes. A growing body of evidence supports a crosstalk between cytokinin and nutrient signaling pathways, such as nitrate availability. Cytokinin signaling regulates sulfur-responsive gene expression, but the underlying molecular mechanisms and their impact on sulfur-containing metabolites have not been systematically explored. Using a combination of genetic and pharmacological tools, we investigated the interplay between cytokinin signaling and sulfur homeostasis. Exogenous cytokinin triggered sulfur starvation-like gene expression accompanied by a decrease in sulfate and glutathione content. This process was uncoupled from the activity of the major transcriptional regulator of sulfate starvation signaling SULFUR LIMITATION 1 and an important glutathione-degrading enzyme, γ-glutamyl cyclotransferase 2;1, expression of which was robustly up-regulated by cytokinin. Conversely, glutathione accumulation was observed in mutants lacking the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE 3 and in cytokinin-deficient plants. Cytokinin-deficient plants displayed improved root growth upon exposure to glutathione-depleting chemicals which was attributed to a higher capacity to maintain glutathione levels. These results shed new light on the interplay between cytokinin signaling and sulfur homeostasis. They position cytokinin as an important modulator of sulfur uptake, assimilation, and remobilization in plant defense against xenobiotics and root growth.

The SLIM1 transcription factor affects sugar signaling during sulfur deficiency in Arabidopsis

The homeostasis of major macronutrient metabolism needs to be tightly regulated, especially when the availability of one or more nutrients fluctuates in the environment. Both sulfur metabolism and glucose signaling are important processes throughout plant growth and development, as well as during stress responses. Still, very little is known about how these processes affect each other, although they are positively connected. Here, we showed in Arabidopsis that the crucial transcription factor of sulfur metabolism, SLIM1, is involved in glucose signaling during shortage of sulfur. The germination rate of the slim1_KO mutant was severely affected by high glucose and osmotic stress. The expression of SLIM1-dependent genes in sulfur deficiency appeared to be additionally induced by a high concentration of either mannitol or glucose, but also by sucrose, which is not only the source of glucose but another signaling molecule. Additionally, SLIM1 affects PAP1 expression during sulfur deficiency by directly binding to its promoter. The lack of PAP1 induction in such conditions leads to much lower anthocyanin production. Taken together, our results indicate that SLIM1 is involved in the glucose response by modulating sulfur metabolism and directly controlling PAP1 expression in Arabidopsis during sulfur deficiency stress.

Sulfate-TOR signaling controls transcriptional reprogramming for shoot apex activation

Plants play a primary role for the global sulfur cycle in the earth ecosystems by reduction of inorganic sulfate from the soil to organic sulfur-containing compounds. How plants sense and transduce the sulfate availability to mediate their growth remains largely unclear. The target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator of nutrient sensing and metabolic signaling to control cell proliferation and growth in all eukaryotes. By tissue-specific Western blotting and RNA-sequencing analysis, we investigated sulfate-TOR signal pathway in regulating shoot apex development. Here, we report that inorganic sulfate exhibits high potency activating TOR and cell proliferation to promote true leaf development in Arabidopsis in a glucose-energy parallel pathway. Genetic and metabolite analyses suggest that this sulfate activation of TOR is independent from the sulfate-assimilation process and glucose-energy signaling. Significantly, tissue specific transcriptome analyses uncover previously unknown sulfate-orchestrating genes involved in DNA replication, cell proliferation and various secondary metabolism pathways, which largely depends on TOR signaling. Systematic comparison between the sulfate- and glucose-TOR controlled transcriptome further reveals that TOR kinase, as the central growth integrator, responds to different nutrient signals to control both shared and unique transcriptome networks, therefore, precisely modulates plant proliferation, growth and stress responses.

Salt Stress Tolerance in Casuarina glauca: Insights from the Branchlets Transcriptome

Climate change and the accelerated rate of population growth are imposing a progressive degradation of natural ecosystems worldwide. In this context, the use of pioneer trees represents a powerful approach to reverse the situation. Among others, N₂-fixing actinorhizal trees constitute important elements of plant communities and have been successfully used in land reclamation at a global scale. In this study, we have analyzed the transcriptome of the photosynthetic organs of Casuarina glauca (branchlets) to unravel the molecular mechanisms underlying salt stress tolerance. For that, C. glauca plants supplied either with chemical nitrogen (KNO₃⁺) or nodulated by Frankia (NOD⁺) were exposed to a gradient of salt concentrations (200, 400, and 600 mM NaCl) and RNA-Seq was performed. An average of ca. 25 million clean reads was obtained for each group of plants, corresponding to 86,202 unigenes. The patterns of differentially expressed genes (DEGs) clearly separate two groups: (i) control- and 200 mM NaCl-treated plants, and (ii) 400 and 600 mM NaCl-treated plants. Additionally, although the number of total transcripts was relatively high in both plant groups, the percentage of significant DEGs was very low, ranging from 6 (200 mM NaCl/NOD⁺) to 314 (600 mM NaCl/KNO₃⁺), mostly involving down-regulation. The vast majority of up-regulated genes was related to regulatory processes, reinforcing the hypothesis that some ecotypes of C. glauca have a strong stress-responsive system with an extensive set of constitutive defense mechanisms, complemented by a tight mechanism of transcriptional and post-transcriptional regulation. The results suggest that the robustness of the stress response system in C. glauca is regulated by a limited number of genes that tightly regulate detoxification and protein/enzyme stability, highlighting the complexity of the molecular interactions leading to salinity tolerance in this species.

WGCNA Identifies a Comprehensive and Dynamic Gene Co-Expression Network That Associates with Smut Resistance in Sugarcane

Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (susceptible) upon S. scitamineum infection. Data analysis revealed 20,273 (12,659 up-regulated and 7614 down-regulated) and 11,897 (7806 up-regulated and 4091 down-regulated) differentially expressed genes (DEGs) in YT93-159 and ROC22, respectively. A co-expression network was then constructed by weighted gene co-expression network analysis (WGCNA), which identified 5010 DEGs in 15 co-expressed gene modules. Four of the 15 modules, namely, Skyblue, Salmon, Darkorange, and Grey60, were significantly associated with smut resistance. The GO and KEGG enrichment analyses indicated that the DEGs involving in these four modules could be enriched in stress-related metabolic pathways, such as MAPK and hormone signal transduction, plant-pathogen interaction, amino acid metabolism, glutathione metabolism, and flavonoid, and phenylpropanoid biosynthesis. In total, 38 hub genes, including six from the Skyblue module, four from the Salmon module, 12 from the Darkorange module, and 16 from the Grey60 module, were screened as candidate hub genes by calculating gene connectivity in the corresponding network. Only 30 hub genes were amplifiable with RT-qPCR, of which 27 were up-regulated upon S. scitamineum infection. The results were consistent with the trend of gene expression in RNA-Seq, suggesting their positive roles in smut resistance. Interestingly, the expression levels of AOX, Cyb5, and LAC were higher in ROC22 than in YT93-159, indicating these three genes may act as negative regulators in response to S. scitamineum infection. This study revealed the transcriptome dynamics in sugarcane challenged by S. scitamineum infection and provided gene targets for smut resistance breeding in sugarcane.

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

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

Glutathione degradation activity of γ-glutamyl peptidase 1 manifests its dual roles in primary and secondary sulfur metabolism in Arabidopsis

Glutathione (GSH) functions as a major sulfur repository and hence occupies an important position in primary sulfur metabolism. GSH degradation results in sulfur reallocation and is believed to be carried out mainly by γ-glutamyl cyclotransferases (GGCT2;1, GGCT2;2, and GGCT2;3), which, however, do not fully explain the rapid GSH turnover. Here, we discovered that γ-glutamyl peptidase 1 (GGP1) contributes to GSH degradation through a yeast complementation assay. Recombinant proteins of GGP1, as well as GGP3, showed high degradation activity of GSH, but not of oxidized glutathione (GSSG), in vitro. Notably, the GGP1 transcripts were highly abundant in rosette leaves, in agreement with the ggp1 mutants constantly accumulating more GSH regardless of nutritional conditions. Given the lower energy requirements of the GGP- than the GGCT-mediated pathway, the GGP-mediated pathway could be a more efficient route for GSH degradation than the GGCT-mediated pathway. Therefore, we propose a model wherein cytosolic GSH is degraded chiefly by GGP1 and likely also by GGP3. Another noteworthy fact is that GGPs are known to process GSH conjugates in glucosinolate and camalexin synthesis; indeed, we confirmed that the ggp1 mutant contained higher levels of O-acetyl-l-Ser, a signaling molecule for sulfur starvation, and lower levels of glucosinolates and their degradation products. The predicted structure of GGP1 further provided a rationale for this hypothesis. In conclusion, we suggest that GGP1 and possibly GGP3 play vital roles in both primary and secondary sulfur metabolism.

Tris(methylthio)methane produced by Mortierella hyalina affects sulfur homeostasis in Arabidopsis

Microbial volatiles are important factors in symbiotic interactions with plants. Mortierella hyalina is a beneficial root-colonizing fungus with a garlic-like smell, and promotes growth of Arabidopsis seedlings. GC–MS analysis of the M. hyalina headspace and NMR analysis of the extracted essential oil identified the sulfur-containing volatile tris(methylthio)methane (TMTM) as the major compound. Incorporation of the sulfur from the fungal volatile into plant metabolism was shown by ³⁴S labeling experiments. Under sulfur deficiency, TMTM down-regulated sulfur deficiency-responsive genes, prevented glucosinolate (GSL) and glutathione (GSH) diminishment, and sustained plant growth. However, excess TMTM led to accumulation of GSH and GSL and reduced plant growth. Since TMTM is not directly incorporated into cysteine, we propose that the volatile from M. hyalina influences the plant sulfur metabolism by interfering with the GSH metabolism, and alleviates sulfur imbalances under sulfur stress.

The Iron Deficiency-Regulated Small Protein Effector FEP3/IRON MAN1 Modulates Interaction of BRUTUS-LIKE1 With bHLH Subgroup IVc and POPEYE Transcription Factors

In light of climate change and human population growth one of the most challenging tasks is to generate plants that are Fe-efficient, resilient to low Fe supply and Fe-biofortified. For such endeavors, it is crucial to understand the regulation of Fe acquisition and allocation in plants. One open question is how identified Fe-regulatory proteins comprising positive and negative regulators act together to steer Fe homeostasis. bHLH transcription factors (TFs) belonging to the subgroups IVb and IVc can initiate a bHLH cascade controlling the -Fe response in roots. In Arabidopsis thaliana, the -Fe-induced genes are sub-divided into several gene co-expression clusters controlled by different sets of TFs. Some of the co-expressed genes encode regulatory E3 ligase proteins BRUTUS (BTS)/BTS-LIKE (BTSL) and small proteins belonging to the group of FE UPTAKE-INDUCING PEPTIDE/IRON MAN (FEP/IMA). Recently, it was described that FEP1/IMA3 and FEP3/IMA1 proteins inhibit the repression of bHLH factors by BTS. We had postulated that -Fe-regulated co-expression clusters provide new information about regulatory protein interaction complexes. Here, we report a targeted yeast two-hybrid screen among 23 proteins of the -Fe response. This identified a novel protein interactome involving another E3 ligase, namely BTSL1, basic helix-loop-helix (bHLH) protein POPEYE (PYE) and transcription factors of the subgroup IVc as well as FEP3/IMA1. Because of the difficulty in stable BTSL1 protein expression in plant cells, we used a yeast two hybrid-based deletion mapping, homology modeling and molecular docking, to pinpoint interaction sites in BTSL1 and FEP3/IMA1. bHLH IVc TFs have similar residues at their C-terminus as FEP3/IMA1 interacting sites. FEP3/IMA1 attenuated interaction of BTSL1 and bHLH proteins in a yeast three-hybrid assay, in line with physiological data pointing to enhanced Fe acquisition and allocation in FEP3/IMA1 overexpression and btsl1 btsl2 mutant plants. Hence, exploiting -Fe-induced gene co-expression networks identified FEP3/IMA1 as a small effector protein that binds and inhibits the BTSL1 complex with PYE and bHLH subgroup IVc proteins. Structural analysis resolved interaction sites. This information helps improving models of Fe regulation and identifying novel targets for breeding of Fe-efficient crops.

In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2

Arabidopsis thaliana sulfur deficiency-induced 1 and sulfur deficiency-induced 2 (SDI1 and SDI2) are involved in partitioning sulfur among metabolite pools during sulfur deficiency, and their transcript levels strongly increase in this condition. However, little is currently known about the cis- and trans-factors that regulate SDI expression. We aimed at identifying DNA sequence elements (cis-elements) and transcription factors (TFs) involved in regulating expression of the SDI genes. We performed in silico analysis of their promoter sequences cataloging known cis-elements and identifying conserved sequence motifs. We screened by yeast-one-hybrid an arrayed library of Arabidopsis TFs for binding to the SDI1 and SDI2 promoters. In total, 14 candidate TFs were identified. Direct association between particular cis-elements in the proximal SDI promoter regions and specific TFs was established via electrophoretic mobility shift assays: sulfur limitation 1 (SLIM1) was shown to bind SURE cis-element(s), the basic domain/leucine zipper (bZIP) core cis-element was shown to be important for HY5-homolog (HYH) binding, and G-box binding factor 1 (GBF1) was shown to bind the E box. Functional analysis of GBF1 and HYH using mutant and over-expressing lines indicated that these TFs promote a higher transcript level of SDI1 in vivo. Additionally, we performed a meta-analysis of expression changes of the 14 TF candidates in a variety of conditions that alter SDI expression. The presented results expand our understanding of sulfur pool regulation by SDI genes.

Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice

Sulfur (S) is an essential mineral nutrient required for plant growth and development. Plants usually face temporal and spatial variation in sulfur availability, including the heterogeneous sulfate content in soils. As sessile organisms, plants have evolved sophisticated mechanisms to modify their gene expression and physiological processes in order to optimize S acquisition and usage. Such plasticity relies on a complicated network to locally sense S availability and systemically respond to S status, which remains poorly understood. Here, we took advantage of a split-root system and performed transcriptome-wide gene expression analysis on rice plants in S deficiency followed by sulfate resupply. S deficiency altered the expressions of 6749 and 1589 genes in roots and shoots, respectively, accounting for 18.07% and 4.28% of total transcripts detected. Homogeneous sulfate resupply in both split-root halves recovered the expression of 27.06% of S-deficiency-responsive genes in shoots, while 20.76% of S-deficiency-responsive genes were recovered by heterogeneous sulfate resupply with only one split-root half being resupplied with sulfate. The local sulfate resupply response genes with expressions only recovered in the split-root half resupplied with sulfate but not in the other half remained in S deficiency were identified in roots, which were mainly enriched in cellular amino acid metabolic process and root growth and development. Several systemic response genes were also identified in roots, whose expressions remained unchanged in the split-root half resupplied with sulfate but were recovered in the other split-root half without sulfate resupply. The systemic response genes were mainly related to calcium signaling and auxin and ABA signaling. In addition, a large number of S-deficiency-responsive genes exhibited simultaneous local and systemic responses to sulfate resupply, such as the sulfate transporter gene OsSULTR1;1 and the O-acetylserine (thiol) lyase gene, highlighting the existence of a systemic regulation of sulfate uptake and assimilation in S deficiency plants followed by sulfate resupply. Our studies provided a comprehensive transcriptome-wide picture of a local and systemic response to heterogeneous sulfate resupply, which will facilitate an understanding of the systemic regulation of S homeostasis in rice.

Sulfur signaling and starvation response in Arabidopsis

As sessile organisms, plants have developed sophisticated mechanism to sense and utilize nutrients from the environment, and modulate their growth and development according to the nutrient availability. Research in the past two decades revealed that nutrient assimilation is not occurring spontaneously, but nutrient signaling networks are complexly regulated and integrate sensing and signaling, gene expression, and metabolism to ensure homeostasis and coordination with plant energy conversion and other processes. Here, we review the importance of the macronutrient sulfur (S) and compare the knowledge of S signaling with other important macronutrients, such as nitrogen (N) and phosphorus (P). We focus on key advances in understanding sulfur sensing and signaling, uptake and assimilation, and we provide new analysis of published literature, to identify core genes regulated by the key transcriptional factor in S starvation response, SLIM1/EIL3, and compare the impact on other nutrient deficiency and stresses on S-related genes.

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

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

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.

Sulfur in Seeds: An Overview

Sulfur is a growth-limiting and secondary macronutrient as well as an indispensable component for several cellular components of crop plants. Over the years various scientists have conducted several experiments on sulfur metabolism based on different aspects of plants. Sulfur metabolism in seeds has immense importance in terms of the different sulfur-containing seed storage proteins, the significance of transporters in seeds, the role of sulfur during the time of seed germination, etc. The present review article is based on an overview of sulfur metabolism in seeds, in respect to source to sink relationships, S transporters present in the seeds, S-regulated seed storage proteins and the importance of sulfur at the time of seed germination. Sulfur is an essential component and a decidable factor for seed yield and the quality of seeds in terms of oil content in oilseeds, storage of qualitative proteins in legumes and has a significant role in carbohydrate metabolism in cereals. In conclusion, a few future perspectives towards a more comprehensive knowledge on S metabolism/mechanism during seed development, storage and germination have also been stated.

Genome-Wide Association Reveals Trait Loci for Seed Glucosinolate Accumulation in Indian Mustard (Brassica juncea L.)

Glucosinolates (GSLs) are sulphur- and nitrogen-containing secondary metabolites implicated in the fitness of Brassicaceae and appreciated for their pungency and health-conferring properties. In Indian mustard (Brassica juncea L.), GSL content and composition are seed-quality-determining traits affecting its economic value. Depending on the end use, i.e., condiment or oil, different GSL levels constitute breeding targets. The genetic control of GSL accumulation in Indian mustard, however, is poorly understood, and current knowledge of GSL biosynthesis and regulation is largely based on Arabidopsis thaliana. A genome-wide association study was carried out to dissect the genetic architecture of total GSL content and the content of two major GSLs, sinigrin and gluconapin, in a diverse panel of 158 Indian mustard lines, which broadly grouped into a South Asia cluster and outside-South-Asia cluster. Using 14,125 single-nucleotide polymorphisms (SNPs) as genotyping input, seven distinct significant associations were discovered for total GSL content, eight associations for sinigrin content and 19 for gluconapin. Close homologues of known GSL structural and regulatory genes were identified as candidate genes in proximity to peak SNPs. Our results provide a comprehensive map of the genetic control of GLS biosynthesis in Indian mustard, including priority targets for further investigation and molecular marker development.

Sulfur deficiency-induced genes affect seed protein accumulation and composition under sulfate deprivation

Sulfur deficiency-induced proteins SDI1 and SDI2 play a fundamental role in sulfur homeostasis under sulfate-deprived conditions (-S) by downregulating glucosinolates. Here, we identified that besides glucosinolate regulation under -S, SDI1 downregulates another sulfur pool, the S-rich 2S seed storage proteins in Arabidopsis (Arabidopsis thaliana) seeds. We identified that MYB28 directly regulates 2S seed storage proteins by binding to the At2S4 promoter. We also showed that SDI1 downregulates 2S seed storage proteins by forming a ternary protein complex with MYB28 and MYC2, another transcription factor involved in the regulation of seed storage proteins. These findings have significant implications for the understanding of plant responses to sulfur deficiency.

Improvement of glucosinolates by metabolic engineering in Brassica crops

Glucosinolates (GSLs) are a class of sulfur- and nitrogen-containing, and amino acid-derived important secondary metabolites, which mainly present in plants of Brassicaceae family, including Brassica crops, such as broccoli, cabbage, and oilseed rape. The bioactive GSL metabolites confer benefits to plant defense, human health, and the unique flavor of some Brassica crops. However, certain GSL profiles have adverse effects and are known as anti-nutritional factors. This has attracted mounting attempts to increase beneficial GSLs and reduce detrimental ones in the most commonly consumed Brassica crops. We provide a comprehensive overview of metabolic engineering applied in Brassica crops to achieve this purpose, including modulation of GSL biosynthesis, ablation of GSL hydrolysis, inhibition of GSL transport processes, and redirection of metabolic flux to GSL. Moreover, advances in omics approaches, i.e., genomics, transcriptome, and metabolome, applied in the elucidation of GSL metabolism in Brassica crops, as well as promising and potential genome-editing technologies are also discussed.

Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach

Background

Glucosinolates (GSLs) are plant secondary metabolites that contain nitrogen-containing compounds. They are important in the plant defense system and known to provide protection against cancer in humans. Currently, increasing the amount of data generated from various omics technologies serves as a hotspot for new gene discovery. However, sometimes sequence similarity searching approach is not sufficiently effective to find these genes; hence, we adapted a network clustering approach to search for potential GSLs genes from the Arabidopsis thaliana co-expression dataset.

Methods

We used known GSL genes to construct a comprehensive GSL co-expression network. This network was analyzed with the DPClusOST algorithm using a density of 0.5. 0.6. 0.7, 0.8, and 0.9. Generating clusters were evaluated using Fisher’s exact test to identify GSL gene co-expression clusters. A significance score (SScore) was calculated for each gene based on the generated p-value of Fisher’s exact test. SScore was used to perform a receiver operating characteristic (ROC) study to classify possible GSL genes using the ROCR package. ROCR was used in determining the AUC that measured the suitable density value of the cluster for further analysis. Finally, pathway enrichment analysis was conducted using ClueGO to identify significant pathways associated with the GSL clusters.

Results

The density value of 0.8 showed the highest area under the curve (AUC) leading to the selection of thirteen potential GSL genes from the top six significant clusters that include IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1, and At3g14220. A total of Four potential genes (MTO1, SIR, SAL1, and IMDH3) were identified from the pathway enrichment analysis on the significant clusters. These genes are directly related to GSL-associated pathways such as sulfur metabolism and valine, leucine, and isoleucine biosynthesis. This approach demonstrates the ability of the network clustering approach in identifying potential GSL genes which cannot be found from the standard similarity search.

Metabolism and Regulatory Functions of O-Acetylserine, S-Adenosylmethionine, Homocysteine, and Serine in Plant Development and Environmental Responses

The metabolism of an organism is closely related to both its internal and external environments. Metabolites can act as signal molecules that regulate the functions of genes and proteins, reflecting the status of these environments. This review discusses the metabolism and regulatory functions of O-acetylserine (OAS), S-adenosylmethionine (AdoMet), homocysteine (Hcy), and serine (Ser), which are key metabolites related to sulfur (S)-containing amino acids in plant metabolic networks, in comparison to microbial and animal metabolism. Plants are photosynthetic auxotrophs that have evolved a specific metabolic network different from those in other living organisms. Although amino acids are the building blocks of proteins and common metabolites in all living organisms, their metabolism and regulation in plants have specific features that differ from those in animals and bacteria. In plants, cysteine (Cys), an S-containing amino acid, is synthesized from sulfide and OAS derived from Ser. Methionine (Met), another S-containing amino acid, is also closely related to Ser metabolism because of its thiomethyl moiety. Its S atom is derived from Cys and its methyl group from folates, which are involved in one-carbon metabolism with Ser. One-carbon metabolism is also involved in the biosynthesis of AdoMet, which serves as a methyl donor in the methylation reactions of various biomolecules. Ser is synthesized in three pathways: the phosphorylated pathway found in all organisms and the glycolate and the glycerate pathways, which are specific to plants. Ser metabolism is not only important in Ser supply but also involved in many other functions. Among the metabolites in this network, OAS is known to function as a signal molecule to regulate the expression of OAS gene clusters in response to environmental factors. AdoMet regulates amino acid metabolism at enzymatic and translational levels and regulates gene expression as methyl donor in the DNA and histone methylation or after conversion into bioactive molecules such as polyamine and ethylene. Hcy is involved in Met-AdoMet metabolism and can regulate Ser biosynthesis at an enzymatic level. Ser metabolism is involved in development and stress responses. This review aims to summarize the metabolism and regulatory functions of OAS, AdoMet, Hcy, and Ser and compare the available knowledge for plants with that for animals and bacteria and propose a future perspective on plant research.

Cross-Species Metabolic Profiling of Floral Specialized Metabolism Facilitates Understanding of Evolutional Aspects of Metabolism Among Brassicaceae Species

Plants produce a variety of floral specialized (secondary) metabolites with roles in several physiological functions, including light-protection, attraction of pollinators, and protection against herbivores. Pigments and volatiles synthesized in the petal have been focused on and characterized as major chemical factors influencing pollination. Recent advances in plant metabolomics have revealed that the major floral specialized metabolites found in land plant species are hydroxycinnamates, phenolamides, and flavonoids albeit these are present in various quantities and encompass diverse chemical structures in different species. Here, we analyzed numerous floral specialized metabolites in 20 different Brassicaceae genotypes encompassing both different species and in the case of crop species different cultivars including self-compatible (SC) and self-incompatible (SI) species by liquid chromatography-mass spectrometry (LC-MS). Of the 228 metabolites detected in flowers among 20 Brassicaceae species, 15 metabolite peaks including one phenylacyl-flavonoids and five phenolamides were detected and annotated as key metabolites to distinguish SC and SI plant species, respectively. Our results provide a family-wide metabolic framework and delineate signatures for compatible and incompatible genotypes thereby providing insight into evolutionary aspects of floral metabolism in Brassicaceae species.

Proteomics of developing pea seeds reveals a complex antioxidant network underlying the response to sulfur deficiency and water stress

Pea is a legume crop producing protein-rich seeds and is increasingly in demand for human consumption and animal feed. The aim of this study was to explore the proteome of developing pea seeds at three key stages covering embryogenesis, the transition to seed-filling, and the beginning of storage-protein synthesis, and to investigate how the proteome was influenced by S deficiency and water stress, applied either separately or combined. Of the 3184 proteins quantified by shotgun proteomics, 2473 accumulated at particular stages, thus providing insights into the proteome dynamics at these stages. Differential analyses in response to the stresses and inference of a protein network using the whole proteomics dataset identified a cluster of antioxidant proteins (including a glutathione S-transferase, a methionine sulfoxide reductase, and a thioredoxin) possibly involved in maintaining redox homeostasis during early seed development and preventing cellular damage under stress conditions. Integration of the proteomics data with previously obtained transcriptomics data at the transition to seed-filling revealed the transcriptional events associated with the accumulation of the stress-regulated antioxidant proteins. This transcriptional defense response involves genes of sulfate homeostasis and assimilation, thus providing candidates for targeted studies aimed at dissecting the signaling cascade linking S metabolism to antioxidant processes in developing seeds.

Transcriptome, proteome, and metabolome reveal the mechanism of tolerance to selenate toxicity in Cardamine violifolia

Cardamine violifolia was found here to accumulate selenium (Se) to over 9000 mg kg^-1 dry weight. To investigate the mechanism of Se accumulation and tolerance in C. violifolia, metabolome, transcriptome, and proteome technologies were applied to C. violifolia seedlings treated with selenate. Several sulfate transporter (Sultr) genes (Sultr1;1, Sultr1;2, and Sultr2;1) and sulfur assimilatory enzyme genes showed high expression levels in response to selenate. Many calcium protein and cysteine-rich kinase genes of C. violifolia were downregulated, whereas selenium-binding protein 1 (SBP1) and protein sulfur deficiency-induced 2 (SDI2) of C. violifolia were upregulated by selenate. The expression of genes involved in the ribosome and posttranslational modifications and chaperones in C. violifolia were also detected in response to selenate. Based on the results of this study and previous findings, we suggest that the downregulated expression of calcium proteins and cysteine-rich kinases, and the upregulated expression of SBP1 and SDI2, were important contributors to the Se tolerance of C. violifolia. The downregulation of cysteine-rich kinases and calcium proteins would enhance Se tolerance of C. violifolia is a novel proposition that has not been reported on other Se hyperaccumulators. This study provides us novel insights to understand Se accumulation and tolerance in plants.

Regulation of glucosinolate biosynthesis

Glucosinolates are secondary defense metabolites produced by plants of the order Brassicales, which includes the model species Arabidopsis and many crop species. In the past 13 years, the regulation of glucosinolate synthesis in plants has been intensively studied, with recent research revealing complex molecular mechanisms that connect glucosinolate production with responses to other central pathways. In this review, we discuss how the regulation of glucosinolate biosynthesis is ecologically relevant for plants, how it is controlled by transcription factors, and how this transcriptional machinery interacts with hormonal, environmental, and epigenetic mechanisms. We present the central players in glucosinolate regulation, MYB and basic helix-loop-helix transcription factors, as well as the plant hormone jasmonate, which together with other hormones and environmental signals allow the coordinated and rapid regulation of glucosinolate genes. Furthermore, we highlight the regulatory connections between glucosinolates, auxin, and sulfur metabolism and discuss emerging insights and open questions on the regulation of glucosinolate biosynthesis.

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.

Coordinating Sulfur Pools under Sulfate Deprivation

Plants display manifold metabolic changes on sulfate deficiency (S deficiency) with all sulfur-containing pools of primary and secondary metabolism affected. O-Acetylserine (OAS), whose levels are rapidly altered on S deficiency, is correlated tightly with novel regulators of plant sulfur metabolism that have key roles in balancing plant sulfur pools, including the Sulfur Deficiency Induced genes (SDI1 and SDI2), More Sulfur Accumulation1 (MSA1), and GGCT2;1. Despite the importance of OAS in the coordination of S pools under stress, mechanisms of OAS perception and signaling have remained elusive. Here, we put particular focus on the general OAS-responsive genes but also elaborate on the specific roles of SDI1 and SDI2 genes, which downregulate the glucosinolate (GSL) pool size. We also highlight the key open questions in sulfur partitioning.

The Transcription Factor EIL1 Participates in the Regulation of Sulfur-Deficiency Response

Sulfur, an indispensable constituent of many cellular components, is a growth-limiting macronutrient for plants. Thus, to successfully adapt to changing sulfur availability and environmental stress, a sulfur-deficiency response helps plants to cope with the limited supply. On the transcriptional level, this response is controlled by SULFUR LIMITATION1 (SLIM1), a member of the ETHYLENE-INSENSITIVE3-LIKE (EIL) transcription factor family. In this study, we identified EIL1 as a second transcriptional activator regulating the sulfur-deficiency response, subordinate to SLIM1/EIL3. Our comprehensive RNA sequencing analysis in Arabidopsis (Arabidopsis thaliana) allowed us to obtain a complete picture of the sulfur-deficiency response and quantify the contributions of these two transcription factors. We confirmed the key role of SLIM1/EIL3 in controlling the response, particularly in the roots, but showed that in leaves more than 50% of the response is independent of SLIM1/EIL3 and EIL1. RNA sequencing showed an additive contribution of EIL1 to the regulation of the sulfur-deficiency response but also identified genes specifically regulated through EIL1. SLIM1/EIL3 seems to have further functions (e.g. in the regulation of genes responsive to hypoxia or mediating defense at both low and normal sulfur supply). These results contribute to the dissection of mechanisms of the sulfur-deficiency response and provide additional possibilities to improve adaptation to sulfur-deficiency conditions.

Sulfur Homeostasis in Plants

Sulfur (S) is an essential macronutrient for plant growth and development. S is majorly absorbed as sulfate from soil, and is then translocated to plastids in leaves, where it is assimilated into organic products. Cysteine (Cys) is the first organic product generated from S, and it is used as a precursor to synthesize many S-containing metabolites with important biological functions, such as glutathione (GSH) and methionine (Met). The reduction of sulfate takes place in a two-step reaction involving a variety of enzymes. Sulfate transporters (SULTRs) are responsible for the absorption of SO42- from the soil and the transport of SO42- in plants. There are 12-16 members in the S transporter family, which is divided into five categories based on coding sequence homology and biochemical functions. When exposed to S deficiency, plants will alter a series of morphological and physiological processes. Adaptive strategies, including cis-acting elements, transcription factors, non-coding microRNAs, and phytohormones, have evolved in plants to respond to S deficiency. In addition, there is crosstalk between S and other nutrients in plants. In this review, we summarize the recent progress in understanding the mechanisms underlying S homeostasis in plants.

Glucosinolate Biosynthesis and the Glucosinolate–Myrosinase System in Plant Defense

Insect pests represent a major global challenge to important agricultural crops. Insecticides are often applied to combat such pests, but their use has caused additional challenges such as environmental contamination and human health issues. Over millions of years, plants have evolved natural defense mechanisms to overcome insect pests and pathogens. One such mechanism is the production of natural repellents or specialized metabolites like glucosinolates. There are three types of glucosinolates produced in the order Brassicales: aliphatic, indole, and benzenic glucosinolates. Upon insect herbivory, a “mustard oil bomb” consisting of glucosinolates and their hydrolyzing enzymes (myrosinases) is triggered to release toxic degradation products that act as insect deterrents. This review aims to provide a comprehensive summary of glucosinolate biosynthesis, the “mustard oil bomb”, and how these metabolites function in plant defense against pathogens and insects. Understanding these defense mechanisms will not only allow us to harness the benefits of this group of natural metabolites for enhancing pest control in Brassicales crops but also to transfer the “mustard oil bomb” to non-glucosinolate producing crops to boost their defense and thereby reduce the use of chemical pesticides.

The Eruca sativa Genome and Transcriptome: A Targeted Analysis of Sulfur Metabolism and Glucosinolate Biosynthesis Pre and Postharvest

Rocket (Eruca sativa) is a source of health-related metabolites called glucosinolates (GSLs) and isothiocyanates (ITCs) but little is known of the genetic and transcriptomic mechanisms responsible for regulating pre and postharvest accumulations. We present the first de novo reference genome assembly and annotation, with ontogenic and postharvest transcriptome data relating to sulfur assimilation, transport, and utilization. Diverse gene expression patterns related to sulfur metabolism, GSL biosynthesis, and glutathione biosynthesis are present between inbred lines of rocket. A clear pattern of differential expression determines GSL abundance and the formation of hydrolysis products. One breeding line sustained GSL accumulation and hydrolysis product formation throughout storage. Multiple copies of MYB28, SLIM1, SDI1, and ESM1 have increased and differential expression postharvest, and are associated with GSLs and hydrolysis product formation. Two glucosinolate transporter gene (GTR2) copies were found to be associated with increased GSL accumulations in leaves. Monosaccharides (which are essential for primary metabolism and GSL biosynthesis, and contribute to the taste of rocket) were also quantified in leaves, with glucose concentrations significantly correlated with the expression of numerous GSL-related genes. Significant negative correlations were observed between the expression of glutathione synthetase (GSH) genes and those involved in GSL metabolism. Breeding line "B" showed increased GSH gene expression and low GSL content compared to two other lines where the opposite was observed. Co-expression analysis revealed senescence (SEN1) and oxidative stress-related (OXS3) genes have higher expression in line B, suggesting that postharvest deterioration is associated with low GSL concentrations.

Integration analysis of PacBio SMRT- and Illumina RNA-seq reveals candidate genes and pathway involved in selenium metabolism in hyperaccumulator Cardamine violifolia

BACKGROUND

Cardamine violifolia, native to China, is one of the selenium (Se) hyperaccumulators. The mechanism of Se metabolism and tolerance remains unclear, and only limited genetic information is currently available. Therefore, we combined a PacBio single-molecule real-time (SMRT) transcriptome library and the Illumina RNA-seq data of sodium selenate (Na₂SeO₄)-treated C. violifolia to further reveal the molecular mechanism of Se metabolism.

RESULTS

The concentrations of the total, inorganic, and organic Se in C. violifolia seedlings significantly increased as the Na₂SeO₄ treatment concentration increased. From SMRT full-length transcriptome of C. violifolia, we obtained 26,745 annotated nonredundant transcripts, 14,269 simple sequence repeats, 283 alternative splices, and 3407 transcription factors. Fifty-one genes from 134 transcripts were identified to be involved in Se metabolism, including transporter, assimilatory enzyme, and several specific genes. Analysis of Illumina RNA-Seq data showed that a total of 948 differentially expressed genes (DEGs) were filtered from the four groups with Na₂SeO₄ treatment, among which 11 DEGs were related to Se metabolism. The enrichment analysis of KEGG pathways of all the DEGs showed that they were significantly enriched in five pathways, such as hormone signal transduction and plant-pathogen interaction pathways. Four genes related to Se metabolism, adenosine triphosphate sulfurase 1, adenosine 5'-phosphosulfate reductase 3, cysteine (Cys) desulfurase 1, and serine acetyltransferase 2, were regulated by lncRNAs. Twenty potential hub genes (e.g., sulfate transporter 1;1, Cys synthase, methionine gamma-lyase, and Se-binding protein 1) were screened and identified to play important roles in Se accumulation and tolerance in C. violifolia as concluded by weighted gene correlation network analysis. Based on combinative analysis of expression profiling and annotation of genes as well as Se speciation and concentration in C. violifolia under the treatments with different Na₂SeO₄ concentrations, a putative Se metabolism and assimilation pathway in C. violifolia was proposed.

CONCLUSION

Our data provide abundant information on putative gene transcriptions and pathway involved in Se metabolism of C. violifolia. The findings present a genetic resource and provide novel insights into the mechanism of Se hyperaccumulation in C. violifolia.

Integrating multiple omics to identify common and specific molecular changes occurring in Arabidopsis under chronic nitrate and sulfate limitations

Plants have fundamental dependences on nitrogen and sulfur and frequently have to cope with chronic limitations when their supply is sub-optimal. This study aimed at characterizing the metabolomic, proteomic, and transcriptomic changes occurring in Arabidopsis leaves under chronic nitrate (Low-N) and chronic sulfate (Low-S) limitations in order to compare their effects, determine interconnections, and examine strategies of adaptation. Metabolite profiling globally revealed opposite effects of Low-S and Low-N on carbohydrate and amino acid accumulations, whilst proteomic data showed that both treatments resulted in increases in catabolic processes, stimulation of mitochondrial and cytosolic metabolism, and decreases in chloroplast metabolism. Lower abundances of ribosomal proteins and translation factors under Low-N and Low-S corresponded with growth limitation. At the transcript level, the major and specific effect of Low-N was the enhancement of expression of defence and immunity genes. The main effect of chronic Low-S was a decrease in transcripts of genes involved in cell division, DNA replication, and cytoskeleton, and an increase in the expression of autophagy genes. This was consistent with a role of target-of-rapamycin kinase in the control of plant metabolism and cell growth and division under chronic Low-S. In addition, Low-S decreased the expression of several NLP transcription factors, which are master actors in nitrate sensing. Finally, both the transcriptome and proteome data indicated that Low-S repressed glucosinolate synthesis, and that Low-N exacerbated glucosinolate degradation. This showed the importance of glucosinolate as buffering molecules for N and S management.

Proteasomal Degradation of Proteins Is Important for the Proper Transcriptional Response to Sulfur Deficiency Conditions in Plants

Plants are continuously exposed to different abiotic and biotic stresses; therefore, to protect themselves, they depend on the fast reprogramming of large gene repertoires to prioritize the expression of a given stress-induced gene set over normal cellular household genes. The activity of the proteasome, a large proteolytic complex that degrades proteins, is vital to coordinate the expression of such genes. Proteins are labeled for degradation by the action of E3 ligases that site-specifically alter their substrates by adding chains of ubiquitin. Recent publications have revealed an extensive role of ubiquitination in the utilization of nutrients. This study presents the transcriptomic profiles of sulfur-deficient rosettes and roots of Arabidopsis thaliana rpt2a mutant with proteasomal malfunction. We found that genes connected with sulfur metabolism are regulated to the lesser extent in rpt2a mutant while genes encoding transfer RNAs and small nucleolar RNAs are highly upregulated. Several genes encoding E3 ligases are specifically regulated by sulfur deficiency. Furthermore, we show that a key transcription factor of sulfur deficiency response, Sulfur LIMitation1, undergoes proteasomal degradation and is able to interact with F-box protein, EBF1.