Molecular mechanisms of regulation of sulfate assimilation: first steps on a long road

Performance of vertical flow constructed wetland for the treatment of effluent from a brassware industry in city of Fez, Morocco: a laboratory scale study

Brassware industry constitutes the second most polluting industrial sector in Fez city, Morocco, owing to its high heavy metal load. The aim of this study is to examine and evaluate the performance of vertical flow constructed wetlands in treating brassware effluents using various plant species. Ten treatment systems were planted with four types of plants: Chrysopogon zizanioides, Typha latifolia, Phragmites australis, and Vitex agnus-castus, while another system remained unplanted. These systems underwent evaluation by measuring various parameters, including pH, electrical conductivity, suspended solids, chemical oxygen demand, biological oxygen demand, sulfates, orthophosphates, total Kjeldhal nitrogen, ammonium, nitrates, nitrites, and heavy metals such as silver, copper, and nickel, using standard methods over of ten weeks. The results obtained demonstrate effectiveness of these systems. When planted with Ch. zizanioides, the systems achieved elimination rates of 83.64%, 98.55%, 91.48%, 86.82%, 80.31%, 96.54%, 98%, and 98.82% for suspended solids, ammonium, nitrites, BOD5, sulfates, orthophosphates, silver, and nickel, respectively. System with V. agnus-castus showed significant reductions in nitrate and copper, with rates of 84.48% and 99.10%, respectively. Considerable decrease in pH and electrical conductivity values was observed in all systems, with a notable difference between planted and control systems regarding effectiveness of treatment for other parameters.

Temporal dynamics of stress response in Halomonas elongata to NaCl shock: physiological, metabolomic, and transcriptomic insights

BACKGROUND

The halophilic bacterium Halomonas elongata is an industrially important strain for ectoine production, with high value and intense research focus. While existing studies primarily delve into the adaptive mechanisms of this bacterium under fixed salt concentrations, there is a notable dearth of attention regarding its response to fluctuating saline environments. Consequently, the stress response of H. elongata to salt shock remains inadequately understood.

RESULTS

This study investigated the stress response mechanism of H. elongata when exposed to NaCl shock at short- and long-time scales. Results showed that NaCl shock induced two major stresses, namely osmotic stress and oxidative stress. In response to the former, within the cell's tolerable range (1-8% NaCl shock), H. elongata urgently balanced the surging osmotic pressure by uptaking sodium and potassium ions and augmenting intracellular amino acid pools, particularly glutamate and glutamine. However, ectoine content started to increase until 20 min post-shock, rapidly becoming the dominant osmoprotectant, and reaching the maximum productivity (1450 ± 99 mg/L/h). Transcriptomic data also confirmed the delayed response in ectoine biosynthesis, and we speculate that this might be attributed to an intracellular energy crisis caused by NaCl shock. In response to oxidative stress, transcription factor cysB was significantly upregulated, positively regulating the sulfur metabolism and cysteine biosynthesis. Furthermore, the upregulation of the crucial peroxidase gene (HELO_RS18165) and the simultaneous enhancement of peroxidase (POD) and catalase (CAT) activities collectively constitute the antioxidant defense in H. elongata following shock. When exceeding the tolerance threshold of H. elongata (1-13% NaCl shock), the sustained compromised energy status, resulting from the pronounced inhibition of the respiratory chain and ATP synthase, may be a crucial factor leading to the stagnation of both cell growth and ectoine biosynthesis.

CONCLUSIONS

This study conducted a comprehensive analysis of H. elongata's stress response to NaCl shock at multiple scales. It extends the understanding of stress response of halophilic bacteria to NaCl shock and provides promising theoretical insights to guide future improvements in optimizing industrial ectoine production.

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.

Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF

Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.

Photorespiration: regulation and new insights on the potential role of persulfidation

Photorespiration has been considered a 'futile' cycle in C3 plants, necessary to detoxify and recycle the metabolites generated by the oxygenating activity of Rubisco. However, several reports indicate that this metabolic route plays a fundamental role in plant metabolism and constitutes a very interesting research topic. Many open questions still remain with regard to photorespiration. One of these questions is how the photorespiratory process is regulated in plants and what factors contribute to this regulation. In this review, we summarize recent advances in the regulation of the photorespiratory pathway with a special focus on the transcriptional and post-translational regulation of photorespiration and the interconnections of this process with nitrogen and sulfur metabolism. Recent findings on sulfide signaling and protein persulfidation are also described.

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.

Diversity and roles of cysteine desulfurases in photosynthetic organisms

As sulfur is part of many essential protein cofactors such as iron-sulfur clusters, molybdenum cofactors, or lipoic acid, its mobilization from cysteine represents a fundamental process. The abstraction of the sulfur atom from cysteine is catalysed by highly conserved pyridoxal 5'-phosphate-dependent enzymes called cysteine desulfurases. The desulfuration of cysteine leads to the formation of a persulfide group on a conserved catalytic cysteine and the concomitant release of alanine. Sulfur is then transferred from cysteine desulfurases to different targets. Numerous studies have focused on cysteine desulfurases as sulfur-extracting enzymes for iron-sulfur cluster synthesis in mitochondria and chloroplasts but also for molybdenum cofactor sulfuration in the cytosol. Despite this, knowledge about the involvement of cysteine desulfurases in other pathways is quite rudimentary, particularly in photosynthetic organisms. In this review, we summarize current understanding of the different groups of cysteine desulfurases and their characteristics in terms of primary sequence, protein domain architecture, and subcellular localization. In addition, we review the roles of cysteine desulfurases in different fundamental pathways and highlight the gaps in our knowledge to encourage future work on unresolved issues especially in photosynthetic organisms.

Unravelling microbial drivers of the sulfate-reduction process inside landfill using metagenomics

Hydrogen sulfide (H₂S) is one of the common landfill odor. This research demonstrates that the sulfate transformation behavior is significantly enhanced during the landfill process, accompanied by a shift in microbial structure. The relative abundance of dissimilatory sulfate reduction (DSR) and thiosulfate oxidation by SOX (sulfur-oxidation) complex gradually decreases through the landfill processes while the assimilatory sulfate reduction (ASR) demonstrates the opposite behavior. The major module for landfill sulfate reduction is ASR, accounting for 31.72% ± 2.84% of sulfate metabolism. Based on the functional genes for the sulfate pathway, the drivers for sulfate biotransformation in landfills were determined and further identified their contribution in the sulfate metabolism during landfill processes. Pseudomonas, Methylocaldum, Bacillus, Methylocystis and Hyphomicrobium were the top 5 contributors for ASR pathway, and only one genus Pseudomonas was found for DSR pathway. Among the 26 high-quality metagenome-assembled genomes of sulfate functional species, 24 were considered novel species for sulfuric metabolism. Overall, this study provides unique insight into the sulfate transformation process related to the H₂S odor control in landfill management.

Transcriptome and QTL mapping analyses of major QTL genes controlling glucosinolate contents in vegetable- and oilseed-type Brassica rapa plants

Glucosinolates (GSLs) are secondary metabolites providing defense against pathogens and herbivores in plants, and anti-carcinogenic activity against human cancer cells. Profiles of GSLs vary greatly among members of genus Brassica. In this study, we found that a reference line of Chinese cabbage (B. rapa ssp. pekinensis), 'Chiifu' contains significantly lower amounts of total GSLs than the oilseed-type B. rapa (B. rapa ssp. trilocularis) line 'LP08'. This study aimed to identify the key regulators of the high accumulation of GSLs in Brassica rapa plants using transcriptomic and linkage mapping approaches. Comparative transcriptome analysis showed that, in total, 8,276 and 9,878 genes were differentially expressed between 'Chiifu' and 'LP08' under light and dark conditions, respectively. Among 162 B. rapa GSL pathway genes, 79 were related to GSL metabolism under light conditions. We also performed QTL analysis using a single nucleotide polymorphism-based linkage map constructed using 151 F₅ individuals derived from a cross between the 'Chiifu' and 'LP08' inbred lines. Two major QTL peaks were successfully identified on chromosome 3 using high-performance liquid chromatography to obtain GSL profiles from 97 F₅ recombinant inbred lines. The MYB-domain transcription factor gene BrMYB28.1 (Bra012961) was found in the highest QTL peak region. The second highest peak was located near the 2-oxoacid-dependent dioxygenase gene BrGSL-OH.1 (Bra022920). This study identified major genes responsible for differing profiles of GSLs between 'Chiifu' and 'LP08'. Thus, our study provides molecular insights into differences in GSL profiles between vegetative- and oilseed-type B. rapa plants.

Unique features of regulation of sulfate assimilation in monocots

Sulfate assimilation is an essential pathway of plant primary metabolism, regulated by the demand for reduced sulfur (S). The S-containing tripeptide glutathione (GSH) is the key signal for such regulation in Arabidopsis, but little is known about the conservation of these regulatory mechanisms beyond this model species. Using two model monocot species, C3 rice (Oryza sativa) and C4Setaria viridis, and feeding of cysteine or GSH, we aimed to find out how conserved are the regulatory mechanisms described for Arabidopsis in these species. We showed that while in principle the regulation is similar, there are many species-specific differences. For example, thiols supplied by the roots are translocated to the shoots in rice but remain in the roots of Setaria. Cysteine and GSH concentrations are highly correlated in Setaria, but not in rice. In both rice and Setaria, GSH seems to be the signal for demand-driven regulation of sulfate assimilation. Unexpectedly, we observed cysteine oxidation to sulfate in both species, a reaction that does not occur in Arabidopsis. This reaction is dependent on sulfite oxidase, but the enzyme(s) releasing sulfite from cysteine still need to be identified. Altogether our data reveal a number of unique features in the regulation of S metabolism in the monocot species and indicate the need for using multiple taxonomically distinct models to better understand the control of nutrient homeostasis, which is important for generating low-input crop varieties.

Using bioelectrohydrogenesis left-over residues as a future potential fertilizer for soil amendment

In this current research, the left-over residues collected from the dark fermentation-microbial electrolysis cells (DF-MEC) integrated system solely biocatalyzed by activated sludge during the bioconversion of the agricultural straw wastes into hydrogen energy, was investigated for its feasibility to be used as a potential alternative biofertilizer to the commonly costly inorganic ones. The results revealed that the electrohydrogenesis left-over residues enriched various plant growth-promoting microbial communities including Enterobacter (8.57%), Paenibacillus (1.18%), Mycobacterium (0.77%), Pseudomonas (0.65%), Bradyrhizobium (0.12%), Azospirillum (0.11%), and Mesorhizobium (0.1%) that are generally known for their ability to produce different essential phytohormones such as indole-3-acetic acid/indole acetic acid (IAA) and Gibberellins for plant growth. Moreover, they also contain both phosphate-solubilizing and nitrogen-fixing microbial communities that remarkably provide an adequate amount of assimilable phosphorus and nitrogen required for enhanced plants or crop growth. Furthermore, macro-, and micronutrients (including N, P, K, etc.) were all analyzed from the residues and detected adequate appreciate concentrations required for plant growth promotions. The direct application of MEC-effluent as fertilizer in this current study conspicuously promoted plant growth (Solanum lycopersicum L. (tomato), Capsicum annuum L. (chilli), and Solanum melongena L. (brinjal)) and speeded up flowering and fruit-generating processes. Based on these findings, electrohydrogenesis residues could undoubtedly be considered as a potential biofertilizer. Thus, this technology provides a new approach to agricultural residue control and concomitantly provides a sustainable, cheap, and eco-friendly biofertilizer that could replace the chemical costly fertilizers.

Protective mechanisms of sulfur against arsenic phytotoxicity in Brassica napus by regulating thiol biosynthesis, sulfur-assimilation, photosynthesis, and antioxidant response

The contamination of agricultural soils with Arsenic (As) is a significant environmental stress that restricts plant growth, metabolism, and productivity worldwide. The present study examined the role of elemental sulfur (S⁰) in protecting Brassica napus plants from Arsenic (As) toxicity. Arsenic (100, and 200 mg As kg^-1 soil) in soil caused detrimental effects on five Brassica napus cultivars (Neelam, Teri-Uttam Jawahar, Him Sarson, GSC-101, and NUDB 26-11). The As toxicity inhibited the growth and photosynthesis indices in all cultivars with more deterioration effects in NUDB 26-11. Plant absorption and uptake of As caused the generation of oxidative injury by accumulating the reactive oxygen species (ROS), which simultaneously decreased the plant defence capability and ultimately the photosynthesis. Application of sulfur (S⁰, 100 or 200 mg S kg^-1 soil) alleviated the negative impacts and toxicity of As on the photosynthesis and growth matrices of plants, especially under high S level. S⁰ also boosted the antioxidant potential of plants and toned-down lipid peroxidation and ROS aggravation such as superoxide anion (O₂^•-) and H₂O₂, hydrogen peroxide, in As affected plants. In general, S⁰ at 200 mg kg^-1 soil more perceptibly increased the functionality of antioxidant enzymes, and non-enzymatic antioxidants, metal chelators and non-protein thiols. Further amendment of soil with S⁰ at fifteen days before seed sowing affected by As-induced toxic effects (added to soil at the time of sowing) considerably intensified the endogenous hydrogen sulfide (H₂S) content and its regenerating enzymes D-cysteine desulfhydrase (DCD) and L-cysteine desulfhydrase (LCD) that further strengthened the defense capability of plants to withstand As-stress. Our results suggest the role of H₂S in the S-induced defense operation of the B. napus plants in restraining As toxicity. The current study shows that S⁰ as a source of S might be used to promote the growth of B. napus plants in polluted agricultural soils.

Physiological metabolic topology analysis of Halomonas elongata DSM 2581T in response to sodium chloride stress

The halophilic bacterium Halomonas elongata DSM 2581^T generally adapts well to high level of salinity by biosynthesizing ectoine, which functions as an important compatible solute protecting the cell against external salinity environment. Halophilic bacteria have specific metabolic activities under high-salt conditions and are gradually applied in various industries. The present study focuses on investigating the physiological and metabolic mechanism of Halomonas elongata DSM 2581^T driven by the external salinity environment. The physiological metabolic dynamics under salt stress were investigated to evaluate the effect of NaCl stress on the metabolism of H. elongata. The obtained results demonstrated that ectoine biosynthesis transited from a non-growth-related process to a growth-related process when the NaCl concentration varied from 1% to 13% (w/v). The maximum biomass (X_m =41.37 g/L), and highest ectoine production (P_m =12.91 g/L) were achieved under 8% NaCl. Moreover, the maximum biomass (X_m ) and the maximum specific growth rates (μ_m ) showed a first rising and then declining trend with the increased NaCl stress. Furthermore, the transcriptome analysis of H. elongata under different NaCl concentrations demonstrated that both 8% and 13% NaCl conditions resulted in increased expressions of genes involved in the pentose phosphate pathway (PPP), Entner-Doudoroff (ED) pathway, Flagellar assembly pathway and ectoine metabolism, but negatively affected the tricarboxylic acid (TCA) cycle and Fatty acid metabolism. At last, the proposed possible adaptation mechanism under the optimum NaCl concentration in H. elongata was described. This article is protected by copyright. All rights reserved.

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.

Assessing the Effect of Silicon Supply on Root Sulfur Uptake in S-Fed and S-Deprived Brassica napus L

Silicon (Si) is known to alleviate many nutritional stresses. However, in Brassica napus, which is a highly S-demanding species, the Si effect on S deficiency remains undocumented. The aim of this study was to assess whether Si alleviates the negative effects of S deficiency on Brassica napus and modulates root sulfate uptake capacity and S accumulation. For this, Brassica napus plants were cultivated with or without S and supplied or not supplied with Si. The effects of Si on S content, growth, expression of sulfate transporter genes (BnaSultr1.1; BnaSultr1.2) and sulfate transporters activity in roots were monitored. Si supply did not mitigate growth or S status alterations due to S deprivation but moderated the expression of BnaSultr1.1 in S-deprived plants without affecting the activity of root sulfate transporters. The effects of Si on the amount of S taken-up and on S transporter gene expression were also evaluated after 72 h of S resupply. In S-deprived plants, S re-feeding led to a strong decrease in the expression of both S transporter genes as expected, except in Si-treated plants where BnaSultr1.1 expression was maintained over time. This result is discussed in relation to the similar amount of S accumulated regardless of the Si treatment.

Whole-Genome and Transcriptome Sequencing-Based Characterization of Bacillus Cereus NR1 From Subtropical Marine Mangrove and Its Potential Role in Sulfur Metabolism

Sulfur, organosulfur compounds, and sulfides are essential parts of life. Microbial sulfate assimilation is among the most active and ancient metabolic activities in the sulfur cycle that operates in various ecosystems. We analyzed the molecular basis of bacterial characterization. NR1 was isolated and purified from mangrove sediments. Whole-genome sequencing indicated that the NR1 isolate was closely related to Bacillus cereus. The genome contained 5,305 functional genes with a total length of 5,420,664 bp, a GC content of 35.62%, 42 rRNA, and 107 tRNA. DBT-grown cultures exhibited DBT utilization, fleeting emergence of DBT sulfone (DBTO2), and formation of 2-hydroxybiphenyl (2-HBP). Molecular analysis of the PCR products’ dsz operon revealed the presence of dszA, dszB, and dszC genes, which encoded for NR1’s 90% DBT desulfurization activity. Furthermore, 17 sulfur metabolism-related genes, including genes involved in assimilation sulfate reduction, APS and PAPS, and the cys, ssu, and TST gene families, were identified. In sulfate media, alkenesulfonate was converted to sulfite and inhibited ssu enzymes. Downregulated cysK variants were associated with nrnA expression and the regulation of L-cysteine synthesis. These findings established a scientific foundation for further research and application of bacteria to mangrove rehabilitation and ecological treatment by evaluating the bacterial characterization and sulfur degradation metabolic pathway. We used whole-genome and transcriptome sequencing to examine their genetic characteristics.

MicroRNA Mediated Plant Responses to Nutrient Stress

To complete their life cycles, plants require several minerals that are found in soil. Plant growth and development can be affected by nutrient shortages or high nutrient availability. Several adaptations and evolutionary changes have enabled plants to cope with inappropriate growth conditions and low or high nutrient levels. MicroRNAs (miRNAs) have been recognized for transcript cleavage and translational reduction, and can be used for post-transcriptional regulation. Aside from regulating plant growth and development, miRNAs play a crucial role in regulating plant’s adaptations to adverse environmental conditions. Additionally, miRNAs are involved in plants’ sensory functions, nutrient uptake, long-distance root transport, and physiological functions related to nutrients. It may be possible to develop crops that can be cultivated in soils that are either deficient in nutrients or have extreme nutrient supplies by understanding how plant miRNAs are associated with nutrient stress. In this review, an overview is presented regarding recent advances in the understanding of plants’ responses to nitrogen, phosphorus, potassium, sulfur, copper, iron, boron, magnesium, manganese, zinc, and calcium deficiencies via miRNA regulation. We conclude with future research directions emphasizing the modification of crops for improving future food security.

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.

Foliar element distributions in Guadua bamboo, a major forest dominant in southwestern Amazonia

Silica is the best-known component filling the spaces that form phytoliths in many plants, but phytoliths may also contain other elements. We used scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM–EDX) to map element distributions in the leaves of Guadua bamboo, which is a successful competitor in southwestern Amazonian forests. We emphasize immobile elements that can be mineralized (silicon and calcium) as well as potassium, an abundant mobile nutrient with many vital functions. We discovered high silicon (Si) content with little or no calcium (Ca) or potassium (K) in bulliform cells, bilobate shaped short cells and stomata, all of which can form phytoliths, and moderately high Si content in the bundle sheet, prickle tips and papillae. K often surrounded Si-loaded cells, Si and K had overlapping distributions in the intercostal areas near vein margins, and Ca showed abundant spotted distribution in the intercostal areas. The dark inside content of the costal zones of some samples in light microscopy showed no mineralization but prominently contained sulfur. Adjacent fusoid cells showed different Si, K and Ca combinations, which may suggest potentially variable functions of these cells. Widespread Si deposition strengthens Guadua bamboo leaves and may help it to outcompete tree species during periods of drought.

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.

Changes in ATP Sulfurylase Activity in Response to Altered Cyanobacteria Growth Conditions

We investigated variations in cell growth and ATP Sulfurylase (ATPS) activity when two cyanobacterial strains-Synechocystis sp. PCC6803 and Synechococcus sp. WH7803-were grown in conventional media, and media with low ammonium, low sulfate and a high CO₂/low O₂ atmosphere. In both organisms, a transition and adaptation to the reconstructed environmental media resulted in a decrease in ATPS activity. This variation appears to be decoupled from growth rate, suggesting the enzyme is not rate-limiting in S assimilation and raising questions about the role of ATPS redox regulation in cell physiology and throughout Earth history.

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.

Interaction Between Macro- and Micro-Nutrients in Plants

Nitrogen (N), phosphorus (P), sulfur (S), zinc (Zn), and iron (Fe) are some of the vital nutrients required for optimum growth, development, and productivity of plants. The deficiency of any of these nutrients may lead to defects in plant growth and decreased productivity. Plant responses to the deficiency of N, P, S, Fe, or Zn have been studied mainly as a separate event, and only a few reports discuss the molecular basis of biological interaction among the nutrients. Macro-nutrients like N, P, and/or S not only show the interacting pathways for each other but also affect micro-nutrient pathways. Limited reports are available on the investigation of two-by-two or multi-level nutrient interactions in plants. Such studies on the nutrient interaction pathways suggest that an MYB-like transcription factor, phosphate starvation response 1 (PHR1), acts as a master regulator of N, P, S, Fe, and Zn homeostasis. Similarly, light-responsive transcription factors were identified to be involved in modulating nutrient responses in Arabidopsis. This review focuses on the recent advances in our understanding of how plants coordinate the acquisition, transport, signaling, and interacting pathways for N, P, S, Fe, and Zn nutrition at the molecular level. Identification of the important candidate genes for interactions between N, P, S, Fe, and/or Zn metabolic pathways might be useful for the breeders to improve nutrient use efficiency and yield/quality of crop plants. Integrated studies on pathways interactions/cross-talks between macro- and micro-nutrients in the agronomically important crop plants would be essential for sustainable agriculture around the globe, particularly under the changing climatic conditions.

Interaction Between Sulfur and Iron in Plants

It is well known that S interacts with some macronutrients, such as N, P, and K, as well as with some micronutrients, such as Fe, Mo, Cu, Zn, and B. From our current understanding, such interactions could be related to the fact that: (i) S shares similar chemical properties with other elements (e.g., Mo and Se) determining competition for the acquisition/transport process (SULTR transporter family proteins); (ii) S-requiring metabolic processes need the presence of other nutrients or regulate plant responses to other nutritional deficiencies (S-containing metabolites are the precursor for the synthesis of ethylene and phytosiderophores); (iii) S directly interacts with other elements (e.g., Fe) by forming complexes and chemical bonds, such as Fe-S clusters; and (iv) S is a constituent of organic molecules, which play crucial roles in plants (glutathione, transporters, etc.). This review summarizes the current state of knowledge of the interplay between Fe and S in plants. It has been demonstrated that plant capability to take up and accumulate Fe strongly depends on S availability in the growth medium in both monocots and dicot plants. Moreover, providing S above the average nutritional need enhances the Fe content in wheat grains, this beneficial effect being particularly pronounced under severe Fe limitation. On the other hand, Fe shortage induces a significant increase in the demand for S, resulting in enhanced S uptake and assimilation rate, similar to what happens under S deficiency. The critical evaluation of the recent studies on the modulation of Fe/S interaction by integrating old and new insights gained on this topic will help to identify the main knowledge gaps. Indeed, it remains a challenge to determine how the interplay between S and Fe is regulated and how plants are able to sense environmental nutrient fluctuations and then to adapt their uptake, translocation, assimilation, and signaling. A better knowledge of the mechanisms of Fe/S interaction might considerably help in improving crop performance within a context of limited nutrient resources and a more sustainable agriculture.

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.

Appraisal of H2S metabolism in Arabidopsis thaliana: In silico analysis at the subcellular level

Hydrogen sulfide (H₂S) has become a new signal molecule in higher plants which seems to be involved in almost all physiological processes from seed germination, root and plant growth until flowering and fruit ripening. Moreover, H₂S also participates in the mechanism of response against adverse environmental stresses. However, its basic biochemistry in plant cells can be considered in a nascent stage. Using the available information of the model plant Arabidopsis thaliana, the goal of the present study is to provide a broad overview of H₂S metabolism and to display an in silico analysis of the 26 enzymatic components involved in the metabolism of H₂S and their subcellular compartmentation (cytosol, chloroplast and mitochondrion) thus providing a wide picture of the cross-talk inside the organelles and amongst them and, consequently, to get a better understanding of the cellular and tissue implications of H₂S. This information will be also relevant for other crop species, especially those whose whole genome is not yet available.

Impairment of MET transcriptional activators, MET4 and MET31 induced lipid accumulation in Saccharomyces cerevisiae

The genes involved in the methionine pathway are closely associated with phospholipid homeostasis in yeast. The impact of the deletion of methionine (MET) transcriptional activators (MET31, MET32 and MET4) in lipid homeostasis is studied. Our lipid profiling data showed that aberrant phospholipid and neutral lipid accumulation occurred in met31∆ and met4∆ strains with low Met. The expression pattern of phospholipid biosynthetic genes such as CHO2, OPI3 and triacylglycerol (TAG) biosynthetic gene, DGA1 were upregulated in met31∆, and met4∆ strains when compared to wild type (WT). The accumulation of triacylglycerol and sterol esters (SE) content supports the concomitant increase in lipid droplets in met31∆ and met4∆ strains. However, excessive supplies of methionine (1 mM) in the cells lacking the MET transcriptional activators MET31 and MET4 ameliorates the abnormal lipogenesis and causes aberrant lipid accumulation. These findings implicate the methionine accessibility plays a pivotal role in lipid metabolism in the yeast model.

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.

MAPPS: A Web-Based Tool for Metabolic Pathway Prediction and Network Analysis in the Postgenomic Era

Comparative and evolutionary analyses of metabolic networks have a wide range of applications, ranging from research into metabolic evolution through to practical applications in drug development, synthetic biology, and biodegradation. We present MAPPS: Metabolic network Analysis and Pathway Prediction Server (https://mapps.lums.edu.pk), a web-based tool to study functions and evolution of metabolic networks using traditional and 'omics data sets. MAPPS provides diverse functionalities including an interactive interface, graphical visualization of results, pathway prediction and network comparison, identification of potential drug targets, in silico metabolic engineering, host-microbe interactions, and ancestral network building. Importantly, MAPPS also allows users to upload custom data, thus enabling metabolic analyses on draft and custom genomes, and has an 'omics pipeline to filter pathway results, making it relevant in today's postgenomic era.

Inorganic Nitrogen Form Determines Nutrient Allocation and Metabolic Responses in Maritime Pine Seedlings

Nitrate and ammonium are the main forms of inorganic nitrogen available to plants. The present study aimed to investigate the metabolic changes caused by ammonium and nitrate nutrition in maritime pine (Pinus pinaster Ait.). Seedlings were grown with five solutions containing different proportions of nitrate and ammonium. Their nitrogen status was characterized through analyses of their biomass, different biochemical and molecular markers as well as a metabolite profile using ¹H-NMR. Ammonium-fed seedlings exhibited higher biomass than nitrate-fed-seedlings. Nitrate mainly accumulated in the stem and ammonium in the roots. Needles of ammonium-fed seedlings had higher nitrogen and amino acid contents but lower levels of enzyme activities related to nitrogen metabolism. Higher amounts of soluble sugars and L-arginine were found in the roots of ammonium-fed seedlings. In contrast, L-asparagine accumulated in the roots of nitrate-fed seedlings. The differences in the allocation of nitrate and ammonium may function as metabolic buffers to prevent interference with the metabolism of photosynthetic organs. The metabolite profiles observed in the roots suggest problems with carbon and nitrogen assimilation in nitrate-supplied seedlings. Taken together, this new knowledge contributes not only to a better understanding of nitrogen metabolism but also to improving aspects of applied mineral nutrition for conifers.

Transcriptome analysis reveals insight into molecular hydrogen-induced cadmium tolerance in alfalfa: the prominent role of sulfur and (homo)glutathione metabolism

BACKGROUND

Hydrogen gas (H2) is hypothesised to play a role in plants that are coping with stresses by regulating signal transduction and gene expression. Although the beneficial role of H2 in plant tolerance to cadmium (Cd) has been investigated previously, the corresponding mechanism has not been elucidated. In this report, the transcriptomes of alfalfa seedling roots under Cd and/or hydrogen-rich water (HRW) treatment were first analysed. Then, the sulfur metabolism pathways were focused on and further investigated by pharmacological and genetic approaches.

RESULTS

A total of 1968 differentially expressed genes (DEGs) in alfalfa seedling roots under Cd and/or HRW treatment were identified by RNA-Seq. The DEGs were classified into many clusters, including glutathione (GSH) metabolism, oxidative stress, and ATP-binding cassette (ABC) transporters. The results validated by RT-qPCR showed that the levels of relevant genes involved in sulfur metabolism were enhanced by HRW under Cd treatment, especially the genes involved in (homo)glutathione metabolism. Additional experiments carried out with a glutathione synthesis inhibitor and Arabidopsis thaliana cad2-1 mutant plants suggested the prominent role of glutathione in HRW-induced Cd tolerance. These results were in accordance with the effects of HRW on the contents of (homo)glutathione and (homo)phytochelatins and in alleviating oxidative stress under Cd stress. In addition, the HRW-induced alleviation of Cd toxicity might also be caused by a decrease in available Cd in seedling roots, achieved through ABC transporter-mediated secretion.

CONCLUSIONS

Taken together, the results of our study indicate that H2 regulated the expression of genes relevant to sulfur and glutathione metabolism and enhanced glutathione metabolism which resulted in Cd tolerance by activating antioxidation and Cd chelation. These results may help to elucidate the mechanism governing H2-induced Cd tolerance in alfalfa.

Lack of FIBRILLIN6 in Arabidopsis thaliana affects light acclimation and sulfate metabolism

Arabidopsis thaliana contains 13 fibrillins (FBNs), which are all localized to chloroplasts. FBN1 and FBN2 are involved in photoprotection of photosystem II, and FBN4 and FBN5 are thought to be involved in plastoquinone transport and biosynthesis, respectively. The functions of the other FBNs remain largely unknown. To gain insight into the function of FBN6, we performed coexpression and Western analyses, conducted fluorescence and transmission electron microscopy, stained reactive oxygen species (ROS), measured photosynthetic parameters and glutathione levels, and applied transcriptomics and metabolomics. Using coexpression analyses, FBN6 was identified as a photosynthesis-associated gene. FBN6 is localized to thylakoid and envelope membranes, and its knockout results in stunted plants. The delayed-growth phenotype cannot be attributed to altered basic photosynthesis parameters or a reduced CO₂ assimilation rate. Under moderate light stress, primary leaves of fbn6 plants begin to bleach and contain enlarged plastoglobules. RNA sequencing and metabolomics analyses point to an alteration in sulfate reduction in fbn6. Indeed, glutathione content is higher in fbn6, which in turn confers cadmium tolerance of fbn6 seedlings. We conclude that loss of FBN6 leads to perturbation of ROS homeostasis. FBN6 enables plants to cope with moderate light stress and affects cadmium tolerance.

An Alkane Sulfonate Monooxygenase Is Required for Symbiotic Nitrogen Fixation by Bradyrhizobium diazoefficiens (syn. Bradyrhizobium japonicum) USDA110T

Sulfur (S)-containing molecules play an important role in symbiotic nitrogen fixation and are critical components of nitrogenase and other iron-S proteins. S deficiency inhibits symbiotic nitrogen fixation by rhizobia. However, despite its importance, little is known about the sources of S that rhizobia utilize during symbiosis. We previously showed that Bradyrhizobium diazoefficiens USDA110T can assimilate both inorganic and organic S and that genes involved in organic S utilization are expressed during symbiosis. Here, we show that a B. diazoefficiens USDA110T mutant with a sulfonate monooxygenase (ssuD) insertion is defective in nitrogen fixation. Microscopy analyses revealed that the ΔssuD mutant was defective in root hair infection and that ΔssuD mutant bacteroids showed degradation compared to the wild-type strain. Moreover, the ΔssuD mutant was significantly more sensitive to hydrogen peroxide-mediated oxidative stress than the wild-type strain. Taken together, these results show that the ability of rhizobia to utilize organic S plays an important role in symbiotic nitrogen fixation. Since nodules have been reported to be an important source of reduced S used during symbiosis and nitrogen fixation, further research will be needed to determine the mechanisms involved in the regulation of S assimilation by rhizobia.IMPORTANCE Rhizobia form symbiotic associations with legumes that lead to the formation of nitrogen-fixing nodules. Sulfur-containing molecules play a crucial role in nitrogen fixation; thus, the rhizobia inside nodules require large amounts of sulfur. Rhizobia can assimilate both inorganic (sulfate) and organic (sulfonates) sources of sulfur. However, very little is known about rhizobial sulfur metabolism during symbiosis. In this report, we show that sulfonate utilization by Bradyrhizobium diazoefficiens is important for symbiotic nitrogen fixation in both soybean and cowpea. The symbiotic defect is probably due to increased sensitivity to oxidative stress from sulfur deficiency in the mutant strain defective for sulfonate utilization. The results of this study can be extended to other rhizobium-legume symbioses, as sulfonate utilization genes are widespread in these bacteria.

The relationship between sulfur metabolism and tolerance of hexavalent chromium in Scenedesmus acutus (Spheropleales): Role of ATP sulfurylase

Sulfur availability and the end products of its metabolism, cysteine, glutathione and phytochelatins, play an important role in heavy metal tolerance, chromium included. Sulfate and chromate not only compete for the transporters but also for assimilation enzymes and chromium tolerance in various organisms has been associated to differences in this pathway. We investigated the mechanisms of Cr(VI)-tolerance increase induced by S-starvation focusing on the role of ATP sulfurylase (ATS) in two strains of Scenedesmus acutus with different chromium sensitivity. S-starvation enhances the defence potential by increasing sulfate uptake/assimilation and decreasing chromium uptake, thus suggesting a change in the transport system. We isolated two isoforms of the enzyme, SaATS1 and SaATS2, with different sensitivity to sulfur availability, and analysed them in S-sufficient and S-replete condition both in standard and in chromium supplemented medium. SaATS2 expression is different in the two strains and presumably marks a different sulfur perception/exploitation in the Cr-tolerant. Its induction and silencing are compatible with a role in the transient tolerance increase induced by S-starvation. This enzyme can however hardly be responsible for the large cysteine production of the Cr-tolerant strain after starvation, suggesting that cytosolic rather than chloroplastic cysteine production is differently regulated in the two strains.

Remobilization and fate of sulphur in mustard

BACKGROUND AND AIMS

Sulphur (S) is an essential macronutrient involved in numerous metabolic pathways required for plant growth. Crops of the plant family Brassicaceae require more S compared with other crops for optimum growth and yield, with most S ultimately sequestered in the mature seeds as the storage proteins cruciferin and napin, along with the unique S-rich secondary metabolite glucosinolate (GSL). It is well established that S assimilation primarily takes place in the shoots rather than roots, and that sulphate is the major form in which S is transported and stored in plants. We carried out a developmental S audit to establish the net fluxes of S in two lines of Brassica juncea mustard where seed GSL content differed but resulted in no yield penalty.

METHODS

We quantified S pools (sulphate, GSL and total S) in different organs at multiple growth stages until maturity, which also allowed us to test the hypothesis that leaf S, accumulated as a primary S sink, becomes remobilized as a secondary source to meet the requirements of GSL as the dominant seed S sink.

KEY RESULTS

Maximum plant sulphate accumulation had occurred by floral initiation in both lines, at which time most of the sulphate was found in the leaves, confirming its role as the primary S sink. Up to 52 % of total sulphate accumulated by the low-GSL plants was lost through senesced leaves. In contrast, S from senescing leaves of the high-GSL line was remobilized to other tissues, with GSL accumulating in the seed from commencement of silique filling until maturity.

CONCLUSION

We have established that leaf S compounds that accumulated as primary S sinks at early developmental stages in condiment type B. juncea become remobilized as a secondary S source to meet the demand for GSL as the dominant seed S sink at maturity.

Sulphur systems biology-making sense of omics data

Systems biology approaches have been applied over the last two decades to study plant sulphur metabolism. These 'sulphur-omics' approaches have been developed in parallel with the advancing field of systems biology, which is characterized by permanent improvements of high-throughput methods to obtain system-wide data. The aim is to obtain a holistic view of sulphur metabolism and to generate models that allow predictions of metabolic and physiological responses. Besides known sulphur-responsive genes derived from previous studies, numerous genes have been identified in transcriptomics studies. This has not only increased our knowledge of sulphur metabolism but has also revealed links between metabolic processes, thus indicating a previously unexpected complex interconnectivity. The identification of response and control networks has been supported through metabolomics and proteomics studies. Due to the complex interlacing nature of biological processes, experimental validation using targeted or systems approaches is ongoing. There is still room for improvement in integrating the findings from studies of metabolomes, proteomes, and metabolic fluxes into a single unifying concept and to generate consistent models. We therefore suggest a joint effort of the sulphur research community to standardize data acquisition. Furthermore, focusing on a few different model plant systems would help overcome the problem of fragmented data, and would allow us to provide a standard data set against which future experiments can be designed and compared.

Signaling by hydrogen sulfide and cyanide through post-translational modification

Two cysteine metabolism-related molecules, hydrogen sulfide and hydrogen cyanide, which are considered toxic, have now been considered as signaling molecules. Hydrogen sulfide is produced in chloroplasts through the activity of sulfite reductase and in the cytosol and mitochondria by the action of sulfide-generating enzymes, and regulates/affects essential plant processes such as plant adaptation, development, photosynthesis, autophagy, and stomatal movement, where interplay with other signaling molecules occurs. The mechanism of action of sulfide, which modifies protein cysteine thiols to form persulfides, is related to its chemical features. This post-translational modification, called persulfidation, could play a protective role for thiols against oxidative damage. Hydrogen cyanide is produced during the biosynthesis of ethylene and camalexin in non-cyanogenic plants, and is detoxified by the action of sulfur-related enzymes. Cyanide functions include the breaking of seed dormancy, modifying the plant responses to biotic stress, and inhibition of root hair elongation. The mode of action of cyanide is under investigation, although it has recently been demonstrated to perform post-translational modification of protein cysteine thiols to form thiocyanate, a process called S-cyanylation. Therefore, the signaling roles of sulfide and most probably of cyanide are performed through the modification of specific cysteine residues, altering protein functions.

Characterization of Entamoeba histolytica adenosine 5'-phosphosulfate (APS) kinase; validation as a target and provision of leads for the development of new drugs against amoebiasis

Background

Amoebiasis, caused by Entamoeba histolytica infection, is a global public health problem. However, available drugs to treat amoebiasis are currently limited, and no effective vaccine exists. Therefore, development of new preventive measures against amoebiasis is urgently needed.

Methodology/Principal findings

Here, to develop new drugs against amoebiasis, we focused on E. histolytica adenosine 5′-phosphosulfate kinase (EhAPSK), an essential enzyme in Entamoeba sulfolipid metabolism. Fatty alcohol disulfates and cholesteryl sulfate, sulfolipids synthesized in Entamoeba, play important roles in trophozoite proliferation and cyst formation. These processes are closely associated with clinical manifestation and severe pathogenesis of amoebiasis and with disease transmission, respectively. We validated a combination approach of in silico molecular docking analysis and an in vitro enzyme activity assay for large scale screening. Docking simulation ranked the binding free energy between a homology modeling structure of EhAPSK and 400 compounds. The 400 compounds were also screened by a 96-well plate-based in vitro APSK activity assay. Among fifteen compounds identified as EhAPSK inhibitors by the in vitro system, six were ranked by the in silico analysis as having high affinity toward EhAPSK. Furthermore, 2-(3-fluorophenoxy)-N-[4-(2-pyridyl)thiazol-2-yl]-acetamide, 3-phenyl-N-[4-(2-pyridyl)thiazol-2-yl]-imidazole-4-carboxamide, and auranofin, which were identified as EhAPSK inhibitors by both in silico and in vitro analyses, halted not only Entamoeba trophozoite proliferation but also cyst formation. These three compounds also dose-dependently impaired the synthesis of sulfolipids in E. histolytica.

Conclusions/Significance

Hence, the combined approach of in silico and in vitro-based EhAPSK analyses identified compounds that can be evaluated for their effects on Entamoeba. This can provide leads for the development of new anti-amoebic and amoebiasis transmission-blocking drugs. This strategy can also be applied to identify specific APSK inhibitors, which will benefit research into sulfur metabolism and the ubiquitous pathway terminally synthesizing essential sulfur-containing biomolecules.

Amoebiasis is a parasitic disease caused by Entamoeba histolytica that is an important health problem worldwide because of high morbidity and mortality rates. However, clinical options are inadequate; therefore, developing new preventive measures, such as anti-amoebic drugs, is urgently needed. In general, for the development of new drugs, the identification of appropriate leads and targets is a prerequisite. Here, to develop new drugs against amoebiasis, we focused on E. histolytica adenosine 5′-phosphosulfate kinase (EhAPSK), an essential enzyme in sulfur metabolism. An EhAPSK-based combination approach of computer-based in silico and laboratory-based in vitro analyses enabled us to screen 400 chemicals, from which we identified 15 that inhibit EhAPSK activity. Furthermore, among them, three compounds halted biological processes in Entamoeba that are closely associated with the clinical manifestation and pathogenesis of amoebiasis and with disease transmission. Hence, this study provides leads as well as a target for the development of new drugs against amoebiasis. This study also provides a basis to identify inhibitors for use in the study of sulfur metabolism, an important topic in general biochemistry and physiology.

Integration of sulfate assimilation with carbon and nitrogen metabolism in transition from C3 to C4 photosynthesis

The first product of sulfate assimilation in plants, cysteine, is a proteinogenic amino acid and a source of reduced sulfur for plant metabolism. Cysteine synthesis is the convergence point of the three major pathways of primary metabolism: carbon, nitrate, and sulfate assimilation. Despite the importance of metabolic and genetic coordination of these three pathways for nutrient balance in plants, the molecular mechanisms underlying this coordination, and the sensors and signals, are far from being understood. This is even more apparent in C4 plants, where coordination of these pathways for cysteine synthesis includes the additional challenge of differential spatial localization. Here we review the coordination of sulfate, nitrate, and carbon assimilation, and show how they are altered in C4 plants. We then summarize current knowledge of the mechanisms of coordination of these pathways. Finally, we identify urgent questions to be addressed in order to understand the integration of sulfate assimilation with carbon and nitrogen metabolism particularly in C4 plants. We consider answering these questions to be a prerequisite for successful engineering of C4 photosynthesis into C3 crops to increase their efficiency.

Transcriptional Reprogramming of Pea Leaves at Early Reproductive Stages

Pea (Pisum sativum L.) is an important source of dietary proteins. Nutrient recycling from leaves contributes to the accumulation of seed proteins and is a pivotal determinant of protein yields in this grain legume. The aim of this study was to unveil the transcriptional regulations occurring in pea leaves before the sharp decrease in chlorophyll breakdown. As a prelude to this study, a time-series analysis of ¹⁵N translocation at the whole plant level was performed, which indicated that nitrogen recycling among organs was highly dynamic during this period and varied depending on nitrate availability. Leaves collected on vegetative and reproductive nodes were further analyzed by transcriptomics. The data revealed extensive transcriptome changes in leaves of reproductive nodes during early seed development (from flowering to 14 days after flowering), including an up-regulation of genes encoding transporters, and particularly of sulfate that might sustain sulfur metabolism in leaves of the reproductive part. This developmental period was also characterized by a down-regulation of cell wall-associated genes in leaves of both reproductive and vegetative nodes, reflecting a shift in cell wall structure. Later on, 27 days after flowering, genes potentially switching the metabolism of leaves toward senescence were pinpointed, some of which are related to ribosomal RNA processing, autophagy, or transport systems. Transcription factors differentially regulated in leaves between stages were identified and a gene co-expression network pointed out some of them as potential regulators of the above-mentioned biological processes. The same approach was conducted in Medicago truncatula to identify shared regulations with this wild legume species. Altogether the results give a global view of transcriptional events in leaves of legumes at early reproductive stages and provide a valuable resource of candidate genes that could be targeted by reverse genetics to improve nutrient remobilization and/or delay catabolic processes leading to senescence.

Sulfation pathways from red to green

Sulfur is present in the amino acids cysteine and methionine and in a large range of essential coenzymes and cofactors and is therefore essential for all organisms. It is also a constituent of sulfate esters in proteins, carbohydrates, and numerous cellular metabolites. The sulfation and desulfation reactions modifying a variety of different substrates are commonly known as sulfation pathways. Although relatively little is known about the function of most sulfated metabolites, the synthesis of activated sulfate used in sulfation pathways is essential in both animal and plant kingdoms. In humans, mutations in the genes encoding the sulfation pathway enzymes underlie a number of developmental aberrations, and in flies and worms, their loss-of-function is fatal. In plants, a lower capacity for synthesizing activated sulfate for sulfation reactions results in dwarfism, and a complete loss of activated sulfate synthesis is also lethal. Here, we review the similarities and differences in sulfation pathways and associated processes in animals and plants, and we point out how they diverge from bacteria and yeast. We highlight the open questions concerning localization, regulation, and importance of sulfation pathways in both kingdoms and the ways in which findings from these "red" and "green" experimental systems may help reciprocally address questions specific to each of the systems.

Knock-Down of the Phosphoserine Phosphatase Gene Effects Rather N- Than S-Metabolism in Arabidopsis thaliana

The aim of present study was to elucidate the significance of the phosphorylated pathway of Ser production for Cys biosynthesis in leaves at day and night and upon cadmium (Cd) exposure. For this purpose, Arabidopsis wildtype plants as control and its psp mutant knocked-down in phosphoserine phosphatase (PSP) were used to test if (i) photorespiratory Ser is the dominant precursor of Cys synthesis in autotrophic tissue in the light, (ii) the phosphorylated pathway of Ser production can take over Ser biosynthesis in leaves at night, and (iii) Cd exposure stimulates Cys and glutathione (GSH) biosynthesis and effects the crosstalk of S and N metabolism, irrespective of the Ser source. Glycine (Gly) and Ser contents were not affected by reduction of the psp transcript level confirming that the photorespiratory pathway is the main route of Ser synthesis. The reduction of the PSP transcript level in the mutant did not affect day/night regulation of sulfur fluxes while day/night fluctuation of sulfur metabolite amounts were no longer observed, presumably due to slower turnover of sulfur metabolites in the mutant. Enhanced contents of non-protein thiols in both genotypes and of GSH only in the psp mutant were observed upon Cd treatment. Mutation of the phosphorylated pathway of Ser biosynthesis caused an accumulation of alanine, aspartate, lysine and a decrease of branched-chain amino acids. Knock-down of the PSP gene induced additional defense mechanisms against Cd toxicity that differ from those of WT plants.

The Photorespiratory BOU Gene Mutation Alters Sulfur Assimilation and Its Crosstalk With Carbon and Nitrogen Metabolism in Arabidopsis thaliana

This study was aimed at elucidating the significance of photorespiratory serine (Ser) production for cysteine (Cys) biosynthesis. For this purpose, sulfur (S) metabolism and its crosstalk with nitrogen (N) and carbon (C) metabolism were analyzed in wildtype Arabidopsis and its photorespiratory bou-2 mutant with impaired glycine decarboxylase (GDC) activity. Foliar glycine and Ser contents were enhanced in the mutant at day and night. The high Ser levels in the mutant cannot be explained by transcript abundances of genes of the photorespiratory pathway or two alternative pathways of Ser biosynthesis. Despite enhanced foliar Ser, reduced GDC activity mediated a decline in sulfur flux into major sulfur pools in the mutant, as a result of deregulation of genes of sulfur reduction and assimilation. Still, foliar Cys and glutathione contents in the mutant were enhanced. The use of Cys for methionine and glucosinolates synthesis was reduced in the mutant. Reduced GDC activity in the mutant downregulated Calvin Cycle and nitrogen assimilation genes, upregulated key enzymes of glycolysis and the tricarboxylic acid (TCA) pathway and modified accumulation of sugars and TCA intermediates. Thus, photorespiratory Ser production can be replaced by other metabolic Ser sources, but this replacement deregulates the cross-talk between S, N, and C metabolism.

A Program for Iron Economy during Deficiency Targets Specific Fe Proteins

Iron (Fe) is an essential element for plants, utilized in nearly every cellular process. Because the adjustment of uptake under Fe limitation cannot satisfy all demands, plants need to acclimate their physiology and biochemistry, especially in their chloroplasts, which have a high demand for Fe. To investigate if a program exists for the utilization of Fe under deficiency, we analyzed how hydroponically grown Arabidopsis (Arabidopsis thaliana) adjusts its physiology and Fe protein composition in vegetative photosynthetic tissue during Fe deficiency. Fe deficiency first affected photosynthetic electron transport with concomitant reductions in carbon assimilation and biomass production when effects on respiration were not yet significant. Photosynthetic electron transport function and protein levels of Fe-dependent enzymes were fully recovered upon Fe resupply, indicating that the Fe depletion stress did not cause irreversible secondary damage. At the protein level, ferredoxin, the cytochrome-b₆f complex, and Fe-containing enzymes of the plastid sulfur assimilation pathway were major targets of Fe deficiency, whereas other Fe-dependent functions were relatively less affected. In coordination, SufA and SufB, two proteins of the plastid Fe-sulfur cofactor assembly pathway, were also diminished early by Fe depletion. Iron depletion reduced mRNA levels for the majority of the affected proteins, indicating that loss of enzyme was not just due to lack of Fe cofactors. SufB and ferredoxin were early targets of transcript down-regulation. The data reveal a hierarchy for Fe utilization in photosynthetic tissue and indicate that a program is in place to acclimate to impending Fe deficiency.

Integrative Transcriptomic Analysis Uncovers Novel Gene Modules That Underlie the Sulfate Response in Arabidopsis thaliana

Sulfur is an essential nutrient for plant growth and development. Sulfur is a constituent of proteins, the plasma membrane and cell walls, among other important cellular components. To obtain new insights into the gene regulatory networks underlying the sulfate response, we performed an integrative meta-analysis of transcriptomic data from five different sulfate experiments available in public databases. This bioinformatic approach allowed us to identify a robust set of genes whose expression depends only on sulfate availability, indicating that those genes play an important role in the sulfate response. In relation to sulfate metabolism, the biological function of approximately 45% of these genes is currently unknown. Moreover, we found several consistent Gene Ontology terms related to biological processes that have not been extensively studied in the context of the sulfate response; these processes include cell wall organization, carbohydrate metabolism, nitrogen compound transport, and the regulation of proteolysis. Gene co-expression network analyses revealed relationships between the sulfate-responsive genes that were distributed among seven function-specific co-expression modules. The most connected genes in the sulfate co-expression network belong to a module related to the carbon response, suggesting that this biological function plays an important role in the control of the sulfate response. Temporal analyses of the network suggest that sulfate starvation generates a biphasic response, which involves that major changes in gene expression occur during both the early and late responses. Network analyses predicted that the sulfate response is regulated by a limited number of transcription factors, including MYBs, bZIPs, and NF-YAs. In conclusion, our analysis identified new candidate genes and provided new hypotheses to advance our understanding of the transcriptional regulation of sulfate metabolism in plants.

A Program for Iron Economy during Deficiency Targets Specific Fe Proteins

Iron (Fe) is an essential element for plants, utilized in nearly every cellular process. Because the adjustment of uptake under Fe limitation cannot satisfy all demands, plants need to acclimate their physiology and biochemistry, especially in their chloroplasts, which have a high demand for Fe. To investigate if a program exists for the utilization of Fe under deficiency, we analyzed how hydroponically grown Arabidopsis (Arabidopsis thaliana) adjusts its physiology and Fe protein composition in vegetative photosynthetic tissue during Fe deficiency. Fe deficiency first affected photosynthetic electron transport with concomitant reductions in carbon assimilation and biomass production when effects on respiration were not yet significant. Photosynthetic electron transport function and protein levels of Fe-dependent enzymes were fully recovered upon Fe resupply, indicating that the Fe depletion stress did not cause irreversible secondary damage. At the protein level, ferredoxin, the cytochrome-b₆f complex, and Fe-containing enzymes of the plastid sulfur assimilation pathway were major targets of Fe deficiency, whereas other Fe-dependent functions were relatively less affected. In coordination, SufA and SufB, two proteins of the plastid Fe-sulfur cofactor assembly pathway, were also diminished early by Fe depletion. Iron depletion reduced mRNA levels for the majority of the affected proteins, indicating that loss of enzyme was not just due to lack of Fe cofactors. SufB and ferredoxin were early targets of transcript down-regulation. The data reveal a hierarchy for Fe utilization in photosynthetic tissue and indicate that a program is in place to acclimate to impending Fe deficiency.

Uniqueness of Entamoeba sulfur metabolism: sulfolipid metabolism that plays pleiotropic roles in the parasitic life cycle

Sulfur metabolism is ubiquitous and terminally synthesizes various biomolecules that are crucial for organisms, such as sulfur-containing amino acids and co-factors, sulfolipids and sulfated saccharides. Entamoeba histolytica, a protozoan parasite responsible for amoebiasis, possesses the unique sulfur metabolism features of atypical localization and its terminal product being limited to sulfolipids. Here, we present an overall scheme of E. histolytica sulfur metabolism by relating all sulfotransferases and sulfatases to their substrates and products. Furthermore, a novel sulfur metabolite, fatty alcohol disulfates, was identified and shown to play an important role in trophozoite proliferation. Cholesteryl sulfate, another synthesized sulfolipid, was previously demonstrated to play an important role in encystation, a differentiation process from proliferative trophozoite to dormant cyst. Entamoeba survives by alternating between these two distinct forms; therefore, Entamoeba sulfur metabolism contributes to the parasitic life cycle via its terminal products. Interestingly, this unique feature of sulfur metabolism is not conserved in the nonparasitic close relative of Entamoeba, Mastigamoeba, because lateral gene transfer-mediated acquisition of sulfatases and sulfotransferases, critical enzymes conferring this feature, has only occurred in the Entamoeba lineage. Hence, our findings suggest that sulfolipid metabolism has a causal relationship with parasitism.

The Sulfate Supply Maximizing Arabidopsis Shoot Growth Is Higher under Long- than Short-Term Exposure to Cadmium

The processes involved in cadmium detoxification in plants deeply affect sulfate uptake and thiol homeostasis and generate increases in the plant nutritional request for sulfur. Here, we present an analysis of the dependence of Arabidopsis growth on the concentration of sulfate in the growing medium with the aim of providing evidence on how plants optimize growth at a given sulfate availability. Results revealed that short-term (72 h) exposure to a broad range of Cd concentrations (0.1, 1, and 10 μM) inhibited plant growth but did not produce any significant effects on the growth pattern of both shoots and roots in relation to the external sulfate. Conversely, long-term (22 days) exposure to 0.1 μM Cd significantly changed the pattern of fresh weight accumulation of the shoots in relation to the external sulfate, without affecting that of the roots, although their growth was severely inhibited by Cd. Moreover, under long-term exposure to Cd, increasing the sulfate external concentration up to the critical value progressively reduced the inhibitory effects exerted by Cd on shoot growth, indicating the existence of sulfate-dependent adaptive responses protecting the shoot tissues against Cd injury. Transcriptional induction of the high-affinity sulfate transporter genes (SULTR1; 1 and SULTR1; 2) involved in sulfate uptake by roots was a common adaptive response to both short- and long-term exposure to Cd. Such a response was closely related to the total amount of non-protein thiols accumulated by a single plant under short-term exposure to Cd, but did not showed any clear relation with thiols under long-term exposure to Cd. In this last condition, Cd exposure did not change the level of non-protein thiols per plant and thus did not alter the nutritional need for sulfur. In conclusion, our results indicate that long term-exposure to Cd, although it induces sulfate uptake, decreases the capacity of the Arabidopsis roots to efficiently absorb the sulfate ions available in the growing medium making the adaptive response of SULTR1; 1 and SULTR1; 2 "per se" not enough to optimize the growth at sulfate external concentrations lower than the critical value.