Genome-wide analyses of ATP sulfurylase (ATPS) genes in higher plants and expression profiles in sorghum (Sorghum bicolor) under cadmium and salinity stresses

Nitrate enhances cadmium accumulation through modulating sulfur metabolism in sweet sorghum

Sweet sorghum deploys tremendous potential for phytoremediation of cadmium (Cd)-polluted soils. Nitrate increases Cd accumulation in sweet sorghum, but the mechanism underlying this is still elusive. Sulfur-containing metabolites have been corroborated to play important roles in Cd tolerance in plants. Thus, whether sulfur metabolism contributed to nitrate-increased Cd accumulation in sweet sorghum was investigated in the present study. Two-way ANOVA analysis showed that most sulfur-containing metabolites concentrations and relevant enzymes activities were regulated by nitrate, Cd and interplay of nitrate and Cd. By using grey correlation analysis and Pearson correlation coefficient, Cd accumulation in shoots as affected by nitrate was also mainly ascribed to sulfur metabolism. ATP sulfurylase (ATPS) activities and non-protein thiol (NPT) concentrations in leaves were the two prominent factors that positively correlated with Cd accumulation in shoots. Excess nitrate elevated ATPS activities in leaves which contributed to increased NPT and phytochelatins (PCs) concentrations in leaves. Nitrate enhanced Cd accumulation in shoots of sweet sorghum under a low level of Cd treatment. Intriguingly, Cd accumulation in shoots of sweet sorghum was similar between a low level and a high level of Cd treatment. Principal Components Analysis (PCA) based on 34 parameters failed to separate the low Cd treatment from the high Cd treatment either, suggesting sweet sorghum is exclusively suitable for phytoremediation of slight Cd-polluted arable lands. Taken together, enhanced Cd accumulation in shoots of sweet sorghum by excess nitrate application is closely correlated with sulfur metabolism containing elevated ATPS activities, NPT and PCs concentrations in leaves.

Transcriptome analysis of mulberry (Morus alba L.) leaves to identify differentially expressed genes associated with post-harvest shelf-life elongation

Present study deals with molecular expression patterns responsible for post-harvest shelf-life extension of mulberry leaves. Quantitative profiling showed retention of primary metabolite and accumulation of stress markers in NS7 and CO7 respectively. The leaf mRNA profiles was sequenced using the Illumina platform to identify DEGs. A total of 3413 DEGs were identified between the treatments. Annotation with Arabidopsis database has identified 1022 DEGs unigenes. STRING generated protein-protein interaction, identified 1013 DEGs nodes with p < 1.0e-16. KEGG classifier has identified genes and their participating biological processes. MCODE and BiNGO detected sub-networking and ontological enrichment, respectively at p ≤ 0.05. Genes associated with chloroplast architecture, photosynthesis, detoxifying ROS and RCS, and innate-immune response were significantly up-regulated, responsible for extending shelf-life in NS7. Loss of storage sucrose, enhanced activity of senescence-related hormones, accumulation of xenobiotics, and development of osmotic stress inside tissue system was the probable reason for tissue deterioration in CO7. qPCR validation of DEGs was in good agreement with RNA sequencing results, indicating the reliability of the sequencing platform. Present outcome provides a molecular insight regarding involvement of genes in self-life extension, which might help the sericulture industry to overcome their pre-existing problems related to landless farmers and larval feeding during monsoon.

Gene Identification, expression analysis and molecular docking of ATP sulfurylase in the selenization pathway of Cardamine hupingshanensis

BACKGROUND

ATP sulfurylase (ATPS) is a crucial enzyme for the selenate assimilation pathway in plants.

RESULTS

In this study, genome-wide and comparative analyses of ATPS in Cardamine hupingshanensis, including sequence and structural analyses, were performed. The expression of ChATPS gene family members in C. hupingshanensis under selenium (Se) stress was also investigated, and our results suggest that ChATPS1-2 play key roles in the response to Se stress. Nine ATPS genes were found from C. hupingshanensis, which share highly conserved sequences with ATPS from Arabidopsis thaliana. In addition, we performed molecular docking of ATP sulfurylase in complex with compounds ATP, selenate, selenite, sulfate, and sulfite. ChAPS3-1 was found to have stronger binding energies with all compounds tested. Among these complexes, amino acid residues Arg, Gly, Ser, Glu, and Asn were commonly present.

CONCLUSION

Our study reveals the molecular mechanism of C. hupingshanensis ATP sulfurylase interacting with selenate, which is essential for understanding selenium assimilation. This information will guide further studies on the function of the ChATPS gene family in the selenium stress response and lay the foundation for the selenium metabolic pathway in higher plants.

State-of-the-art OMICS strategies against toxic effects of heavy metals in plants: A review

Environmental pollution of heavy metals (HMs), mainly due to anthropogenic activities, has received growing attention in recent decades. HMs, especially the non-essential carcinogenic ones, including chromium (Cr), cadmium (Cd), mercury (Hg), aluminum (Al), lead (Pb), and arsenic (As), have appeared as the most significant air, water, and soil pollutants, which adversely affect the quantity, quality, and security of plant-based food all over the world. Plants exposed to HMs could experience significant decline in growth and yield. To avoid or tolerate the toxic effects of HMs, plants have developed complicated defense mechanisms, including absorption and accumulation of HMs in cell organelles, immobilization by forming complexes with organic chelates, extraction by using numerous transporters, ion channels, signalling cascades, and transcription elements, among others. OMICS strategies have developed significantly to understand the mechanisms of plant transcriptomics, genomics, proteomics, metabolomics, and ionomics to counter HM-mediated stress stimuli. These strategies have been considered to be reliable and feasible for investigating the roles of genomics (genomes), transcriptomic (coding), mRNA transcripts (non-coding), metabolomics (metabolites), and ionomics (metal ions) to enhance stress resistance or tolerance in plants. The recent developments in the mechanistic understandings of the HMs-plant interaction in terms of their absorption, translocation, and toxicity invasions at the molecular and cellular levels, as well as plants' response and adaptation strategies against these stressors, are summarized in the present review. Transcriptomics, genomics, metabolomics, proteomics, and ionomics for plants against HMs toxicities are reviewed, while challenges and future recommendations are also discussed.

Physiological, anatomical, and transcriptional responses of mulberry (Morus alba L.) to Cd stress in contaminated soil

Mulberry has been widely studied for its capacity to tolerate heavy metals. However, the anatomical and molecular response mechanisms of Cd detoxification and transportation in mulberry have not been fully elucidated. In this study, the anatomical characteristics, Cd and mineral element uptake and transport, and transcriptome profiling of mulberry were studied under Cd stress. The results showed that mulberry possessed strong detoxification and self-protection abilities against Cd stress. The growth and photosynthetic pigment contents of mulberry were only slightly affected when the soil Cd content was less than 37.0 mg/kg, while the Ca and Mg contents in the mulberry roots were clearly (p < 0.05) increased by 37.85%-40.87% and 36.63%-53.06% in 37.0-55.4 mg/kg Cd-contaminated soil. Meanwhile, the relationships between antioxidant enzyme activities, such as peroxidase, catalase, and ascorbate peroxidase, and Cd content in plants were positive. Furthermore, the structures of leaf cells, root and stem tissues were largely intact; simultaneously, the increase in osmiophilic particles and the dissolution of starch granules in mulberry leaves significantly responded to Cd stress. Clusters of Orthologous Groups of proteins (COG) and Gene Ontology (GO) classification analysis indicated that mulberry can enhance the catalytic activity, regulate the transport and metabolism of inorganic ions, and strengthen its antioxidant enzyme activity and defense mechanism to decrease Cd intoxication. Large numbers of differentially expressed genes associated with cell wall biosynthesis, antioxidant enzyme activities, glutathione metabolism, chelation, plant hormone signal transduction, and the mitogen-activated protein kinase (MAPK) signaling pathway were upregulated under Cd stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that plant hormone signal transduction was significantly (p < 0.05) enriched in roots, stems, and leaves of mulberry, and abscisic acid and ethylene can mediate MAPK signaling pathways to increase plant tolerance to Cd stress. The results suggested that the physiological, cellular and tissue, and transcriptional regulation of mulberry can facilitate its stress adaptation in Cd-contaminated soil.

De novo Transcriptome Assembly and Comparative Analysis Highlight the Primary Mechanism Regulating the Response to Selenium Stimuli in Oats (Avena sativa L.)

Selenium is an essential microelement for humans and animals. The specific processing technique of oats can maximize the preservation of its nutrients. In this study, to understand the genetic response of oats in a high-selenium environment, oats were treated with sodium selenate for 24 h, and transcriptome analysis was performed. A total of 211,485,930 clean reads composing 31.30 Gb of clean data were retained for four samples. After assembly, 186,035 unigenes with an average length of 727 bp were generated, and the N50 length was 1,149 bp. Compared with that in the control group, the expression of 7,226 unigenes in the treatment group was upregulated, and 2,618 unigenes were downregulated. Based on the sulfur assimilation pathway and selenocompound metabolic pathway, a total of 27 unigenes related to selenate metabolism were identified. Among them, the expression of both key genes APS (ATP sulfurylase) and APR (adenosine 5'-phosphosulfate reductase) was upregulated more than 1,000-fold under selenate treatment, while that of CBL (cystathionine-β-synthase) was upregulated 3.12-fold. Based on the transcriptome analysis, we suspect that the high-affinity sulfur transporter Sultr1;2 plays a key role in selenate uptake in oats. A preliminary regulatory mechanism explains the oat response to selenate treatment was ultimately proposed based on the transcriptome analysis and previous research.