Transcriptomic analysis reveals key genes and pathways corresponding to Cd and Pb in the hyperaccumulator Arabis paniculata

Identification and functional characterization of ABC transporters for selenium accumulation and tolerance in soybean

ATP-binding cassette (ABC) transporters were crucial for various physiological processes like nutrition, development, and environmental interactions. Selenium (Se) is an essential micronutrient for humans, and its role in plants depends on applied dosage. ABC transporters are considered to participate in Se translocation in plants, but detailed studies in soybean are still lacking. We identified 196 ABC genes in soybean transcriptome under Se exposure using next-generation sequencing and single-molecule real-time sequencing technology. These proteins fell into eight subfamilies: 8 GmABCA, 51 GmABCB, 39 GmABCC, 5 GmABCD, 1 GmABCE, 10 GmABCF, 74 GmABCG, and 8 GmABCI, with amino acid length 121-3022 aa, molecular weight 13.50-341.04 kDa, and isoelectric point 4.06-9.82. We predicted a total of 15 motifs, some of which were specific to certain subfamilies (especially GmABCB, GmABCC, and GmABCG). We also found predicted alternative splicing in GmABCs: 60 events in selenium nanoparticles (SeNPs)-treated, 37 in sodium selenite (Na2SeO3)-treated samples. The GmABC genes showed differential expression in leaves and roots under different application of Se species and Se levels, most of which are belonged to GmABCB, GmABCC, and GmABCG subfamilies with functions in auxin transport, barrier formation, and detoxification. Protein-protein interaction and weighted gene co-expression network analysis suggested functional gene networks with hub ABC genes, contributing to our understanding of their biological functions. Our results illuminate the contributions of GmABC genes to Se accumulation and tolerance in soybean and provide insight for a better understanding of their roles in soybean as well as in other plants.

Comparative transcriptomic analysis revealed important processes underlying the static magnetic field effects on Arabidopsis

Static magnetic field (SMF) plays important roles in various biological processes of many organisms including plants, though the molecular mechanism remains largely unclear. Here in this study, we evaluated different magnetic setups to test their effects on growth and development on Arabidopsis (Arabidopsis thaliana), and discovered that plant growth was significantly enhanced by inhomogeneous SMF generated by a regular triangular prism magnet perpendicular to the direction of gravity. Comparative transcriptomic analysis revealed that auxin synthesis and signal transduction genes were upregulated by SMF exposure. SMF also facilitated plants to maintain the iron homeostasis. The expression of iron metabolism-related genes was downregulated by SMF, however, the iron content in plant tissues remains relatively unchanged. Furthermore, SMF exposure also helped the plants to reduce ROS level and synergistically maintain the oxidant balance by enhanced activity of antioxidant enzymes and accumulation of nicotinamide. Taken together, our data suggested that SMF is involved in regulating the growth and development of Arabidopsis thaliana through maintaining iron homeostasis and balancing oxidative stress, which could be beneficial for plant survival and growth. The work presented here would extend our understanding of the mechanism and the regulatory network of how magnetic field affects the plant growth, which would provide insights into the development of novel plant synthetic biology technologies to engineer stress-resistant and high-yielding crops.

Transporters and phytohormones analysis reveals differential regulation of ryegrass (Lolium perenne L.) in response to cadmium and arsenic stresses

Cadmium (Cd) and arsenic (As) are two highly toxic heavy metals and metalloids that coexist in many situations posing severe threats to plants. Our investigation was conducted to explore the different regulatory mechanisms of ryegrass (Lolium perenne L.) responding to individual and combined Cd and As stresses in hydroponics. Results showed that the ryegrass well-growth phenotype was not affected by Cd stress of 10 mg·L-1. However, As of 10 mg·L-1 caused rapid water loss, proline surge, and chlorosis in shoots, suggesting that ryegrass was highly sensitive to As. Transcriptomic analysis revealed that the transcription factor LpIRO2 mediated the upregulation of ZIP1 and YSL6 that played an important role in Cd tolerance. We found that the presence of As caused the overexpression of LpSWT12, a process potentially regulated by bHLH14, to mitigate hyperosmolarity. Indoleacetic acid (IAA) and abscisic acid (ABA) contents and expression of their signaling-related genes were significantly affected by As stress rather than Cd. We predict a regulatory network to illustrate the interaction between transporters, transcription factors, and signaling transduction, and explain the antagonism of Cd and As toxicity. This present work provides a research basis for plant protection from Cd and As pollution.

Effects of different cellular and subcellular characteristics on the atmospheric Pb uptake, distribution and morphology in Tillandsia usneoides leaves

Lead (Pb) is a widespread highly toxic and persistent environmental pollutant. Plant leaves play a key role in accumulating atmospheric Pb, but its distribution in different cells and subcellular structures and the factors affecting it have been little studied. Here, Tillandsia usneoides, an indicator plant for atmospheric heavy metals, was treated with an aerosol generation device to analyze Pb contents in different cells (three types of cells in leaf surface scales, epidermal cells, mesophyll cells, vascular bundle cells), subcellular structures (cell wall, cell membrane, vacuoles, and organelles) and cell wall components (pectin, hemicellulose 1 and 2, and cellulose). Results show the different cells of T. usneoides leaves play distinct roles in the process of Pb retention. The outermost wing cells are structures that capture external pollutants, while mesophyll cells, as the aggregation site after material transport, ring cells, disc cells, epidermal cells, and vascular cells are material transporters. Pb was only detected in the cell wall and pectin, indicating the cell wall was the dominant subcellular structure for Pb retention, while pectin was the main component affecting Pb retention. FTIR analysis of cell wall components indicated the esterified carboxyl (CO) functional group in pectin may function in absorbing Pb. Pb entered leaf cells mainly in the form of low toxicity and activity to enhance its resistance.

Transcriptome Profiling, Physiological and Biochemical Analyses Reveal Comprehensive Insights in Cadmium Stress in Brassica carinata L

With the constant progress of urbanization and industrialization, cadmium (Cd) has emerged as one of the heavy metals that pollute soil and water. The presence of Cd has a substantial negative impact on the growth and development of both animals and plants. The allotetraploid Brasscia. carinata, an oil crop in the biofuel industry, is known to produce seeds with a high percentage of erucic acid; it is also known for its disease resistance and widespread adaptability. However, there is limited knowledge regarding the tolerance of B. carinata to Cd and its physiological responses and gene expressions under exposure to Cd. Here, we observed that the tested B. carinata exhibited a strong tolerance to Cd (1 mmol/L CdCl2 solution) and exhibited a significant ability to accumulate Cd, particularly in its roots, with concentrations reaching up to 3000 mg/kg. Additionally, we found that the total oil content of B. carinata seeds harvested from the Cd-contaminated soil did not show a significant change, but there were noticeable alterations in certain constituents. The activities of antioxidant enzymes, including catalase (CAT), superoxide dismutase (SOD), peroxidase (POD), and ascorbate peroxidase (APX), were observed to significantly increase after treatment with different concentrations of CdCl2 solutions (0.25 mmol/L, 0.5 mmol/L, and 1 mmol/L CdCl2). This suggests that these antioxidant enzymes work together to enhance Cd tolerance. Comparative transcriptome analysis was conducted to identify differentially expressed genes (DEGs) in the shoots and roots of B. carinata when exposed to a 0.25 mmol/L CdCl2 solution for 7 days. A total of 631 DEGs were found in the shoots, while 271 DEGs were found in the roots. It was observed that these selected DEGs, which responded to Cd stress, also showed differential expression after exposure to PbCl2. This suggests that B. carinata may employ a similar molecular mechanism when tolerating these heavy metals. The functional annotation of the DEGs showed enrichment in the categories of 'inorganic ion transport and metabolism' and 'signal transduction mechanisms'. Additionally, the DEGs involved in 'tryptophan metabolism' and 'zeatin biosynthesis' pathways were found to be upregulated in both the shoots and roots of B. carinata, suggesting that the plant can enhance its tolerance to Cd by promoting the biosynthesis of plant hormones. These results highlight the strong Cd tolerance of B. carinata and its potential use as a Cd accumulator. Overall, our study provides valuable insights into the mechanisms underlying heavy metal tolerance in B. carinata.

A WRKY transcription factor, PyWRKY71, increased the activities of antioxidant enzymes and promoted the accumulation of cadmium in poplar

Cadmium (Cd) pollution poses significant threats to the ecological environment and human health. Currently, phytoremediation is recognized as an environmentally friendly approach for mitigating Cd pollution, with increasing attention on the utilization of transgenic plants in Cd-contaminated soil remediation. In this study, we isolated and cloned PyWRKY71 from Populus yunnanensis and conducted a pot experiment to validate its enhanced functionality in conferring Cd tolerance to woody plants (poplar). During the experiment, the increase in plant height of the OE-87 line (overexpression poplar) was 1.46 times than that of the wild type (WT). Moreover, PyWRKY71 significantly promoted the accumulation of Cd in poplar, especially in the roots, where the Cd content in the OE-45 and OE-87 lines was 1.42 times than that in the WT. The chlorophyll content of transgenic poplar leaves was higher than that of the WT, reflecting a protective mechanism of PyWRKY71. Additionally, the activities of other antioxidants, including POD, SOD, CAT, and MDA, were elevated in transgenic poplars, bolstering their tolerance to Cd stress. In summary, PyWRKY71 exhibits substantial potential in regulating plant tolerance to Cd stress. This study not only provides a solid scientific foundation but also introduces a novel modified poplar variety for the remediation of Cd pollution.

Full-Length Transcriptome Sequencing Analysis and Characterization of WRKY Transcription Factors Responsive to Cadmium Stress in Arabis paniculata

Arabis paniculata is a newly discovered hyperaccumulator known for its ability to accumulate multiple metals. WRKY proteins play a significant role in plant responses to various stresses, including cadmium (Cd) stress. However, there is limited research on the molecular biology of Arabis paniculata, especially regarding the WRKY family. In this study, we conducted third-generation sequencing for functional annotation and structural analysis of Arabis paniculata. We obtained 41,196 high-quality isoforms from the full-length transcriptome, with an average length of 1043 bp. A total of 26,670 genes were predicted against NR, Swissprot, KOG, and KEGG databases. Functional comparison using the KOG database revealed excellent annotation in 25 functional categories, with general function prediction (1822 items) being the most predominant. MISA analysis identified 12,593 SSR loci, with single nucleotide repeats being the largest category (44.83% of the total). Moreover, our predictions provide insights into 20,022 coding sequences (CDS), 811 transcription factors, and 17,963 LncRNAs. In total, 34 WRKY gene sequences were identified in Arabis paniculata. Bioinformatics analysis revealed diverse numbers of amino acids in these WRKYs (113 to 545 aa), and a conserved WRKYGQK sequence within the N-terminus of the WRKY protein. Furthermore, all WRKYs were found to be localized in the nucleus. Phylogenetic analysis classified the WRKY genes into three categories: I (14 members), II (17 members), and III (3 members). Category II was subsequently divided into four sub-categories: II-a (8 members), II-b (1 member), II-c (1 member), and II-d (7 members). Our quantitative real-time polymerase chain reaction (qRT-PCR) experiments revealed that ApWRKY23 and ApWRKY34 exhibited the highest expression levels at the 24-h time point, suggesting their potential role as the candidate genes for Cd stress response. These findings contribute to our understanding of the genomic information of Arabis paniculata and provide a basis for the analysis of its genetic diversity. Additionally, this study paves the way for a comprehensive exploration of the molecular mechanisms underlying the WRKY genes in Arabis paniculata under Cd stress conditions.

Overexpression of ApHIPP26 from the Hyperaccumulator Arabis paniculata Confers Enhanced Cadmium Tolerance and Accumulation to Arabidopsis thaliana

Cadmium (Cd) is a toxic heavy metal that seriously affects metabolism after accumulation in plants, and it also causes adverse effects on humans through the food chain. The HIPP gene family has been shown to be highly tolerant to Cd stress due to its special domain and molecular structure. This study described the Cd-induced gene ApHIPP26 from the hyperaccumulator Arabis paniculata. Its subcellular localization showed that ApHIPP26 was located in the nucleus. Transgenic Arabidopsis overexpressing ApHIPP26 exhibited a significant increase in main root length and fresh weight under Cd stress. Compared with wild-type lines, Cd accumulated much more in transgenic Arabidopsis both aboveground and underground. Under Cd stress, the expression of genes related to the absorption and transport of heavy metals underwent different changes in parallel, which were involved in the accumulation and distribution of Cd in plants, such as AtNRAMP6 and AtNRAMP3. Under Cd stress, the activities of antioxidant enzymes (superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase) in the transgenic lines were higher than those in the wild type. The physiological and biochemical indices showed that the proline and chlorophyll contents in the transgenic lines increased significantly after Cd treatment, while the malondialdehyde (MDA) content decreased. In addition, the gene expression profile analysis showed that ApHIPP26 improved the tolerance of Arabidopsis to Cd by regulating the changes of related genes in plant hormone signal transduction pathway. In conclusion, ApHIPP26 plays an important role in cadmium tolerance by alleviating oxidative stress and regulating plant hormones, which provides a basis for understanding the molecular mechanism of cadmium tolerance in plants and provides new insights for phytoremediation in Cd-contaminated areas.

Plant growth-promoting bacteria modulate gene expression and induce antioxidant tolerance to alleviate synergistic toxicity from combined microplastic and Cd pollution in sorghum

Microplastics (MPs) can act as carriers for environmental pollutants; therefore, MPs combined with heavy metal pollution are attracting increasing attention from researchers. In this study, the potential of the plant growth-promoting bacterium Bacillus sp. SL-413 to mitigate the stress caused by exposure to both MPs and cadmium (Cd) in sorghum plants was investigated. The effects of inoculation on sorghum biomass were investigated using hydroponic experiments, and evaluation of Cd accumulation and enzyme activity changes and transcriptomics approaches were used to analyze its effect on sorghum gene expression. The results showed that combined polyethylene (PE) and Cd pollution reduced the length and the fresh and dry weights of sorghum plants and thus exerted a synergistic toxic effect. However, inoculation with the strains alleviated the stress caused by the combined pollution and significantly increased the biomass. Inoculation increased the dry weights of the aboveground and belowground parts by 11.5-44.6% and 14.9-38.4%, respectively. Plant physiological measurements indicated that inoculation reduced the reactive oxygen species (ROS) content of sorghum by 10.5-27.2% and thereby alleviated oxidative stress. Transcriptome sequencing showed that exposure to combined Cd+MP contamination induced downregulation of gene expression, particularly that of genes related to amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, and plant hormone signal transduction, in sorghum. However, inoculation with Bacillus sp. SL-413 resulted in an increase in the proportion of upregulated genes involved in signal transduction, antioxidant defense, cell wall biology, and other metabolic pathways, which included the phenylpropanoid biosynthesis, photosynthesis, flavonoid biosynthesis, and MAPK signaling pathways. The upregulation of these genes promoted the tolerance of sorghum under combined Cd+MP pollution stress and alleviated the stress induced by these conditions. This study provides the first demonstration that plant growth-promoting bacteria can alleviate the stress caused by combined pollution with MPs and Cd by regulating plant gene expression. These findings provide a reference for the combined plant-microbial remediation of MPs and Cd.

Endophytic Bacillus sp. AP10 harboured in Arabis paniculata mediates plant growth promotion and manganese detoxification

Phytoremediation of heavy metal-polluted soils assisted by plant-associated endophytes, is a suitable method for plant growth and manganese (Mn) removal in contaminated soils. This investigation was conducted to evaluate the Mn-resistant endophytic resources of the Mn hyperaccumulator Arabis paniculata and their functions in the phytoremediation of Mn²⁺ toxicity. This study isolated an endophytic bacterium with high Mn resistance and indole-3-acetic acid (IAA) production form A. paniculata and identified it as Bacillus sp. AP10 using 16 S rRNA gene sequencing analysis. The effects of Bacillus sp. AP10 on the alleviation of Mn²⁺ toxicity in Arabidopsis thaliana seedlings and the molecular mechanisms were further investigated using biochemical tests and RNA-seq analysis. Under Mn²⁺ stress, Bacillus sp. AP10 increased the biomass, chlorophyll content and the translocation factor (TF) values of Mn in the aerial parts, while decreased the malondialdehyde (MDA) content of A. thaliana seedlings compared with that of control plants. The differentially expressed genes (DEGs) and enrichment analysis showed that Bacillus sp. AP10 could significantly increase the expression of key genes involved in cell-wall loosening, which may improve plant growth under Mn stress. Superoxide dismutase (SOD)-encoding genes were detected as DEGs after AP10 treatment. Moreover, AP10 regulated the expression of genes responsible for phenylpropanoid pathway, which may promote antioxidant flavonoids accumulation for reactive oxygen species (ROS) scavenging to improve Mn tolerance. The activation of ATP-binding cassette (ABC) transporter gene expression especially ABCB1 after AP10 stimulation, explained the elevation of metal ion binding or transport related to enhanced Mn accumulation in plants. Futhermore, AP10 might alleviate Mn toxicity through enhancing abscisic acid (ABA) responsive gene expression and ABA biosynthesis. These findings provide new insights into the functions and regulatory mechanism of Bacillus sp. AP10 in promoting plant growth, and tolerance, improving Mn accumulation and alleviating Mn²⁺ toxicity in plants. The application of Bacillus sp. AP10 as potential phytoremediators may be a promising strategy in Mn²⁺ contaminated fields. AVAILABILITY OF DATA AND MATERIALS: The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.