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.

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

Soil and water are increasingly at risk of contamination from the toxic heavy metals lead (Pb) and cadmium (Cd). Arabis paniculata (Brassicaceae) is a hyperaccumulator of heavy metals (HMs) found widely distributed in areas impacts by mining activities. However, the mechanism by which A. paniculata tolerates HMs is still uncharacterized. For this experiment, we employed RNA sequencing (RNA-seq) in order to find Cd (0.25 mM)- and Pb (2.50 mM)-coresponsive genes A. paniculata. In total, 4490 and 1804 differentially expressed genes (DEGs) were identified in root tissue, and 955 and 2209 DEGs were identified in shoot tissue, after Cd and Pb exposure, respectively. Interestingly in root tissue, gene expression corresponded similarly to both Cd and Pd exposure, of which 27.48% were co-upregulated and 41.00% were co-downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses showed that the co-regulated genes were predominantly involved in transcription factors (TFs), cell wall biosynthesis, metal transport, plant hormone signal transduction, and antioxidant enzyme activity. Many critical Pb/Cd-induced DEGs involved in phytohormone biosynthesis and signal transduction, HM transport, and transcription factors were also identified. Especially the gene ABCC9 was co-downregulated in root tissues but co-upregulated in shoot tissues. The co-downregulation of ABCC9 in the roots prevented Cd and Pb from entering the vacuole rather than the cytoplasm for transporting HMs to shoots. While in shoots, the ABCC9 co-upregulated results in vacuolar Cd and Pb accumulation, which may explain why A. paniculata is a hyperaccumulator. These results will help to reveal the molecular and physiological processes underlying tolerance to HM exposure in the hyperaccumulator A. paniculata, and aid in future efforts to utilize this plant in phytoremediation.

Characterisation of manganese toxicity tolerance in Arabis paniculata

Manganese (Mn) contamination limits the production and quality of crops, and affects human health by disrupting the food chain. Arabis paniculata is a pioneer species of Brassicaceae found in mining areas, and has the ability to accumulate heavy metals. However, little is known about the genetic mechanisms of Mn tolerance in A. paniculata. In this study, we found that Mn tolerance and ability to accumulate Mn were higher in A. paniculata than in Arabidopsis thaliana. The mechanisms underlying the response and recovery of A. paniculata to Mn toxicity were further investigated using transcriptome analysis. A total of 69,862,281 base pair clean reads were assembled into 61,627 high-quality unigenes, of which 41,591 (67.5%) and 39,297 (63.8%) were aligned in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO), respectively. In response to Mn toxicity, genes were expressed in twelve distinct patterns, which can be divided into four general categories: initial, stable, dose-dependent, and lineage. Genes that were differentially expressed during Mn response and recovery belong to several dominant KEGG pathways. An early response to Mn toxicity in A. paniculata includes the upregulation of genes involved in glutathione metabolism. ATP-binding cassette (ABC) transporter proteins were up-regulated during the entire response phase, and genes involved in glycerophospholipid metabolism were up-regulated during the late phase of the Mn response. Genes in the phenylpropanoid pathway were differentially expressed in the repair process after Mn treatment. These findings reveal ideal material and genetic resources for phytoremediation in Mn-contaminated areas and highlight new knowledge and theoretical perspectives on the mechanisms of Mn tolerance.

Two phases of response to long-term moderate heat: Variation in thermotolerance between Arabidopsis thaliana and its relative Arabis paniculata

Long-term moderate heat is often experienced by plants and will become even more common in the future due to global warming. However, the responses of plants to this stress have not been characterised. In the present study, growth between Arabidopsis thaliana and its relative Arabis paniculata upon long-term exposure to moderate heat was compared. It was found that the latter was more tolerant than the former, and the patterns of physiological and biochemical responses of both plants presented two phases. The early phase involved no significant visible morphological and physiological changes. It occurred during the first third of the heat treatment and was extended when the stress was attenuated. During the later phase, the plants died or were damaged. Heat shock proteins were dramatically induced at the early phase and gradually decreased at the later phase in A. thaliana. By contrast, the levels were induced and maintained in A. paniculata. Profiling of membrane lipids found that the two plants exhibited opposite patterns of lipid remodelling at the early phase: A. paniculata synthesised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylinositol and showed a rapid decrease in the degree of lipid unsaturation, while A. thaliana degraded its lipids at the early phase and showed an accelerated degradation at the later phase. These biochemical adjustments during the early phase could favor the thermotolerance of A. paniculata. These results suggest that this species could thus be a model for the study of resistance to long-term moderate heat, through a strategy by which plants can adapt to long-term moderate heat.