Comparative transcriptome analysis reveals different functions of Kandelia obovata superoxide dismutases in regulation of cadmium translocation

Integrated transcriptome and metabolomics analyses revealed key functional genes in Canna indica under Cr stress

Chromium (Cr) can interfere with plant gene expression, change the content of metabolites and affect plant growth. However, the molecular response mechanism of wetland plants at different time sequences under Cr stress has yet to be fully understood. In this study, Canna indica was exposed to 100 mg/kg Cr-contaminated soil for 0, 7, 14, and 21 days and analyzed using untargeted metabolomics (LC-MS) and transcriptomics. The results showed that Cr stress increased the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX) and peroxidase (POD), the contents of glutathione (GSH), malondialdehyde (MDA), and oxygen free radical (ROS), and inhibited the biosynthesis of photosynthetic pigments, thus leading to changes in plant growth and biomass. Metabonomics analysis showed that Cr stress mainly affected 12 metabolic pathways, involving 38 differentially expressed metabolites, including amino acids, phenylpropane, and flavonoids. By transcriptome analysis, a total of 16,247 differentially expressed genes (DEGs, 7710 up-regulated genes, and 8537 down-regulated genes) were identified, among which, at the early stage of stress (Cr contaminate seven days), C. indica responds to Cr toxicity mainly through galactose, starch and sucrose metabolism. With the extension of stress time, plant hormone signal transduction and MAPK signaling pathway in C. indica in the Cr14 (Cr contaminate 14 days) treatment group were significantly affected. Finally, in the late stage of stress (Cr21), C. indica co-defuses Cr toxicity by activating its Glutathione metabolism and Phenylpropanoid biosynthesis. In conclusion, this study revealed the molecular response mechanism of C. indica to Cr stress at different times through multi-omics methods.

Comprehensive physiology and proteomics analysis revealed the resistance mechanism of rice (Oryza sativa L) to cadmium stress

Cadmium contamination can lead to a decrease in crop yield and quality. However, Cd-tolerant rice can improve rice resistance genes, improve crop tolerance to heavy metals, and protect plants from oxidative damage. In this study, Japonica rice: Chunyou 987 and Indica rice: Chuanzhong you 3607 were used to reveal the molecular response mechanism of Cd-tolerant rice under cadmium concentration of 3 mg/kg through comparative experiments combined with physiology and proteomics. The results showed that compared with indica rice, japonica rice showed more robust resistance to Cd stress and effectively retained many Cd ions in roots. Moreover, it enhanced its enzymatic and non-enzymatic anti-oxidative stress mechanism, which increased the activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) by 47.37%, 21.75%, and 55.42%, respectively. The contents of non-enzymatic antioxidant substances ascorbic acid (AsA), glutathione (GSH), cysteine (Cys), proline (PRO), anthocyanins (OPC), and flavonoids were increased by 25.32%, 42.67%, 21.43%, 50.81%, 33.23%, and 72.16%, respectively. Through proteomics analysis, it was found that in response to the damage caused by cadmium stress, Japonica rice makes Photosynthesis functional proteins (psbO and PetH), Photosynthesis antenna proteins (LHCA and ASCAB9), Carbon fixation functional proteins (PEPC and OsAld), Porphyrin metabolism functional proteins (OsRCCR1 and SE5), Glyoxylate and dicarboxylate The expression of metabolism functional proteins (CATC and GLO4.) and Glutathione metabolism functional proteins (APX8 and OsGSTU13) were significantly up-regulated, which stimulated the antioxidant stress mechanism and photosynthetic system, and constructed a robust energy supply system to ensure the normal metabolic activities of life. Strengthening the mechanisms of plant homeostasis. In summary, this study revealed the molecular mechanism of tolerance to Cd stress in japonica rice, and the results of this study will provide a possible way to improve Cd-resistant rice seedlings.

Integrative physiological, transcriptomic, and metabolomic analysis of Abelmoschus manihot in response to Cd toxicity

Rapid industrialization and urbanization have caused severe soil contamination with cadmium (Cd) necessitating effective remediation strategies. Phytoremediation is a widely adopted technology for remediating Cd-contaminated soil. Previous studies have shown that Abelmoschus manihot has a high Cd accumulation capacity and tolerance indicating its potential for Cd soil remediation. However, the mechanisms underlying its response to Cd stress remain unclear. In this study, physiological, transcriptomic, and metabolomic analyses were conducted to explore the response of A. manihot roots to Cd stress at different time points. The results revealed that Cd stress significantly increased malondialdehyde (MDA) levels in A. manihot, which simultaneously activated its antioxidant defense system, enhancing the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) by 19.73%-50%, 22.87%-38.89%, and 32.31%-45.40% at 12 h, 36 h, 72 h, and 7 days, respectively, compared with those in the control (CK). Moreover, transcriptomic and metabolomic analyses revealed 245, 5,708, 9,834, and 2,323 differentially expressed genes (DEGs), along with 66, 62, 156, and 90 differentially expressed metabolites (DEMs) at 12 h, 36 h, 72 h, and 7 days, respectively. Through weighted gene coexpression network analysis (WGCNA) of physiological indicators and transcript expression, eight hub genes involved in phenylpropanoid biosynthesis, signal transduction, and metal transport were identified. In addition, integrative analyses of metabolomic and transcriptomic data highlighted the activation of lipid metabolism and phenylpropanoid biosynthesis pathways under Cd stress suggesting that these pathways play crucial roles in the detoxification process and in enhancing Cd tolerance in A. manihot. This comprehensive study provides detailed insights into the response mechanisms of A. manihot to Cd toxicity.

miR397 regulates cadmium stress response by coordinating lignin polymerization in the root exodermis in Kandelia obovata

Secondary lignification of the root exodermis of Kandelia obovata is crucial for its response to adversity such as high salinity and anaerobic environment, and this lignification is also effective in blocking cadmium transport to the roots. However, how the differences in lignification of root exodermis at different developmental stages respond to Cd stress and its regulatory mechanisms have not been revealed. In this study, after analyzing the root structure and cell wall thickness using a Phenom scanning electron microscope as well as measuring cadmium content in the root cell wall, we found that the exodermis of young and mature roots of K. obovata responded to Cd stress through the polymerization of different lignin monomers, forming two different mechanisms: chelation and blocking. Through small RNA sequencing, RLM-5'-RACE and dual luciferase transient expression system, we found that miR397 targets and regulates KoLAC4/17/7 expression. The expression of KoLAC4/17 promoted the accumulation of guaiacyl lignin during lignification and enhanced the binding of cadmium to the cell wall. Meanwhile, KoLAC7 expression promotes the accumulation of syringyl lignin during lignification, which enhances the obstruction of cadmium and improves the tolerance to cadmium. These findings enhance our understanding of the molecular mechanisms underlying the differential lignification of the root exodermis of K. obovata in response to cadmium stress, and provide scientific guidance for the conservation of mangrove forests under heavy metal pollution.

Combined transcriptomics and metabolomics to analyse the response of Cuminum cyminum L. under Pb stress

Lead (Pb) can disrupt plant gene expression, modify metabolite contents, and influence the growth of plants. Cuminum cyminum L. is highly adaptable to adversity, but molecular mechanism by which it responds to Pb stress is unknown. For this study, transcriptomic and metabolomic sequencing was performed on root tissues of C. cyminum under Pb stress. Our results showed that high Pb stress increased the activity of peroxidase (POD), the contents of malondialdehyde (MDA) and proline by 80.03 %, 174.46 % and 71.24 %, respectively. Meanwhile, Pb stress decreased the activities of superoxide dismutase (SOD) and catalase (CAT) as well as contents of soluble sugars and GSH, which thus affected the growth of C. cyminum. In addition, Pb stress influenced the accumulation and transport of Pb in C. cyminum. Metabolomic results showed that Pb stress affected eight metabolic pathways involving 108 differentially expressed metabolites, primarily amino acids, organic acids, and carbohydrates. The differentially expressed genes identified through transcriptome analysis were mainly involved the oxidation reductase activity, transmembrane transport, phytohormone signaling, and MAPK signaling pathway. The results of this study will help to understand the molecular mechanisms of C. cyminum response to Pb stress, and provide a basis for screening seeds with strong resistance to heavy metals.

Integrated transcriptomics and metabolomics reveal key metabolic pathway responses in Pistia stratiotes under Cd stress

Cadmium (Cd) can interfere with plant gene expression, change the content of metabolites and affect plant growth. In this study, untargeted metabolomics (LC-MS) and RNA-Seq sequencing were performed on root tissues of Pistia stratiotes exposed to Cd stress. The results showed that cadmium stress affected the accumulation and transport of cadmium in plants and increased the content of soluble sugar, the activities of ascorbate peroxidase (APX), and peroxidase (POD) by 34.89%, 41.45%, and 6.71% on average, and decreased the activity of superoxide dismutase (SOD) by 51.51% on average. At the same time, the contents of carotenoid, chlorophyll a, and chlorophyll b decreased by 29.52%, 20.11%, and 13.14%, respectively, Thus affecting the growth and development of plants. Metabolomic analysis showed that Cd stress affected eight metabolic pathways, involving 27 differentially expressed metabolites, mainly including unsaturated fatty acids, amino acids (phenylalanine), nucleotides, sulfur compounds, and flavonoids. By transcriptome analysis, a total of 3107 differentially expressed genes (DEGs, 2666 up-regulated genes, and 441 down-regulated genes) were identified, which were mainly involved in four pathways, among which glutathione metabolism and lignin biosynthesis were the key metabolic pathways. In conclusion, this study reveals the metabolic and transcriptional response mechanisms of P. stratiotes to Cd stress through multi-omics, providing the theoretical basis for the phytoremediation of water contaminated by Cd.

The Effect of Cadmium on Plants in Terms of the Response of Gene Expression Level and Activity

Cadmium (Cd) is a heavy metal that can cause damage to living organisms at different levels. Even at low concentrations, Cd can be toxic to plants, causing harm at multiple levels. As they are unable to move away from areas contaminated by Cd, plants have developed various defence mechanisms to protect themselves. Hyperaccumulators, which can accumulate and detoxify heavy metals more efficiently, are highly valued by scientists studying plant accumulation and detoxification mechanisms, as they provide a promising source of genes for developing plants suitable for phytoremediation techniques. So far, several genes have been identified as being upregulated when plants are exposed to Cd. These genes include genes encoding transcription factors such as iron-regulated transporter-like protein (ZIP), natural resistance associated macrophage protein (NRAMP) gene family, genes encoding phytochelatin synthases (PCs), superoxide dismutase (SOD) genes, heavy metal ATPase (HMA), cation diffusion facilitator gene family (CDF), Cd resistance gene family (PCR), ATP-binding cassette transporter gene family (ABC), the precursor 1-aminocyclopropane-1-carboxylic acid synthase (ACS) and precursor 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) multigene family are also influenced. Thanks to advances in omics sciences and transcriptome analysis, we are gaining more insights into the genes involved in Cd stress response. Recent studies have also shown that Cd can affect the expression of genes related to antioxidant enzymes, hormonal pathways, and energy metabolism.

Characterization and Expression Analysis of Four Cadmium-Tolerance-Associated Genes of Avicennia marina (Forsk.)

Mangroves colonize the intertidal area of estuaries (e.g., Pichavaram, Payardia, and Mai Po) with remarkable cadmium (Cd) pollution. A study on the mechanism of mangrove plant response to Cd pollution can help to understand the adaptive characteristics of plants under Cd stress. This study explored the roles of peroxidase (PRX), pectate lyase (PL), and phytosulfokine (PSK) genes in cadmium tolerance of mangrove Avicennia marina. Full-length sequences of four genes (i.e., AmPRX1, AmPRX2, AmPL, and AmPSK) associated with metal tolerance were identified with suppression subtractive hybridization and rapid amplification of cDNA ends. These genes showed the characteristic features of the respective protein family, indicating functions similar to other plant proteins. Real-time quantitative PCR analysis demonstrated that cadmium exposure resulted in differences in expression patterns among the tissues. Our findings emphasize the complex regulatory mechanism of these four genes in response to trace metal pollution and reveal their functions in metabolic signaling during the stress response.

Role of extracellular polymeric substances in metal sequestration during mangrove restoration

Extracellular polymeric substances (EPS) are widely observed in aquatic ecosystems, however the potential function of EPS on metal sequestration in mangrove wetlands is unclear. Thus, an ecological restoration area (including Sonneratia apetala, Kandelia obovata and unvegetated mudflat) was employed to assess the effect of mangrove reforestation on metal sequestration and the underlying roles played by EPS. The results showed that mangrove restoration directly promoted metal accumulation (e.g., Cr, Cu, Ni, Pb, and Zn) in sediments. However, alleviated metal bioavailability was detected after mangrove reforestation. The changes in metal accumulation and bioavailability were highly correlated with EPS and microbial composition. Mangrove restoration (especially for K. obovata reforestation) also significantly promoted EPS production, in which multiple metal-chelating functional groups (e.g., hydroxyl, carboxyl, and imino) were identified by Fourier infrared spectra. Moreover, the contents of EPS were positively correlated with metal accumulation but negatively correlated with metal bioavailability. The present data further illustrated that the enhancements of Gammaproteobacteria, Bacteroidia, Desulfobulbia, and Desulfobacteria might be important for EPS production. In summary, this is the first study to reveal that the presence of artificial mangroves might act as an efficient barrier in metal sequestration and immobilization by enhancing inherent microbial EPS.

Temporal and tissue-specific transcriptome analyses reveal mechanistic insights into the Solidago canadensis response to cadmium contamination

Understanding the cellular mechanisms mediating invasive plant adaptation to excessive cadmium (Cd) in environments is crucial for designing phytoremediation strategies for Cd-contaminated soils. Here we performed RNA sequencing on the root and leaf tissues of Solidago canadensis stressed by Cd for 0, 12, 24, and 48 h. Tissue-specific gene expression was notably significant, i.e., 76% (1667) of differentially expressed unigenes in the root and 78% (1856) in the leaf were exclusive to each tissue. Distinctive enrichment of gene functions was further observed in each tissue's response. In detail, adaptation of the root to Cd stress involved the up-regulation of genes encoding molecular chaperones (mainly heat shock proteins) and induction of some antioxidants, which may help cells scavenge reactive oxygen species (ROS). In comparison, leaf exposure to Cd ramped up the expression of genes associated with secondary metabolism, comprised mainly of cytochrome P450, but slowed down its photosynthetic functions, which seems to conserve energy for survival. Moreover, we highlighted candidate gene modules that are highly linked to physiological traits. Collectively, these observations suggest that S. canadensis may adopt a multipronged approach to actively cope with Cd stress, with both management of ROS accumulation and metabolic adjustment to optimize energy metabolism.

Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

Mangroves are halophytic plants belonging to diverse angiosperm families that are adapted to highly stressful intertidal zones between land and sea. They are special, unique, and one of the most productive ecosystems that play enormous ecological roles and provide a large number of benefits to the coastal communities. To thrive under highly stressful conditions, mangroves have innovated several key morphological, anatomical, and physio-biochemical adaptations. The evolution of the unique adaptive modifications might have resulted from a host of genetic and molecular changes and to date we know little about the nature of these genetic and molecular changes. Although slow, new information has accumulated over the last few decades on the genetic and molecular regulation of the mangrove adaptations, a comprehensive review on it is not yet available. This review provides up-to-date consolidated information on the genetic, epigenetic, and molecular regulation of mangrove adaptive traits.

An update on redox signals in plant responses to biotic and abiotic stress crosstalk: insights from cadmium and fungal pathogen interactions

Complex signalling pathways are involved in plant protection against single and combined stresses. Plants are able to coordinate genome-wide transcriptional reprogramming and display a unique programme of transcriptional responses to a combination of stresses that differs from the response to single stresses. However, a significant overlap between pathways and some defence genes in the form of shared and general stress-responsive genes appears to be commonly involved in responses to multiple biotic and abiotic stresses. Reactive oxygen and nitrogen species, as well as redox signals, are key molecules involved at the crossroads of the perception of different stress factors and the regulation of both specific and general plant responses to biotic and abiotic stresses. In this review, we focus on crosstalk between plant responses to biotic and abiotic stresses, in addition to possible plant protection against pathogens caused by previous abiotic stress. Bioinformatic analyses of transcriptome data from cadmium- and fungal pathogen-treated plants focusing on redox gene ontology categories were carried out to gain a better understanding of common plant responses to abiotic and biotic stresses. The role of reactive oxygen and nitrogen species in the complex network involved in plant responses to changes in their environment is also discussed.