Microarray-based analysis of gene expression in lycopersicon esculentum seedling roots in response to cadmium, chromium, mercury, and lead

The Recovery of Soybean Plants after Short-Term Cadmium Stress

Background: Cadmium is a non-essential heavy metal, which is toxic even in relatively low concentrations. Although the mechanisms of Cd toxicity are well documented, there is limited information concerning the recovery of plants after exposure to this metal. Methods: The present study describes the recovery of soybean plants treated for 48 h with Cd at two concentrations: 10 and 25 mg/L. In the frame of the study the growth, cell viability, level of membrane damage makers, mineral content, photosynthesis parameters, and global methylation level have been assessed directly after Cd treatment and/or after 7 days of growth in optimal conditions. Results: The results show that exposure to Cd leads to the development of toxicity symptoms such as growth inhibition, increased cell mortality, and membrane damage. After a recovery period of 7 days, the exposed plants showed no differences in relation to the control in all analyzed parameters, with an exception of a slight reduction in root length and changed content of potassium, magnesium, and manganese. Conclusions: The results indicate that soybean plants are able to efficiently recover even after relatively severe Cd stress. On the other hand, previous exposure to Cd stress modulated their mineral uptake.

Enhanced synergistic removal of Cr(VI) and Cd(II) with bi-functional biomass-based composites

Cr(VI) and Cd(II) are typical heavy metal ions and their co-removal is significant. Nitrogen-doped, bi-functional, and biomass-based composites (CP-BA) were successfully applied for efficient and synergistic removal of Cr(VI) and Cd(II). The mutual promotion ratios of adsorption capacity by Cr(VI) and Cd(II) were 161.32 % and 14.13 %, respectively. In addition, all coexisting inorganic anions could extremely promote the removal of Cd(II) with the best promotion ratio upon phosphate ions as high as 80.00 %. The following co-removal mechanisms were deeply revealed: (1) Cr(VI) combined with protonated imine groups could weaken the electrostatic repulsion between CP-BA and Cd(II) by electrostatic shielding, and further promoted the coordination of Cd(II) with hydroxyl, carboxyl and neutral imine groups. (2) Cd(II) which were coordinated to neutral imine groups could form cation bridges, and thus promoted the interaction with Cr(VI) because of the electrostatic attraction. Moreover, the removal capacity for Cr(VI) and Cd(II) did not display obvious reduction even after four cycles. Therefore, CP-BA showed a great potential in the co-removal of inorganic anion-cation complexes from wastewater.

Toxicity of mercury: Molecular evidence

Minamata disease in Japan and the large-scale poisoning by methylmercury (MeHg) in Iraq caused wide public concerns about the risk emanating from mercury for human health. Nowadays, it is widely known that all forms of mercury induce toxic effects in mammals, and increasing evidence supports the concern that environmentally relevant levels of MeHg could impact normal biological functions in wildlife. The information of mechanism involved in mercurial toxicity is growing but knowledge gaps still exist between the adverse effects and mechanisms of action, especially at the molecular level. A body of data obtained from experimental studies on mechanisms of mercurial toxicity in vivo and in vitro points to that disruption of the antioxidant system may play an important role in the mercurial toxic effects. Moreover, the accumulating evidence indicates that signaling transduction, protein or/and enzyme activity, and gene regulation are involving in mediating toxic and adaptive response to mercury exposure. We conducted here a comprehensive review of mercurial toxic effects on wildlife and human, in particular synthesized key findings of molecular pathways involved in mercurial toxicity from the cells to human. We discuss the molecular evidence related mercurial toxicity to the adverse effects, with particular emphasis on the gene regulation. The further studies relying on Omic analysis connected to adverse effects and modes of action of mercury will aid in the evaluation and validation of causative relationship between health outcomes and gene expression.

Cadmium stress alters cytosine methylation status and expression of a select set of genes in Nicotiana benthamiana

In this paper, we evaluated the genotoxicity of cadmium (Cd) in plants by performing a methylation-sensitive amplification polymorphism (MSAP) on the model plant Nicotiana benthamiana. Among 255 loci examined, 14 genes were found to show altered cytosine methylation patterns in response to Cd stress. Four of those genes (NbMORC3, NbHGSNAT, NbMUT, and NbBG) were selected for further analysis due to their predicted roles in plant development. Cd-induced changes of cytosine methylation status in MSAP fragments of selected genes were confirmed using bisulfite sequencing polymerase chain reaction (BSP). In addition, the expression levels of these genes were found to correlate with cadmium dosage, and a knock-down of these four genes via virus-induced genes silencing (VIGS) led to abnormal development and elevated sensitivity to cadmium stress. Silencing of these four genes resulted in altered cadmium accumulation in different parts of the experimental plants. Our data indicate that cadmium exposure causes dramatic changes in the cytosine methylation status of the plant genome, thus affecting the expression of many genes that are vital for plant growth and are involved in cadmium stress response.

Heterologous expression of TuCAX1a and TuCAX1b enhances Ca2+ and Zn2+ translocation in Arabidopsis

TuCAX1a and TuCAX1b improved Ca²⁺ and Zn²⁺ translocation and TuCAX1b enhanced Ca²⁺, Zn²⁺, Mn²⁺ and Fe²⁺ content when exposed to Cd²⁺; Cd²⁺ translocation was inhibited under Ca²⁺ and Zn²⁺. Cation/H⁺ antiporters (CAXs) are involved in the translocation of Ca²⁺ and various metal ions in higher plants. In the present study, TuCAX1a and TuCAX1b, two cation/H⁺ antiporters, were isolated from the diploid wheat Triticum urartu, and their metal cation translocation functions investigated. TuCAX1a and TuCAX1b showed abundant tissue-specific expression in the internode and beard, respectively, and their expression levels were increased in shoots exposed to Cd²⁺, Zn²⁺ and Ca²⁺. Plant phenotype analysis showed that overexpression of TuCAX1a and TuCAX1b could improve the tolerance of Arabidopsis to exogenous Ca²⁺ and Zn²⁺. In the plant shoots and roots, the contents of Ca²⁺ and Zn²⁺ were higher than wild-type plants under Ca²⁺ and Zn²⁺ treatments, indicating that TuCAX1a and TuCAX1b can enhance Ca²⁺ and Zn²⁺ translocation. Ca²⁺, Zn²⁺, Mn²⁺ and Fe²⁺ contents showed higher accumulation in TuCAX1b-transgenic Arabidopsis shoots than in wild-type plants exposed to Cd²⁺, and the translocation of Cd²⁺ was inhibited under Ca²⁺ and Zn²⁺. Overall, the present study provides a novel genetic resource for improving the uptake of microelements and reducing accumulation of toxic heavy metals in wheat.

Wheat Cell Number Regulator CNR10 Enhances the Tolerance, Translocation, and Accumulation of Heavy Metals in Plants

Heavy metal contamination affects crop growth and development and can indirectly threaten human health. Therefore, improving the content of microelements and reducing the accumulation of toxic metals by genetic breeding in crops is an effective strategy to solve this environmental problem. Previous reports show plant cadmium resistance (PCR) protein can transport zinc (Zn) and cadmium (Cd). The cell number regulator (CNR) protein, which functions to regulate organ size, has high similarity to, and shares conserved motifs with, PCR. Therefore, CNR may be involved in regulating heavy metal translocation. We isolated TuCNR10 from diploid wheat, Triticum urartu. Real-time quantitative PCR showed TuCNR10 expression increased in the shoots and roots of seedlings under Cd, Zn, and manganese (Mn) stresses. Confocal imaging indicated TuCNR10 was localized at the plasma membrane. Overexpression of TuCNR10 in Arabidopsis and rice enhanced Cd, Zn, and Mn tolerance and improved Cd, Zn, and Mn translocation from roots to shoots. Compared with wild-type rice, rice overexpressing TuCNR10 had lower Cd and higher Zn and Mn contents in grains. These results indicated that TuCNR10 may be a transporter of Cd, Zn, and Mn. TuCNR10 may be a useful genetic resource for microelement fortification and reducing toxic metal accumulation in crops.

Which Genes in a Typical Intertidal Seagrass (Zostera japonica) Indicate Copper-, Lead-, and Cadmium Pollution?

Healthy seagrasses are considered a prime indicator of estuarine and coastal ecosystem function; however, as the only group of flowering plants recolonizing the sea, seagrasses are frequently exposed to anthropogenic heavy metal pollutants, which are associated with high levels of molecular damage. To determine whether biologically relevant concentrations of heavy metals cause systematic alterations in RNA expression patterns, we performed a gene expression study using transcriptome analyses (RNA-seq). We exposed the typical intertidal seagrass Zostera japonica to 0 and 50 μM of copper (Cu), lead (Pb), and cadmium (Cd) under laboratory conditions. A total of 18,266 differentially expressed genes (DEGs) were identified, of which 2001 co-expressed genes directly related by Cu, Pb, and Cd stress. We also examined the effects of short-term heavy metal Cu, Pb, and Cd pulses on the accumulation of metals in Z. japonica and showed metal concentrations were higher in the shoots than in roots. Twelve differentially expressed genes were further analyzed for expression differences using real-time quantitative polymerase chain reaction (RT-qPCR). Our data suggest that as coastal seawater pollution worsens, the sensitive genes identified in this study may be useful biomarkers of sublethal effects and provide fundamental information for Z. japonica resistant gene engineering.

Inorganic Hg toxicity in plants: A comparison of different genotoxic parameters

Inorganic Mercury (Hg) contamination persists an environmental problem, but its cyto- and genotoxicity in plants remains yet unquantified. To determine the extent of Hg-induced cyto- and genotoxicity, and assess most sensitive endpoints in plants, Pisum sativum L. seedlings were exposed for 14 days to different HgCl2 concentrations up to 100 μM. Shoots and roots from hydroponic exposure presented growth impairment and/or morphological disorders for doses >1 μM, being the roots more sensitive. Plant growth, ploidy changes, clastogenicity (HPCV), cell cycle dynamics (G1-S-G2), Comet-tail moment (TM), Comet-TD, Mitotic-index (MI) and cell proliferation index (CPI) were used to evaluate Hg-induced cyto/genotoxicity. Both leaf and root DNA-ploidy levels, assessed by flow cytometry (FCM), remained unaltered after exposure. Root cell cycle impairment occurred at lower doses (≥1 μM) than structural DNA damages (≥10 μM). Cytostatic effects depended on the Hg concentration, with delays during S-phase at lower doses, and arrests at G1 at higher ones. This arrest was paralleled with decreases of both mitotic index (MI) and cell proliferation index (CPI). DNA fragmentation, assessed by the Comet assay parameters of TD and TM, could be visualized for conditions ≥10 μM, while FCM-clastogenic parameter (FPCV) and micronuclei (MNC) were only altered in roots exposed to 100 μM. We demonstrate that inorganic-Hg induced cytostaticity is detectable even at 1 μM (a value found in contaminated sites), while structural DNA breaks/damage are only visualized in plants at concentrations ≥10 μM. We also demonstrate that among the different techniques tested for cyto- and genotoxicity, TD and TM Comet endpoints were more sensitive than FPCV or MNC. Regarding cytostatic effects, cell cycle analysis by FCM, including the difference in % cell cycle phases and CPI were more sensitive than MI or MNC frequency. Our data contribute to better understand Hg cyto- and genotoxicity in plants and to understand the information and sensitivity provided by each of the genotoxic techniques used.

Toxic Effects and Molecular Mechanism of Different Types of Silver Nanoparticles to the Aquatic Crustacean Daphnia magna

Silver nanoparticles (AgNPs) have been assessed to have a high exposure risk for humans and aquatic organisms. Toxicity varies considerably between different types of AgNPs. This study aimed to investigate the toxic effects of AgNPs with different particle sizes (40 and 110 nm) and different surface coatings (sodium citrate and polyvinylpyrrolidone, PVP) on Daphnia magna and their mechanisms of action. The results revealed that the citrate-coated AgNPs were more toxic than PVP-coated AgNPs and that the 40 nm AgNPs were more toxic than the 110 nm AgNPs. Transcriptome analysis further revealed that the toxic effects of AgNPs on D. magna were related to the mechanisms of ion binding and several metabolic pathways, such as the "RNA polymerase" pathway and the "protein digestion and absorption" pathway. Moreover, the principal component analysis (PAC) results found that surface coating was the major factor that determines the toxicities compared to particle size. These results could help us better understand the possible mechanism of AgNP toxicity in aquatic invertebrates at the transcriptome level and establish an important foundation for revealing the broad impacts of nanoparticles on aquatic environments.

Assessment on cadmium and lead in soil based on a rhizosphere microbial community

The soil ecosystem is easily polluted by heavy metals. Cadmium (Cd) and lead (Pb), as the main pollutants of heavy metals, cause much harm to the soil ecosystem. However, the impact of the two chemicals on rhizosphere microorganisms remains almost unknown. The change of catalase (CAT) activity was consistent with the microbial biomass. 16S rRNA gene sequencing was performed on soil samples to study the toxic effect of heavy metals. On performing sequence analysis at the phylum and family taxonomic levels, 32 identified phyla and 303 families were observed. The dominant phylum was Proteobacteria followed by Bacteroidetes, Acidobacteria, and Actinobacteria. The relative abundance of the dominant phyla was obviously changed under the stress of Cd and Pb, suggesting that the heavy metal input had affected the microbial community structure. At the Order and Family levels, there was different variation of richness and diversity in Cd and Pb group as compared to those in the control group. Furthermore, abundance and similarity analysis showed the differences between Cd and Pb, indicating different toxicology effect on rhizosphere microbial communities because of the unique properties. This study provided a novel insight into the composition of microbial communities of rhizosphere, which could be used to evaluate the soil environment.

Influencing Mechanism of Ocean Acidification on Byssus Performance in the Pearl Oyster Pinctada fucata

The byssus is an important adhesive structure by which bivalves robustly adhere to underwater substrates. It is susceptible to carbon dioxide-driven ocean acidification (OA). Previous investigations have documented significant adverse effects of OA on the performance of byssal threads, but the mechanisms remain largely unknown. In this study, multiple approaches were employed to reveal the underlying mechanisms for the effects of OA on byssus production and mechanical properties in the pearl oyster Pinctada fucata. The results showed that OA altered the abundance and secondary structure of byssal proteins and affected the contents of metal ions in distal threads, which together reduced the byssus diameter and amplified byssus nanocavity, causing reductions in mechanical properties (strength and extensibility). Expression analysis of key foot protein genes further confirmed changes in byssal protein abundance. Moreover, comparative transcriptome analysis revealed enrichment of ion transportation- and apoptosis-related categories, up-regulation of apoptosis-related pathways, and down-regulation of the "extracellular matrix-receptor interaction" pathway, which may influence foot locomotion physiology, leading to a decrease in byssus production. This study provides mechanistic insight into the effects of OA on pearl oyster byssus, which should broaden our overall understanding of the impacts of OA on marine ecosystem.

Concentration-dependent alterations in gene expression induced by cadmium in Solanum lycopersicum

Cadmium (Cd) toxicity in agricultural soil has received significant attention because of its higher transformation in the food chain and toxicity to humans. The aim of the present study was to develop sensitive and specific biomarkers for Cd stress. Therefore, transcriptional analyses were performed to investigate concentration-response characteristics of Cd responsive genes identified from a Solanum lycopersicum microarray. The results showed that the lowest observable adverse effect concentrations (LOAECs) of Cd to S. lycopersicum were 1 mg/kg for seed germination, 8 mg/kg for root dry weight, 8 mg/kg for root elongation, and 8 mg/kg for root morphology. Furthermore, the genes were differentially expressed even at the lowest Cd concentrations (0.5 mg/kg), indicating that the detection of Cd in soil at the molecular level is a highly sensitive method. Cd in soil was positively correlated with the expression of the F-box protein PP2-B15 (r = 0.809, p < 0.01) and zinc transporter 4 (r = 0.643, p < 0.01), indicating that these two genes could be selected as indicators of soil Cd contamination.

Microarray analysis and real-time PCR assay developed to find biomarkers for mercury-contaminated soil

The evaluation of mercury (Hg) toxicity in agricultural soil is of great concern because its bioavailability and bioaccumulation in organisms through the food chain can have adverse effects on human health. Therefore, the aim of this study was to develop sensitive biomarkers for Hg stress in agricultural soil. With the results obtained from a high-throughput cDNA microarray, 12 Hg-responsive genes were selected to examine their concentration-dependent responses to Hg stress at different Hg concentrations. The lowest observable adverse effect concentrations (LOAECs) of Hg were 0.8 mg kg-1 for seed germination, 1.6 mg kg-1 for root biomass, 0.8 mg kg-1 for root elongation, and 0.8 mg kg-1 for root morphology, respectively, whereas the lowest Hg treatments (0.1-0.4 mg kg-1) could generally induce differential expression of genes. These results indicated that the detection of Hg in soil at the molecular level is a highly sensitive method. Moreover, the Hg soil content exhibited a significant positive correlation with the relative expression of probable glutathione S-transferase parA (r = 0.637, p = 0.05), chlorophyll a-b binding protein 13, chloroplastic-like (r = 0.689, p = 0.05) and geranylgeranyl pyrophosphate synthase 1 (r = 0.682, p = 0.05), implying that the three genes are good candidates to detect Hg-contaminated soil.

Morphological and transcriptional responses of Lycopersicon esculentum to hexavalent chromium in agricultural soil

The carcinogenic, teratogenic, and mutagenic effects of hexavalent chromium (Cr[VI]) on living organisms through the food chain raise the immediate need to assess the potential toxicological impacts of Cr(VI) on human health. Therefore, the concentration-dependent responses of 12 Cr(VI)-responsive genes selected from a high-throughput Lycopersicon esculentum complementary DNA microarray were examined at different Cr concentrations. The results indicated that most of the genes were differentially expressed from 0.1 mg Cr/kg soil, whereas the lowest-observable-adverse-effect concentrations of Cr(VI) were 1.6 mg Cr/kg soil, 6.4 mg Cr/kg soil, 3.2 mg Cr/kg soil, and 0.4 mg Cr/kg soil for seed germination, root elongation, root biomass, and root morphology, respectively, implying that the transcriptional method was more sensitive than the traditional method in detecting Cr(VI) toxicity. Dose-dependent responses were observed for the relative expression of expansin (p = 0.778), probable chalcone-flavonone isomerase 3 (p = -0.496), and 12S seed storage protein CRD (p = -0.614); therefore, the authors propose the 3 genes as putative biomarkers in Cr(VI)-contaminated soil. Environ Toxicol Chem 2016;35:1751-1758. © 2015 SETAC.

Oxidative stress-induced toxicity of CuO nanoparticles and related toxicogenomic responses in Arabidopsis thaliana

Microarray analysis of toxicogenomic effects of CuO NPs on Arabidopsis thaliana was conducted. Arabidopsis growth was significantly inhibited by CuO NPs (10 and 20 mg/L). CuO NPs (10 and 20 mg/L) caused significant root damage after short-time (0-2 h) exposure while their corresponding Cu(2+) ions (0.80 and 1.35 mg/L) did not show any root damage. After longer exposure times (1 and 2 days), Cu(2+) ions induced obvious root damage, indicating that released Cu(2+) ions from CuO NPs contributed partial toxicity during CuO NPs exposure. After CuO NPs (10 mg/L) exposure for 2 h, reactive oxygen species (ROS) generation in root tips was much higher than that in the corresponding Cu(2+) ions (0.8 mg/L) treatment. The gene ontology categories identified from microarray analysis showed that CuO NPs (10 mg/L) caused 1658 differentially expressed genes (p < 0.01, fold change>3). Of these, 1035 and 623 genes were up-regulated and down-regulated, respectively. 47 genes among all the up-regulated genes were response to oxidative stress, in which 19 genes were also related to "response to abiotic stimulus" and 12 genes were involved in the phenylpropanoid biosynthesis of the KEGG metabolic pathway. The expression of all the selected genes (RHL41, MSRB7, BCB, PRXCA, and MC8) measured using quantitative RT-PCR was consistent with the microarray analysis. CuO NPs contributed much stronger up-regulation of oxidative stress-related genes than the corresponding Cu(2+) ions.

Interactive Effects of Seawater Acidification and Elevated Temperature on the Transcriptome and Biomineralization in the Pearl Oyster Pinctada fucata

Interactive effects of ocean acidification and ocean warming on marine calcifiers vary among species, but little is known about the underlying mechanisms. The present study investigated the combined effects of seawater acidification and elevated temperature (ambient condition: pH 8.1 × 23 °C, stress conditions: pH 7.8 × 23 °C, pH 8.1 × 28 °C, and pH 7.8 × 28 °C, exposure time: two months) on the transcriptome and biomineralization of the pearl oyster Pinctada fucata, which is an important marine calcifier. Transcriptome analyses indicated that P. fucata implemented a compensatory acid-base mechanism, metabolic depression and positive physiological responses to mitigate the effects of seawater acidification alone. These responses were energy-expensive processes, leading to decreases in the net calcification rate, shell surface calcium and carbon content, and changes in the shell ultrastructure. Elevated temperature (28 °C) within the thermal window of P. fucata did not induce significant enrichment of the sequenced genes and conversely facilitated calcification, which was detected to alleviate the negative effects of seawater acidification on biomineralization and the shell ultrastructure. Overall, this study will help elucidate the mechanisms by which pearl oysters respond to changing seawater conditions and predict the effects of global climate change on pearl aquaculture.

Biomarker discovery and gene expression responses in Lycopersicon esculentum root exposed to lead

Gene expression analysis has shown particular promise for the identification of molecular biomarkers that can be used for further evaluation of potential toxicity of chemicals present in agricultural soil. In the study, we focused on the development of molecular markers to detect Pb toxicity in agricultural soil. Using the results obtained from microarray analysis, twelve Pb-responsive genes were selected and tested in different Pb concentrations to examine their concentration-response characteristics using real-time quantitative polymerase chain reaction (RT-qPCR). All the Pb treatments set in our study could generally induce the differential expression of the 12 genes, while the lowest observable adverse effect concentration (LOAEC) of Pb for seed germination, root elongation, biomass and structural modification derived from 1,297, 177, 177, and 1,297 mg Pb/kg soil, respectively, suggesting that the transcriptional approach was more sensitive than the traditional end points of death, growth, and morphology for the evaluation of Pb toxicity. The relative expression of glycoalkaloid metabolism 1 (P=-0.790), ethylene-responsive transcription factor ERF017 (P=-0.686) and CASP-like protein 4C2 (P=-0.652) demonstrates a dose-dependent response with Pb content in roots, implying that the three genes can be used as sensitive bioindicators of Pb stress in Lycopersicon esculentum.

The Transcriptomic Response of Arabidopsis thaliana to Zinc Oxide: A Comparison of the Impact of Nanoparticle, Bulk, and Ionic Zinc

The impact of nanosize was evaluated by comparing of the transcriptomic response of Arabidopsis thaliana roots to ZnO nanoparticles (nZnO), bulk ZnO, and ionic Zn(2+). Microarray analyses revealed 416 up- and 961 down-regulated transcripts (expression difference >2-fold, p [FDR] < 0.01) after a seven-day treatment with nZnO (average particle size 20 nm, concentration 4 mg L(-1)). Exposure to bulk ZnO resulted in 816 up- and 2179 down-regulated transcripts. The most dramatic changes (1711 transcripts up- and 3242 down-regulated) were caused by the presence of ionic Zn(2+) (applied as ZnSO4.7H20 at a concentration of 14.14 mg L(-1), corresponding to the amount of Zn contained in 4 mg L(-1) ZnO). Genes involved in stress response (e.g., to salt, osmotic stress or water deprivation) were the most relatively abundant group of gene transcripts up-regulated by all three Zn treatments while genes involved in cell organization and biogenesis (e.g., tubulins, arabinogalactan proteins) and DNA or RNA metabolism (e.g., histones) were the most relatively abundant groups of down-regulated transcripts. The similarity of the transcription profiles and the increasing number of changed transcripts correlating with the increased concentration of Zn(2+) in cultivation medium indicated that released Zn(2+) may substantially contribute to the toxic effect of nZnO because particle size has not demonstrated a decisive role.