Cadmium-induced genomic instability in Arabidopsis: Molecular toxicological biomarkers for early diagnosis of cadmium stress

Toxicological effects and mechanisms of lithium on growth, photosynthesis and antioxidant system in the freshwater microalga Chromochloris zofingiensis

The growing prevalence of lithium (Li) batteries has drawn public attention to Li as an emerging pollutant. The present study investigates the toxicity of Li+ on Chromochloris zofingiensis, examining physiological, biochemical and omics aspects. Results reveal hormesis effects of Li+ on C. zofingiensis growth. At Li+ concentrations below 5 mg L-1, Li+ can enhance chlorophyll content, mitochondrial activity, and antioxidant capacity, leading to increased dry cell weight and cell number. Conversely, when it exceeded 10 mg L-1, Li+ can reduce chlorophyll content, induce oxidative stress, and disrupt chloroplast and mitochondria structure and function, ultimately impeding cell growth. In addition, under 50 mg L-1 Li+ stress, microalgae optimize absorbed light energy use (increasing Fv/Fm and E TR ) and respond to stress by up-regulating genes in starch and lipid biosynthesis pathways, promoting the accumulation of storage components. Weighted gene co-expression network analysis indicates that peptidylprolyl cis/trans isomerase, GTPase and L-ascorbate oxidase might be the key regulators in response to Li+ stress. This research marks the toxic effects and molecular mechanisms of Li+ on freshwater microalga, which would improve our understanding of Li's toxicology and contributing to the establishment of Li pollution standards.

The role of epigenetic and epitranscriptomic modifications in plants exposed to non-essential metals

Contamination of the soil with non-essential metals and metalloids is a serious problem in many regions of the world. These non-essential metals and metalloids are toxic to all organisms impacting crop yields and human health. Crop plants exposed to high concentrations of these metals leads to perturbed mineral homeostasis, decreased photosynthesis efficiency, inhibited cell division, oxidative stress, genotoxic effects and subsequently hampered growth. Plants can activate epigenetic and epitranscriptomic mechanisms to maintain cellular and organism homeostasis. Epigenetic modifications include changes in the patterns of cytosine and adenine DNA base modifications, changes in cellular non-coding RNAs, and remodeling histone variants and covalent histone tail modifications. Some of these epigenetic changes have been shown to be long-lasting and may therefore contribute to stress memory and modulated stress tolerance in the progeny. In the emerging field of epitranscriptomics, defined as chemical, covalent modifications of ribonucleotides in cellular transcripts, epitranscriptomic modifications are postulated as more rapid modulators of gene expression. Although significant progress has been made in understanding the plant's epigenetic changes in response to biotic and abiotic stresses, a comprehensive review of the plant's epigenetic responses to metals is lacking. While the role of epitranscriptomics during plant developmental processes and stress responses are emerging, epitranscriptomic modifications in response to metals has not been reviewed. This article describes the impact of non-essential metals and metalloids (Cd, Pb, Hg, Al and As) on global and site-specific DNA methylation, histone tail modifications and epitranscriptomic modifications in plants.

Epigenetic Control of Plant Response to Heavy Metals

Plants are sessile organisms that must adapt to environmental conditions, such as soil characteristics, by adjusting their development during their entire life cycle. In case of low-distance seed dispersal, the new generations are challenged with the same abiotic stress encountered by the parents. Epigenetic modification is an effective option that allows plants to face an environmental constraint and to share the same adaptative strategy with their progeny through transgenerational inheritance. This is the topic of the presented review that reports the scientific progress, up to date, gained in unravelling the epigenetic response of plants to soil contamination by heavy metals and metalloids, collectively known as potentially toxic elements. The effect of the microbial community inhabiting the rhizosphere is also considered, as the evidence of a transgenerational transfer of the epigenetic status that contributes to the activation in plants of response mechanisms to soil pollution.

Transcriptomic and Functional Analyses of Two Cadmium Hyper-Enriched Duckweed Strains Reveal Putative Cadmium Tolerance Mechanisms

Cadmium (Cd) is one of the most toxic metals in the environment and exerts deleterious effects on plant growth and production. Duckweed has been reported as a promising candidate for Cd phytoremediation. In this study, the growth, Cd enrichment, and antioxidant enzyme activity of duckweed were investigated. We found that both high-Cd-tolerance duckweed (HCD) and low-Cd-tolerance duckweed (LCD) strains exposed to Cd were hyper-enriched with Cd. To further explore the underlying molecular mechanisms, a genome-wide transcriptome analysis was performed. The results showed that the growth rate, chlorophyll content, and antioxidant enzyme activities of duckweed were significantly affected by Cd stress and differed between the two strains. In the genome-wide transcriptome analysis, the RNA-seq library generated 544,347,670 clean reads, and 1608 and 2045 differentially expressed genes were identified between HCD and LCD, respectively. The antioxidant system was significantly expressed during ribosomal biosynthesis in HCD but not in LCD. Fatty acid metabolism and ethanol production were significantly increased in LCD. Alpha-linolenic acid metabolism likely plays an important role in Cd detoxification in duckweed. These findings contribute to the understanding of Cd tolerance mechanisms in hyperaccumulator plants and lay the foundation for future phytoremediation studies.

Physiological and DNA methylation analysis provides epigenetic insights into kenaf cadmium tolerance heterosis

Soil heavy metal pollution is one of the most challenging problems. Kenaf is an important natural fiber crop with strong heterosis and a higher tolerance to heavy metals. However, little is known about the molecular mechanisms of kenaf heavy metal tolerance, especially the mechanism of genomic DNA methylation regulating heterosis. In this study, kenaf cultivars CP085, CP089, and their hybrid F₁ seedlings were subjected to 300 µM cadmium stress and found obvious heterosis of cadmium resistance in morphology and antioxidant enzyme activity of F₁ hybrid seedlings. Through methylation-sensitive amplification polymorphism (MSAP) analysis, we highlighted that the total DNA methylation level under cadmium decreased by 16.9 % in F₁ and increased by 14.0 % and 3.0 % in parents CP085 and CP089, respectively. The hypomethylation rate was highest (21.84 %), but hypermethylation was lowest (17.24 %) in F₁ compared to parent cultivars. In particular, principal coordinates analysis (PCoA) indicates a significant epigenetic differentiation between F₁ and its parents under cadmium. Furthermore, 21 differentially methylated DNA fragments (DMFs) were analyzed. Especially, the expression of NPF2.7, NADP-ME, NAC71, TPP-D, LRR-RLKs, and DHX51 genes were changed due to cadmium stress and related to cytosine methylation regulation. Finally, the knocked-down of the differentially methylated gene NPF2.7 by virus-induced gene silencing (VIGS) resulted in increased sensitivity of kenaf seedlings under cadmium stress. It is speculated that low DNA methylation levels can regulate gene expression that led to the heterosis of cadmium tolerance in kenaf.

Mitigation mechanism of zinc oxide nanoparticles on cadmium toxicity in tomato

Cadmium (Cd) pollution seriously reduces the yield and quality of vegetables. Reducing Cd accumulation in vegetables is of great significance for improving food safety and sustainable agricultural development. Here, using tomato as the material, we analyzed the effect of foliar spraying with zinc oxide nanoparticles (ZnO NPs) on Cd accumulation and tolerance in tomato seedlings. Foliar spraying with ZnO NPs improved Cd tolerance by increasing photosynthesis efficiency and antioxidative capacity, while it reduced Cd accumulation by 40.2% in roots and 34.5% in leaves but increased Zn content by 33.9% in roots and 78.6% in leaves. Foliar spraying with ZnO NPs also increased the contents of copper (Cu) and manganese (Mn) in the leaves of Cd-treated tomato seedlings. Subsequent metabonomic analysis showed that ZnO NPs exposure alleviated the fluctuation of metabolic profiling in response to Cd toxicity, and it had a more prominent effect in leaves than in roots. Correlation analysis revealed that several differentially accumulated metabolites were positively or negatively correlated with the growth parameters and physiol-biochemical indexes. We also found that flavonoids and alkaloid metabolites may play an important role in ZnO NP-alleviated Cd toxicity in tomato seedlings. Taken together, the results of this study indicated that foliar spraying with ZnO NPs effectively reduced Cd accumulation in tomato seedlings; moreover, it also reduced oxidative damage, improved the absorption of trace elements, and reduced the metabolic fluctuation caused by Cd toxicity, thus alleviating Cd-induced growth inhibition in tomato seedlings. This study will enable us to better understand how ZnO NPs regulate plant growth and development and provide new insights into the use of ZnO NPs for improving growth and reducing Cd accumulation in vegetables.

DNA methylation is enhanced during Cd hyperaccumulation in Noccaea caerulescens ecotype Ganges

In this study, we assess the DNA damage occurring in response to cadmium (Cd) in the Cd hyperaccumulator Noccaea caerulescens Ganges (GA) vs the non-accumulator and close-relative species Arabidopsis thaliana. At this purpose, the alkaline comet assay was utilized to evaluate the Cd-induced variations in nucleoids and the methy-sens comet assay, and semiquantitative real-time (qRT)-PCR were also performed to associate nucleus variations to possible DNA modifications. Cadmium induced high DNA damages in nuclei of A. thaliana while only a small increase in DNA migration was observed in N. caerulescens GA. In addition, in N. caerulescens GA, CpG DNA methylation increase upon Cd when compared to control condition, along with an increase in the expression of MET1 gene, coding for the DNA-methyltransferase. N. caerulescens GA does not show any oxidative stress under Cd treatment, while A. thaliana Cd-treated plants showed an upregulation of transcripts of the respiratory burst oxidase, accumulation of reactive oxygen species, and enhanced superoxide dismutase activity. These data suggest that epigenetic modifications occur in the N. caerulescens GA exposed to Cd to preserve genome integrity, contributing to Cd tolerance.

E2Fs co-participate in cadmium stress response through activation of MSHs during the cell cycle

Cadmium is one of the most common heavy metal contaminants found in agricultural fields. MutSα, MutSβ, and MutSγ are three different MutS-associated protein heterodimer complexes consisting of MSH2/MSH6, MSH2/MSH3, and MSH2/MSH7, respectively. These complexes have different mismatch recognition properties and abilities to support MMR. However, changes in mismatch repair genes (OsMSH2, OsMSH3, OsMSH6, and OsMSH7) of the MutS system in rice, one of the most important food crops, under cadmium stress and their association with E2Fs, the key transcription factors affecting cell cycles, are poorly evaluated. In this study, we systematically categorized six rice E2Fs and confirmed that OsMSHs were the downstream target genes of E2F using dual-luciferase reporter assays. In addition, we constructed four msh mutant rice varieties (msh2, msh3, msh6, and msh7) using the CRISPR-Cas9 technology, exposed these mutant rice seedlings to different concentrations of cadmium (0, 2, and 4 mg/L) and observed changes in their phenotype and transcriptomic profiles using RNA-Seq and qRT-PCR. We found that the difference in plant height before and after cadmium stress was more significant in mutant rice seedlings than in wild-type rice seedlings. Transcriptomic profiling and qRT-PCR quantification showed that cadmium stress specifically mobilized cell cycle-related genes ATR, CDKB2;1, MAD2, CycD5;2, CDKA;1, and OsRBR1. Furthermore, we expressed OsE2Fs in yeasts and found that heterologous E2F expression in yeast strains regulated cadmium tolerance by regulating MSHs expression. Further exploration of the underlying mechanisms revealed that cadmium stress may activate the CDKA/CYCD complex, which phosphorylates RBR proteins to release E2F, to regulate downstream MSHs expression and subsequent DNA damage repairment, thereby enhancing the response to cadmium stress.

Exogenous melatonin enhances soybean (Glycine max (L.) Merr.) seedling tolerance to saline-alkali stress by regulating antioxidant response and DNA damage repair

Saline-alkali (SA) stress induces excessive reactive oxygen species (ROS) accumulation in plant cells, resulting in oxidative damages of membranes, lipids, proteins, and nucleic acids. Melatonin has antioxidant protection effects in living organisms and thus has received a lot of attention. This study aimed to investigate the effect and regulating mechanism of melatonin treatment on soybean tolerance to SA stress. In this study, cultivars Heihe 49 (HH49, SA-tolerant) and Henong 95 (HN95, SA-sensitive) were pot-cultured in SA soil, then treated with MT (0-300 μM) at V1 stage. SA stress induced ROS accumulation and DNA damage in the seedling roots of both cultivars, causing G1/S arrest in HN95 and G2/M arrest in HH49. Melatonin treatment enhanced the activity of antioxidant enzymes in soybean seedling roots and reduced ROS accumulation. Additionally, melatonin treatment upregulated DNA damage repair genes, thus enhancing the reduction of DNA oxidative damage under SA stress. The effects of melatonin treatment were manifested as decreased RAPD polymorphism, 8-hydroxy-2'-deoxyguanine (8-OH-dG) level, and relative density of apurinic sites (AP-sites). Meanwhile, melatonin treatment partially alleviated the SA-induced G1/S arrest in HN95 and G2/M arrest in HH49, thus enhancing soybean seedling tolerance to SA stress.

Multigenerational graphene oxide intoxication results in reproduction disorders at the molecular level of vitellogenin protein expression in Acheta domesticus

The anthropogenic activities may lead to accumulation of graphene oxide (GO) pollution in the environment. Organisms exposed to chronic or multigenerational GO intoxication can present reproduction depletion. Vitellogenin (Vg) has been used as a parameter for evaluating female fertility due to its importance in embryo nutrition. In this study, we used a promising model organism, Acheta domesticus, which was intoxicated with GO in food for three generations. The aim of the study was to investigate the process of Vg synthesis in crickets depending on the exposure time, GO concentration, and age of the females. The results revealed that chronic GO intoxication had adverse effects on the Vg expression pattern. The 1st generation of insects showing low Vg expression was most affected. The 2nd generation of A. domesticus presented a high Vg expression. The last investigated generation seemed to cope with stress caused by GO, and the Vg expression was balanced. We suggest that the epigenetic mechanisms may play a role in the information transfer to the next generations on how to react to the risk factor and keep reproduction at a high rate. We suspect that chronic GO intoxication can disturb the regular formation of the Vg quaternary structure, resulting in consequences for developing an embryo.

The Relationship between Cadmium Toxicity and the Modulation of Epigenetic Traits in Plants

Elevated concentrations of heavy metals such as cadmium (Cd) have a negative impact on staple crop production due to their ability to elicit cytotoxic and genotoxic effects on plants. In order to understand the relationship between Cd stress and plants in an effort to improve Cd tolerance, studies have identified genetic mechanisms which could be important for conferring stress tolerance. In recent years epigenetic studies have garnered much attention and hold great potential in both improving the understanding of Cd stress in plants as well as revealing candidate mechanisms for future work. This review describes some of the main epigenetic mechanisms involved in Cd stress responses. We summarize recent literature and data pertaining to chromatin remodeling, DNA methylation, histone acetylation and miRNAs in order to understand the role these epigenetic traits play in cadmium tolerance. The review aims to provide the framework for future studies where these epigenetic traits may be used in plant breeding and molecular studies in order to improve Cd tolerance.

The exposure of gadolinium at environmental relevant levels induced genotoxic effects in Arabidopsis thaliana (L.)

Rare Earth Elements (REEs) are increasingly being used in agriculture and are also used to produce high end technological devices, thereby increasing their anthropogenic presence in the environment. However, the ecotoxicological mechanism of REEs on organisms is not fully understood. In this study, the effects of gadolinium (Gd) addition on Arabidopsis thaliana (L.) were investigated at both physiological and molecular levels. Four treatments (0, 10, 50 and 200 μmol·L^-1 Gd) were used in the exposure tests. Biomass, root length and chlorophyll content in shoots/roots were measured to investigate the plant's physiological response to Gd stress. Random amplified polymorphic (RAPD)-Polymerase Chain Reaction (PCR) and methylation sensitive arbitrarily primed (MSAP)-PCR were used to investigate changes in genetic variation and DNA methylation of A. thaliana when exposed to Gd. At the physiological level, it was found that low concentration of Gd (10 μmol·L^-1) could significantly increase the plant biomass and root length, while the growth of A. thaliana was significantly inhibited when exposed to 200 μmol·L^-1 of Gd, yet the total soluble protein content in aerial plant parts increased significantly by 24.2% when compared to the control group. Among the 12 primers considered in the RAPD assessment, at the molecular level, only four primers revealed different patterns in their genomic DNA. Compared to the control group, the treatment with 50 μmol·L^-1 of Gd was associated with lower polymorphism, while the treatment with 200 μmol·L^-1 of Gd was associated with higher polymorphism. The polymorphism frequencies for the 50 μmol·L^-1 of Gd and the 200 μmol·L^-1 of Gd were 4.67% and 20.33%, respectively. The MSAP analysis revealed that the demethylation (D) type of Arabidopsis genomic DNA increased significantly under 10 and 50 μmol·L^-1 of Gd, while the methylation (M) type was also significantly increased under 200 μmol·L^-1 of Gd. Generally, the total methylation polymorphism (D+M) increased with an increase of Gd concentration. It was found that high concentrations of Gd appeared to cause DNA damage, but low concentrations of Gd (as low as 10 μmol·L^-1) were associated with DNA methylation change. Further, it was verified by Real time Reverse Transcription PCR (RT-PCR) on the bands detected by the MSAP analysis, that the genes relative to processes including cell cycle, oxidative stress and apoptosis, appeared to be regulated by methylation under Gd stress. These findings reveal new insight regarding ecotoxicity mechanisms of REEs on plants.

Root and Shoot Response to Nickel in Hyperaccumulator and Non-Hyperaccumulator Species

The soil-root interface is the micro-ecosystem where roots uptake metals. However, less than 10% of hyperaccumulators' rhizosphere has been examined. The present study evaluated the root and shoot response to nickel in hyperaccumulator and non-hyperaccumulator species, through the analysis of root surface and biomass and the ecophysiological response of the related aboveground biomass. Ni-hyperaccumulators Alyssoides utriculata (L.) Medik. and Noccaea caerulescens (J. Presl and C. Presl) F.K. Mey. and non-hyperaccumulators Alyssum montanum L. and Thlaspi arvense L. were grown in pot on Ni-spiked soil (0-1000 mg Ni kg^-1, total). Development of root surfaces was analysed with ImageJ; fresh and dry root biomass was determined. Photosynthetic efficiency was performed by analysing the fluorescence of chlorophyll a to estimate the plants' physiological conditions at the end of the treatment. Hyperaccumulators did not show a Ni-dependent decrease in root surfaces and biomass (except Ni 1000 mg kg^-1 for N. caerulescens). The non-hyperaccumulator A. montanum suffers metal stress which threatens plant development, while the excluder T. arvense exhibits a positive ecophysiological response to Ni. The analysis of the root system, as a component of the rhizosphere, help to clarify the response to soil nickel and plant development under metal stress for bioremediation purposes.

Lemna minor, a hyperaccumulator shows elevated levels of Cd accumulation and genomic template stability in binary application of Cd and Ni: a physiological and genetic approach

In this study, to determine whether having potential to be used as hyperaccumulator for Cd and Ni, numerous experiments were designed for conducting assessments for physiological and genotoxic changes along with defining possible alterations on mineral nutrient status of Lemna minor L. by applying Cd-Ni binary treatments (0, 100, 200 and 400 µM). Our study revealed that there were increases in the concentrations of B, Cr, Fe, K, Mg, and Mn whereas decreases were noticed in the concentrations of Na and Zn and the levels of Ca were inversely proportional to Cd-Ni applications showing tendency to increase at the low concentration and to decrease at the high concentration. Randomly Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) analyses revealed that rather than band losses and new band formations, mostly intensity changes in the band profiles, and low polymorphism and high genomic template stability (GTS) were observed. Although, to date, L. minor was defined as an efficient hyperaccumulator/potential accumulator or competent phytoremedial agent by researchers. Our research revealed that L. minor showing high accumulation capability for Cd and having low polymorphism rate and high genomic template stability is a versatile hyperaccumulator, especially for Cd; therefore, highly recommended by us for decontamination of water polluted with Cd. NOVELTY STATEMENTMany studies have been focused on the effects of individual metal ions. However, heavy metal contaminants usually exist as their mixtures in natural aquatic environments. Especially, Cd and Ni coexist in industrial wastes.In this study, the accumulation properties of Lemna minor for both Cd and Ni were investigated and the effects of Cd and Ni on the bioaccumulation of B, Ca, Cu, Fe, Mg, K, Mn, Na, Pb and Zn in L. minor were also determined. This study furthermore aimed to assess the genotoxic effects of Cd and Ni found in being extended concentrations on DNA using the Randomly Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) method.

The cytotoxicity of core-shell or non-shell structure quantum dots and reflection on environmental friendly: A review

Quantum dots are widely applicated into bioindustry and research owing to its superior properties such as broad excitation spectra, narrow bandwidth emission spectra and high resistance to photo-bleaching. However, the toxicity of quantum dots should not be underestimated and aroused widespread concern. The surface properties and size of quantum dots are critical relevant properties on toxicity. Then, the core/shell structure becomes one common way to affect the activity of quantum dots such as enhance biocompatibility and stability. Except those toxicity it induced, the problem it brought into the environment such as the degradation of quantum dot similarly becomes a hot issue. This review initially took a brief scan of current research on the cytotoxicity of QDs and the mechanism behind that over the past five years. Mainly discussion concentrated on the diversity of structure on quantum dots whether played a key role on the cytotoxicty of quantum dots. It also discussed the role of different shells with metal or nonmetal cores and the influence on the environment.

Heavy metals modulate DNA compaction and methylation at CpG sites in the metal hyperaccumulator Arabidopsis halleri

Excess heavy metals affect plant physiology by inducing stress symptoms, however several species have evolved the ability to hyperaccumulate metals in above-ground tissues without phytotoxic effects. In this study we assume that at subcellular level, different strategies were adopted by hyperaccumulator versus the non-accumulator plant species to face the excess of heavy metals. At this purpose the comet assay was used to investigate the nucleoid structure modifications occurring in response to Zn and Cd treatments in the I16 and PL22 populations of the hyperaccumulator Arabidopsis halleri versus the nonaccumulator species Arabidopsis thaliana. Methy-sens comet assay and RT-qPCR were also performed to associate metal induced variations in nucleoids with possible epigenetic modifications. The comet assay showed that Zn induced a mild but non significant reduction in the tail moment in A. thaliana and in both I16 and PL22. Cd treatment induced an increase in DNA migration in nuclei of A. thaliana, whereas no differences in DNA migration was observed for I16, and a significant increase in nucleoid condensation was found in PL22 Cd treated samples. This last population showed higher CpG DNA methylation upon Cd treatment than in control conditions, and an up-regulation of genes involved in symmetric methylation and histone deacetylation. Our data support the hypothesis of a possible role of epigenetic modifications in the hyperaccumulation trait to cope with the high Cd shoot concentrations. In addition, the differences observed between PL22 and I16 could reinforce previous suggestions of divergent strategies for metals detoxification developing in the two metallicolous populations.

DNA damage in Spodoptera exigua after multigenerational cadmium exposure - A trade-off between genome stability and adaptation

Human activity is a serious cause of extensive changes in the environment and a constant reason for the emergence of new stress factors. Thus, to survive and reproduce, organisms must constantly implement a program of adaptation to continuously changing conditions. The research presented here is focused on tracking slow changes occurring in Spodoptera exigua (Lepidoptera: Noctuidae) caused by multigenerational exposure to sub-lethal cadmium doses. The insects received food containing cadmium at concentrations of 5, 11, 22 and 44 μg per g of dry mass of food. The level of DNA stability was monitored by a comet assay in subsequent generations up to the 36th generation. In the first three generations, the level of DNA damage was high, especially in the groups receiving higher doses of cadmium in the diet. In the fourth generation, a significant reduction in the level of DNA damage was observed, which could indicate that the desired stability of the genome was achieved. Surprisingly, however, in subsequent generations, an alternating increase and decrease was found in DNA stability. The observed cycles of changing DNA stability were longer lasting in insects consuming food with a lower Cd content. Thus, a transient reduction in genome stability can be perceived as an opportunity to increase the number of genotypes that undergo selection. This phenomenon occurs faster if the severity of the stress factor is high but is low enough to allow the population to survive.

Transcriptome analysis provides molecular evidences for growth and adaptation of plant roots in cadimium-contaminated environments

Cadmium (Cd) is a detrimental element that can be toxic to plants. The physiological and biochemical responses of plants to Cd stress have been extensively studied, but the molecular mechanisms remain unclear. The present study showed that Cd severely inhibited the growth of roots and shoots and reduced plant biomass of mung bean seedlings. To further investigate the gene profiles and molecular processes in response Cd stress, transcriptome analyses of mung bean roots exposed to 100 μM Cd for 1, 5, and 9 days were performed. Cd treatment significantly decreased global gene expression levels at 5 and 9 d compared with the control. A total of 6737, 10279, and 9672 differentially expressed genes (DEGs) were identified in the 1-, 5-, and 9-day Cd-treated root tissues compared with the controls, respectively. Based on the analysis of DEG function annotation and enrichment, a pattern of mung bean roots response to Cd stress was proposed. The processes detoxification and antioxidative defense were involved in the early response of mung bean roots to Cd. Cd stress downregulated the expressions of a series of genes involved in cell wall biosynthesis, cell division, DNA replication and repair, and photosynthesis, while genes involved in signal transduction and regulation, transporters, secondary metabolisms, defense systems, and mitochondrial processes were upregulated in response to Cd, which might be contributed to the improvement of plant tolerance. Our results provide some novel insights into the molecular processes for growth and adaption of mung bean roots in response to Cd and many candidate genes for further biotechnological manipulations to improve plant tolerance to heavy metals.

Mechanisms used by DNA MMR system to cope with Cadmium-induced DNA damage in plants

Cadmium (Cd) is found widely in soil and is severely toxic for plants, causing oxidative damage in plant cells because of its heavy metal characteristics. The DNA damage response (DDR) is triggered in plants to cope with the Cd stress. The DNA mismatch repair (MMR) system known for its mismatch repair function determines DDR, as mispairs are easily generated by a translesional synthesis under Cd-induced genomic instability. Cd-induced mismatches are recognized by three heterodimeric complexes including MutSα (MSH2/MSH6), MutSβ (MSH2/MSH3), and MutSγ (MSH2/MSH7). MutLα (MLH1/PMS1), PCNA/RFC, EXO1, DNA polymerase δ and DNA ligase participate in mismatch repair in turn. Meanwhile, ATR is preferentially activated by MSH2 to trigger DDR including the regulation of the cell cycle, endoreduplication, cell death, and recruitment of other DNA repair, which enhances plant tolerance to Cd. However, plants with deficient MutS will bypass MMR-mediated DDR and release the multiple-effect MLH1 from requisition of the MMR system, which leads to weak tolerance to Cd in plants. In this review, we systematically illustrate how the plant DNA MMR system works in a Cd-induced DDR, and how MMR genes regulate plant tolerance to Cd. Additionally, we also reviewed multiple epigenetic regulation systems acting on MMR genes under stress.

Suppressor of Gamma Response 1 Modulates the DNA Damage Response and Oxidative Stress Response in Leaves of Cadmium-Exposed Arabidopsis thaliana

Cadmium (Cd) exposure causes an oxidative challenge and inhibits cell cycle progression, ultimately impacting plant growth. Stress-induced effects on the cell cycle are often a consequence of activation of the DNA damage response (DDR). The main aim of this study was to investigate the role of the transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) and three downstream cyclin-dependent kinase inhibitors of the SIAMESE-RELATED (SMR) family in the Cd-induced DDR and oxidative challenge in leaves of Arabidopsis thaliana. Effects of Cd on plant growth, cell cycle regulation and the expression of DDR genes were highly similar between the wildtype and smr4/5/7 mutant. In contrast, sog1-7 mutant leaves displayed a much lower Cd sensitivity within the experimental time-frame and significantly less pronounced upregulations of DDR-related genes, indicating the involvement of SOG1 in the Cd-induced DDR. Cadmium-induced responses related to the oxidative challenge were disturbed in the sog1-7 mutant, as indicated by delayed Cd-induced increases of hydrogen peroxide and glutathione concentrations and lower upregulations of oxidative stress-related genes. In conclusion, our results attribute a novel role to SOG1 in regulating the oxidative stress response and connect oxidative stress to the DDR in Cd-exposed plants.

MSH2 and MSH6 in Mismatch Repair System Account for Soybean (Glycine max (L.) Merr.) Tolerance to Cadmium Toxicity by Determining DNA Damage Response

Our aim was to investigate DNA mismatch repair (MMR) genes regulating cadmium tolerance in two soybean cultivars. Cultivars Liaodou 10 (LD10, Cd-sensitive) and Shennong 20 (SN20, Cd-tolerant) seedlings were grown hydroponically on Murashige and Skoog (MS) media containing 0-2.5 mg·L-1 Cd for 4 days. Cd stress induced less random amplified polymorphism DNA (RAPD) polymorphism in LD10 than in SN20 roots, causing G1/S arrest in LD10 and G2/M arrest in SN20 roots. Virus-induced gene silencing (VIGS) of MLH1 in LD10-TRV-MLH1 plantlets showed markedly diminished G1/S arrest but enhanced root length/area under Cd stress. However, an increase in G1/S arrest and reduction of G2/M arrest occurred in SN20-TRV-MSH2 and SN20-TRV-MSH6 plantlets with decreased root length/area under Cd stress. Taken together, we conclude that the low expression of MSH2 and MSH6, involved in the G2/M arrest, results in Cd-induced DNA damage recognition bypassing the MMR system to activate G1/S arrest with the assistance of MLH1. This then leads to repressed root growth in LD10, explaining the intervarietal difference in Cd tolerance in soybean.

Prospects for incorporation of epigenetic biomarkers in human health and environmental risk assessment of chemicals

Epigenetic mechanisms have gained relevance in human health and environmental studies, due to their pivotal role in disease, gene × environment interactions and adaptation to environmental change and/or contamination. Epigenetic mechanisms are highly responsive to external stimuli and a wide range of chemicals has been shown to determine specific epigenetic patterns in several organisms. Furthermore, the mitotic/meiotic inheritance of such epigenetic marks as well as the resulting changes in gene expression and cell/organismal phenotypes has now been demonstrated. Therefore, epigenetic signatures are interesting candidates for linking environmental exposures to disease as well as informing on past exposures to stressors. Accordingly, epigenetic biomarkers could be useful tools in both prospective and retrospective risk assessment but epigenetic endpoints are currently not yet incorporated into risk assessments. Achieving a better understanding on this apparent impasse, as well as identifying routes to promote the application of epigenetic biomarkers within environmental risk assessment frameworks are the objectives of this review. We first compile evidence from human health studies supporting the use of epigenetic exposure-associated changes as reliable biomarkers of exposure. Then, specifically focusing on environmental science, we examine the potential and challenges of developing epigenetic biomarkers for environmental fields, and discuss useful organisms and appropriate sequencing techniques to foster their development in this context. Finally, we discuss the practical incorporation of epigenetic biomarkers in the environmental risk assessment of chemicals, highlighting critical data gaps and making key recommendations for future research within a regulatory context.

Inhibition of DNA demethylation enhances plant tolerance to cadmium toxicity by improving iron nutrition

Although the alteration of DNA methylation due to abiotic stresses, such as exposure to the toxic metal cadmium (Cd), has been often observed in plants, little is known about whether such epigenetic changes are linked to the ability of plants to adapt to stress. Herein, we report a close linkage between DNA methylation and the adaptational responses in Arabidopsis plants under Cd stress. Exposure to Cd significantly inhibited the expression of three DNA demethylase genes ROS1/DML2/DML3 (RDD) and elevated DNA methylation at the genome-wide level in Col-0 roots. Furthermore, the profile of DNA methylation in Cd-exposed Col-0 roots was similar to that in the roots of rdd triple mutants, which lack RDD, indicating that Cd-induced DNA methylation is associated with the inhibition of RDD. Interestingly, the elevation in DNA methylation in rdd conferred a higher tolerance against Cd stress and improved cellular Fe nutrition in the root tissues. In addition, lowering the Fe supply abolished improved Cd tolerance due to the lack of RDD in rdd. Together, these data suggest that the inhibition of RDD-mediated DNA demethylation in the roots by Cd would in turn enhance plant tolerance to Cd stress by improving Fe nutrition through a feedback mechanism.

Protective role of zinc in Spodoptera exigua larvae under 135-generational cadmium exposure

The aim of this study was to investigate whether zinc supplementation modulates cadmium toxicity in the beet armyworm Spodoptera exigua selected for 135 generations towards cadmium tolerance. To achieve this, larvae originating from three laboratory populations of S. exigua (control strain - C; cadmium-intoxicated for 135 generations strain - Cd, and control strain intoxicated with Cd for 1 generation - CCd) were additionally exposed to zinc in three concentrations (Zn1, 400 μg Zn·g^-1 dry mass of food; Zn2; 200 μg Zn·g^-1 dry mass of food; Zn3, 100 μg Zn·g^-1 dry mass of food). As the markers of toxicity, a life history traits (the duration of L4 and L5 stages), cellular (DNA damage indices) and biochemical parameters (ADP/ATP ratio and ATP and HSP70 concentrations) were chosen. The duration of larval stages of Zn supplemented larvae was prolonged, while cellular and biochemical indicators, in general, appeared to be lower in comparison to the insects from respective reference groups in each laboratory populations. Moreover, the range of the differences depended on zinc concentration in food. We can suspect that zinc supplementation contributed to the protection of S. exigua individuals against negative effects of cadmium intoxication, probably at the cost of growth rate. Significant differences in the response pattern between insects from different laboratory populations indicate that the influence of additional stress factors is dependent on the overall condition of animals and their previous adaptation to other stressors.

The corrosion process caused by the activity of the anaerobic sporulated bacterium Clostridium celerecrescens on API XL 52 steel

The microbial corrosion of oil and gas pipes is one of the problems occurring in the oil industry. Various mechanisms explaining microbial corrosion have been demonstrated. Commonly, biocorrosion is attributed to sulfate-reducing bacteria. Also, it has recently been reported that microbial species can connect their electron transport system to metal electrodes. In this research, two spore-forming bacteria isolated in different years from a gas pipeline were identified by biochemical techniques and by 16S rDNA amplification, sequencing, and comparison with the NCBI database. Isolates were also compared between them using molecular techniques as the restriction patterns, unique for 16S rDNA (ARDRA), and the profile of the amplified bit from the genomic DNA, using an unspecific primer (RAPD). The results obtained showed that both isolates corresponded to Clostridium celerecrescens with a 99% similarity according to the sequence reported on the NCBI database. Also, the ARDRA and RAPD electrophoretic profiles of both strains were identical, and no plasmids were found in the strains. Thus, it can be settled that this bacterium is persistent in the environment prevailing in gas pipelines. Also, it was demonstrated that the bacterial secretion of organic acids contributes to the pitting and general biocorrosion of API XL 52 steel. The rates of corrosion obtained, approximately after 40 days, were correlated with the presence and metabolic activity of C. celerecrescens on the metallic surfaces.

Cadmium and Plant Development: An Agony from Seed to Seed

Anthropogenic pollution of agricultural soils with cadmium (Cd) should receive adequate attention as Cd accumulation in crops endangers human health. When Cd is present in the soil, plants are exposed to it throughout their entire life cycle. As it is a non-essential element, no specific Cd uptake mechanisms are present. Therefore, Cd enters the plant through transporters for essential elements and consequently disturbs plant growth and development. In this review, we will focus on the effects of Cd on the most important events of a plant's life cycle covering seed germination, the vegetative phase and the reproduction phase. Within the vegetative phase, the disturbance of the cell cycle by Cd is highlighted with special emphasis on endoreduplication, DNA damage and its relation to cell death. Furthermore, we will discuss the cell wall as an important structure in retaining Cd and the ability of plants to actively modify the cell wall to increase Cd tolerance. As Cd is known to affect concentrations of reactive oxygen species (ROS) and phytohormones, special emphasis is put on the involvement of these compounds in plant developmental processes. Lastly, possible future research areas are put forward and a general conclusion is drawn, revealing that Cd is agonizing for all stages of plant development.

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.

Cadmium and/or copper excess induce interdependent metal accumulation, DNA methylation, induction of metal chelators and antioxidant defences in the seagrass Zostera marina

In this investigation, we assessed the effects of Cu and/or Cd excess on physiological and metabolic processes of the widespread seagrass Zostera marina. Adult were exposed to low Cd and Cu (0.89 and 0.8 μM, respectively) and high Cd and Cu (8.9 and 2.4 μM, respectively) for 6 d at: Control conditions; low Cu; high Cu; low Cd; high Cd; low Cd and low Cu; and high Cd and high Cu. Photosynthetic performance decreased under single and combined treatments, although effects were more negative under Cu than Cd. Total Cu accumulation was higher than Cd, under single and combined treatments; however, their accumulation was generally lower when applied together, suggesting competition among them. Levels of glutathione (GSH) and phytochelatins (PCs) followed patterns similar to metal accumulation, with up to PC5, displaying adaptations in tolerance. A metallothionein (MET) gene showed upregulation only at high Cd, low Cu, and high Cu. The expression of the enzymes glutathione reductase (GR), ascorbate peroxidase (APX), and catalase (CAT) was greatest at high Cu, and at high Cd and Cu together; the highest expression was under Cu, alone and combined. Both metals induced upregulation of the DNA methyltransferases CMT3 and DRM2, with the highest expression at single Cu. The DNA demethylation ROS1 was overexpressed in treatments containing high Cu, suggesting epigenetic modifications. The results show that under copper and/or cadmium, Z. marina was still biologically viable; certainly based, at least in part, on the induction of metal chelators, antioxidant defences and methylation/demethylation pathways of gene regulation.

Genetic impacts induced by BaP and Pb in Mytilus coruscus: Can RAPD be a validated tool in genotoxicity evaluation both in vivo and in vitro?

Benzo(α)pyrene (BaP) and lead (Pb) are common pollutants discharged greatly in ocean and causing detrimental impacts on marine organisms. Although mussels are one of the most prominent and frequently studied biological models, the research on their genomic alterations induced by the mixture of two totally different chemicals, is still rare. In present study, local marine mussels Mytilus coruscus were exposed in vivo to BaP (53.74 ± 19.79 μg/L), Pb (2.58 ± 0.11 mg/L) and their mixture for 6 days. The genotoxic damages were assessed by comet assay, micronucleus (MNi) test, and random amplified polymorphic DNA (RAPD) analysis. Significantly increased though transitory genomic damage was investigated after the exposure and showed consistency using various detecting methods. Additive genotoxicity was only found after 3 days combined exposure by means of MNi test, suggesting that BaP and Pb may play with alternative biological targets during metabolism and/or interaction with the genome. The geno-stability and the recovery capability were further detected both in vivo and in vitro after challenged by BaP. RAPD results showed coherence in BaP induced genotoxicity, together with time-specific alterations. The genomic instability was found to recover in both in vivo and in vitro exposure scenarios in present study. To our knowledge, this is the first study to focus on the genotoxicitiy induced by BaP, Pb and their mixture by multiple detecting techniques. The attempt to utilize model pollutants and marine organism to validate the potential value of RAPD analysis highlighted that it might be a useful tool in the research of genotoxicology, especially on the effect-mechanism interplay at genetic level.

Epigenetic modifications preserve the hyperaccumulator Noccaea caerulescens from Ni geno-toxicity

The Ni hyperaccumulator Noccaea caerulescens has adapted to live in a naturally stressed environment, evolving a complex pattern of traits to cope with adverse conditions. Evidence is accumulating regarding the important role of epigenetic modifications in regulating plant responses to stress. In this study, we present data from the natural "open-field" adaptation of the Ni hyperaccumulator N. caerulescens to serpentine soil and provide the first evidence of the involvement of epigenetic changes in response to the high Ni content present in plant leaves. The alkaline comet assay revealed the integrity of the nuclei of leaf cells of N. caerulescens grown in a Ni-rich environment, while in the non-tolerant Arabidopsis thaliana exposed to Ni, the nuclei were severely damaged. DNA of N. caerulescens plants grown in situ were considerably hyper-methylated compared to A. thaliana plants exposed to Ni. In addition, qRT-PCR revealed that N. caerulescens MET1, DRM2, and HDA8 genes involved in epigenetic DNA and histone modification were up-regulated in the presence of high Ni content in leaves. Such epigenetic modifications may constitute a defense strategy that prevents genome instability and direct damage to the DNA structure by Ni ion, enabling plants to survive in an extreme environment. Further studies will be necessary to analyze in detail the involvement of DNA methylation and other epigenetic mechanisms in the complex process of metal hyperaccumulation and plants' adaptive response. Environ. Mol. Mutagen. 59:464-475, 2018. © 2018 Wiley Periodicals, Inc.

Pouteria torta: a native species of the Brazilian Cerrado as a bioindicator of glyphosate action

In Brazil, the expansion of agricultural activity and the associated indiscriminate use of herbicides such as glyphosate is directly related to the loss of biodiversity in the Cerrado. The identification of plant species as bioindicators of herbicide action, especially species native to the area, can help in monitoring the impacts of xenobiotics in the remaining Cerrado. Thus, this study was designed to evaluate the possible use of the native Cerrado species Pouteria torta as a bioindicator of glyphosate action via changes in physiological performance. At 16 months after sowing, the effect of glyphosate was evaluated by applying the following doses: 0 (control), 25, 50, 100, 200, 400, 800, and 1200 g a.e. ha-1. In response to glyphosate, P. torta exhibited reductions in photosynthesis and chloroplastid pigment content, as well as accumulation of shikimic acid and the occurrence of chlorosis and necrosis. These changes demonstrate the high sensitivity of P. torta to glyphosate and its potential for use as a bioindicator of this herbicide.

Comparative transcriptome analysis of duckweed (Landoltia punctata) in response to cadmium provides insights into molecular mechanisms underlying hyperaccumulation

Cadmium (Cd) is a detrimental environmental pollutant. Duckweeds have been considered promising candidates for Cd phytoremediation. Although many physiological studies have been conducted, the molecular mechanisms underlying Cd hyperaccumulation in duckweeds are largely unknown. In this study, clone 6001 of Landoltia punctata, which showed high Cd tolerance, was obtained by large-scale screening of over 200 duckweed clones. Subsequently, its growth, Cd flux, Cd accumulation, and Cd distribution characteristics were investigated. To further explore the global molecular mechanism, a comprehensive transcriptome analysis was performed. For RNA-Seq, samples were treated with 20 μM CdCl₂ for 0, 1, 3, and 6 days. In total, 9,461, 9,847, and 9615 differentially expressed unigenes (DEGs) were discovered between Cd-treated and control (0 day) samples. DEG clustering and enrichment analysis identified several biological processes for coping with Cd stress. Genes involved in DNA repair acted as an early response to Cd, while RNA and protein metabolism would be likely to respond as well. Furthermore, the carbohydrate metabolic flux tended to be modulated in response to Cd stress, and upregulated genes involved in sulfur and ROS metabolism might cause high Cd tolerance. Vacuolar sequestration most likely played an important role in Cd detoxification in L. punctata 6001. These novel findings provided important clues for molecular assisted screening and breeding of Cd hyperaccumulating cultivars for phytoremediation.

Biochemical and Genetical Responses of Phoenix dactylifera L. to Cadmium Stress

The cadmium (Cd), a heavy metal, causes toxicity, which leads to hampering the growth and development of the plant. The molecular and biochemical approaches were used for the investigation of antioxidant system response and genotoxicity in date palm (Phoenix dactylifera L.) cv. Sagai in pot experiment having Cd. The root length was more affected than the shoot length as more accumulation of Cd occurs in roots. Fresh weights of root and shoot were reduced significantly in treated plants as compared to the control. The proline content was increased at low concentration of Cd (300 µM-CdCl2) than the medium and high concentrations (600 and 900 µM-CdCl2), respectively. The thiobarbituric acid reactive substances (TBARS) content was increased at 600 and 900 µM-CdCl2 compared to the plants treated at 300 µM-CdCl2 and controls. Antioxidant enzymatic assay was performed under Cd stress and compared with control plants. The catalase (CAT) and superoxide dismutase (SOD) activities were found to be high in plants treated with CdCl2 at 300 µM compared to at 600 and 900 µM-CdCl2, respectively. The genotoxicity of Cd was assessed using the inter-simple sequence repeat (ISSR) marker where all treated and control plants were clustered into three main groups based on genetic similarity. P. dactylifera plants were found to be more divergent at high Cd stress as compared to control and plants treated at low concentration of Cd.

Incorporating Transgenerational Epigenetic Inheritance into Ecological Risk Assessment Frameworks

Chronic exposure to environmental contaminants can induce heritable "transgenerational" modifications to organisms, potentially affecting future ecosystem health and functionality. Incorporating transgenerational epigenetic heritability into risk assessment procedures has been previously suggested. However, a critical review of existing literature yielded numerous studies claiming transgenerational impacts, with little compelling evidence. Therefore, contaminant-induced epigenetic inheritance may be less common than is reported in the literature. We identified a need for multigeneration epigenetic studies that extend beyond what could be deemed "direct exposure" to F1 and F2 gametes and also include subsequent multiple nonexposed generations to adequately evaluate transgenerational recovery times. Also, increased experimental replication is required to account for the highly variable nature of epigenetic responses and apparent irreproducibility of current studies. Further, epigenetic end points need to be correlated with observable detrimental organism changes before a need for risk management can be properly determined. We suggest that epigenetic-based contaminant studies include concentrations lower than current "EC_10-20" or "Lowest Observable Effect Concentrations" for the organism's most sensitive phenotypic end point, as higher concentrations are likely already regulated. Finally, we propose a regulatory framework and optimal experimental design that enables transgenerational epigenetic effects to be assessed and incorporated into conventional ecotoxicological testing.

Effect of cadmium on cytosine hydroxymethylation in gastropod hepatopancreas

5-Hydroxymethylcytosine (5hmC) is an important, yet poorly understood epigenetic DNA modification, especially in invertebrates. Aberrant genome-wide 5hmC levels have been associated with cadmium (Cd) exposure in humans, but such information is lacking for invertebrate bioindicators. Here, we aimed to determine whether this epigenetic mark is present in DNA of the hepatopancreas of the land snail Cantareus aspersus and is responsive to Cd exposure. Adult snails were reared under laboratory conditions and exposed to graded amounts of dietary cadmium for 14 days. Weight gain was used as a sublethal endpoint, whereas survival as a lethal endpoint. Our results are the first to provide evidence for the presence of 5hmC in DNA of terrestrial mollusks; 5hmC levels are generally low with the measured values falling below 0.03%. This is also the first study to investigate the interplay of Cd with DNA hydroxymethylation levels in a non-human animal study system. Cadmium retention in the hepatopancreas of C. aspersus increased from a dietary Cd dose of 1 milligram per kilogram dry weight (mg/kg d. wt). For the same treatment, we identified the only significant elevation in percentage of samples with detectable 5hmC levels despite the lack of significant mortalities and changes in weight gain among treatment groups. These findings indicate that 5hmC is an epigenetic mark that may be responsive to Cd exposure, thereby opening a new aspect to invertebrate environmental epigenetics.