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

Abstract

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.

Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology

“…In Hibiscus cannabinus , increased methylation was associated with increasing chromium levels (Ding et al 2016). In Arabidopsis halleri , cadmium treatments increased CpG methylation of genes responsible for symmetric methylation (Galati et al 2021). In rice, a model for nutrient stress, the expression of Heavy Metal Transporting ATPases (HMAs) was modified and retained over generations and modulated by the methylation of specific TEs (Cong et al 2019).…”

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

“…In particular, the Ganges (GA) ecotype has shown superior Cd accumulation and hypertolerance when compared to other populations studied so far (Assuncão et al 2003). In a previous work, we used alkaline and methy-sens comet assays to show that the Cd hyperacculator and hypertolerant species Arabidopsis halleri, differently to the non-tolerant species Arabidopsis thaliana, condenses its nucleus by DNA methylation in response to Cd treatment, suggesting a role of DNA methylation for proper plant development (Galati et al 2021). In this work, we compared the Cd response in N. caerulescens GA vs the non-tolerant A. thaliana analyzing i) the possible DNA damages by alkaline comet assay; ii) the modulation of DNA methylation by methy-sens comet assay; iii) the superoxide dismutase (SOD) activity and ROS production, measuring the three oxidative stress biomarkers, H 2 O 2 , 7,8-Dihydro-8-oxo-2′-deoxyguanosine (8-oxo-dG) and superoxide anion; and iv) the expression of genes involved in symmetric and non-symmetric DNA methylation and genes coding for enzymes linked to oxidative stress response.…”

“…This assay enables to detect DNA damage even at low concentrations of contaminants (Rodriguez et al 2019) and allows the identification of modifications in the DNA that alters the supercoiling of the molecule, since loops move towards the anode during electrophoresis (Tice et al 2000). In a previous work, the comet assay was employed to compare the effects of Cd exposure on the integrity of leaf cell nuclei in the Cd hypertolerant and hypercaccumulator species Arabidopsis halleri PL22 vs the non-tolerant species A. thaliana, showing a highly condensed nucleus in the hyperacculator species upon Cd treatment and a nucleus degradation in the non-tolerant one (Galati et al 2021). A similar result was observed in the Ni hyperaccumulator N. caerulescens Monte Prinzera population vs the non-tolerant A. thaliana.…”

“…Most known taxa accumulate Ni but few taxa are capable of accumulating Cd 100 times more than the level of toxicity of non-tolerant plants (Manara et al 2020). To better understand the role of DNA methylation in metal tolerance and toxicity, metal hypertolerant and hyperaccumulating species can be used as models (Galati et al 2021;Gullì et al 2018). In particular, the cruciferous plant Noccaea caerulescens is a well-known metal hyperaccumulator.…”

Molecular basis of intraspecific differentiation for heavy metal tolerance in the copper moss Scopelophila cataractae

“…So far, experimental evidence on the contribution of epigenetic mechanisms to plant heavy metal tolerance has shown that DNA methylation could have a direct protective role. For example, metal tolerant plants like Arabidopsis halleri -in response to Cd -and Noccaea caerulescens -in response to Ni showed hypermethylation of DNA and no heavy metal-induced DNA damage 34,35 . Non-tolerant species like the moss Physcomitrium patens , however, showed overall DNA hypomethylation and significant signs of DNA strand breaks in response to Mn 36 .…”