Identification and gene expression analysis of cytosine-5 DNA methyltransferase and demethylase genes in Amaranthus cruentus L. under heavy metal stress

Abstract

Amaranth has become increasingly popular due to its highly nutritious grains and ability to tolerate environmental stress. The mechanism underlying defense and adaptation to environmental stress is a complicated process involving DNA methylation and demethylation. These epigenetic features have been well documented to play an important role in plant stress response, including heavy metal-induced stress. This study was aimed at the identification and analysis of cytosine-5 DNA methyltransferase (C5-MTase) and demethylase (DMTase) genes in Amaranthus cruentus. Eight C5-MTase and two DMTase genes were identified and described in response to individual heavy metals (Cd, Pb, Zn, Mn) and their combination (Cd/Pb, Cd/Zn, Pb/Zn) in root and leaf tissues. Studied heavy metals, individually and in combinations, differentially regulated C5-MTase and DMTase gene expression. Interestingly, most of the genes were transcriptionally altered under Zn exposure. Our results suggest that identified amaranth MTase and DMTase genes are involved in heavy metal stress responses through regulating DNA methylation and demethylation level in amaranth plants.

Molecular characterization and expression analysis of DNA methyltransferase genes during kiwifruit ripening

“…Subcellular localization prediction results presented that thirteen kiwifruit DNMTs were localized in nucleus, two in the chloroplast and one in plasma membrane (Table 1). Similarly, most DNMTs were also located in the nucleus in other plant species, such as wheat (Gahlaut et al, 2020), pineapple (Lin et al, 2022), and amaranth (Lancíková et al, 2023). Due to the importance of protein subcellular localization in determining its function, these predictions offered a clue for possible functions of these DNMTs.…”

“…Nitric oxide enhanced the cold tolerance of peach fruit via mediating DNA methylation (Guo et al, 2023). MTases and DMTases took part in heavy metal stress via controlling DNA methylation levels in amaranth (Lancíková et al, 2023).…”

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

“…Mutants deficient in ROS1 , DML2 and DML3 expression were characterized by higher metal tolerance and lower Cd uptake. In Amaranthus cruentus the expression of eight methylases ( AcDRM2a , AcDRM2b , AcCMT1 , AcCMT2a , AcCMT2b , AcCMT3, AcMET1a and AcMET1b ) and two demethylases ( AcDML2a and AcDML2b ) was assessed under optimal conditions and in response to metal treatment ( Lancíková et al., 2023 ). The most pronounced response was observed in the roots, which constitute the first site of metal action.…”

“…There are convincing premises indicating that these changes can be related to the enhancement of metal tolerance. For example, the metal hyperaccumulator Noccaea caerulescens showed higher DNA methylation level and lower DNA damage when compared with more sensitive but closely related plant species, Arabidopsis thaliana ( Lancíková et al., 2023 ). Differential methylation patterns and higher metal tolerance was also evidenced in kenaf F 1 hybrid when compared with the parental cultivars ( Luo et al., 2023 ).…”

Epigenetic Changes Occurring in Plant Inbreeding

“…For the same purpose, recombinant inbred lines (RIL) from germplasm with high epigenetic diversity are applied [ 15 ]. Another source of natural epigenetic variation are stress-induced changes [ 16 , 17 , 18 ]. One of the strategies used to obtain epigenetic variation is a targeted epigenetic modification, which uses systems such as TALE, ZF proteins or CRISPR-Cas9 to edit the epigenome, enabling changes in the gene expression, e.g., to improve agricultural properties [ 19 , 20 , 21 ].…”