Integrated physiological, transcriptome-wide m6A methylation and proteome analysis reveals molecular mechanisms of tomato root response to cadmium stress

Soil cadmium pollution has increasingly become a serious problem for crop production, which drastically attenuates plant growth and food safety. Although N 6 -methyladenosine (m 6 A) methylation is crucial for plant response to various stresses, the regulatory mechanism underlying m 6 A modification during cadmium (Cd) stress remains unclear. This study investigated the physiological responses, transcriptome-wide m 6 A methylome, and proteome changes in tomato roots exposed to 50 μmol · L −1 CdCl 2 . Excess Cd restricted plant growth, altered the antioxidant system and disrupted mineral nutrient absorption. We identified a negative correlation between m 6 A levels and gene transcription for that 150 out of 198 differentially expressed genes (DEGs) were hypomethylated but mRNA up-regulated. Cd stress also enhanced translational efficiency, particularly for differentially abundant proteins (DAPs). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially m 6 A modified genes (DMGs), DEGs, and DAPs were commonly enriched in phenylpropanoid biosynthesis, glutathione metabolism, and ABC transporters, reflecting cell wall barriers, chelation, and transport of Cd, respectively. Finally, we confirmed the Cd-transport activity of eight putative metal transporters identified in DMGs, DEGs, or DAPs by yeast complementaion experiments, and pharmacologically investigated the effect of m 6 A modification on their expression. Treatment with the m 6 A methylation inhibitor 3-deazaneplanocin A (3-DA) reduced SlIRT1/2 expression and increased SlNRAMP3/SlZIP4 expression, while the m 6 A demethylase inhibitor meclofenamic acid (MA) treatment decreased SlNRAMP3 expression but elevated SlIRT2 expression under Cd stress. Our findings provide novel insights into the interplay between m 6 A modification, transcription, and translation under Cd stress and the associated plant stress response.