Metabolomic analysis reveals the molecular responses to copper toxicity in rice (Oryza sativa)

Copper (Cu) is one of the essential microelements and widely participates in various pathways in plants, but excess Cu in plant cells could induce oxidative stress and harm plant growth. Rice (Oryza sativa) is a main crop food worldwide. The molecular mechanisms of rice in response to copper toxicity are still not well understood. In this study, two-week-old seedlings of the rice cultivar Nipponbare were treated with 100 μM Cu²⁺ (CuSO₄) in the external solution for 10 days. Physiological analysis showed that excess Cu significantly inhibited the growth and biomass of rice seedlings. After Cu treatment, the contents of Mn and Zn were significantly reduced in the roots and shoots, while the Fe content was significantly increased in the roots. Meanwhile, the activities of antioxidant enzymes including SOD and POD were dramatically enhanced after Cu treatment. Based on metabolomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods, 695 metabolites were identified in rice roots. Among these metabolites, 123 metabolites were up-regulated and 297 were down-regulated, respectively. The differential metabolites (DMs) include carboxylic acids and derivatives, benzene and substituted derivatives, carbonyl compounds, cinnamic acids and derivatives, fatty acyls and organ nitrogen compounds. KEGG analysis showed that these DMs were mainly enriched in TCA cycle, purine metabolism and starch and sucrose metabolism pathways. Many intermediates in the TCA cycle and purine metabolism were down-regulated, indicating a perturbed carbohydrate and nucleic acid metabolism. Taken together, the present study provides new insights into the mechanism of rice roots to Cu toxicity.