Mechanisms for increased pH-mediated amelioration of copper toxicity in Citrus sinensis leaves using physiology, transcriptomics and metabolomics

Molecular and Physiological Responses of Citrus sinensis Leaves to Long-Term Low pH Revealed by RNA-Seq Integrated with Targeted Metabolomics

“…Thus, the reduction of Asn, Asp, Ser, Gln, Ala, Thr, GABA, Glu, and TFAAs in low pH-treated leaves was mainly caused by decreased biosynthesis rather than by increased degradation and utilization, because the concentration of total soluble proteins was reduced in leaves [ 4 ]. Low pH-induced decreases in the concentrations of proteins and TFAAs have been obtained in Pennisetum clandestinum [ 51 ], sweet orange [ 4 , 14 ], and Calopogonium mucunoides [ 52 ] leaves.…”

“…There is evidence that low pH (H + -toxicity) can directly impair plant root growth and functions, thus damaging root water and nutrient uptake [ 4 , 6 ]. In addition, low pH has an adverse influence on leaf physiological processes, including water and nutrient uptake [ 4 , 6 , 7 ], photosynthetic pigment biosynthesis, gas exchange [ 8 , 9 , 10 ], photosynthetic electron transport [ 4 , 7 ], production and detoxification of reactive oxygen species (ROS) and aldehydes [ 10 , 11 , 12 ], organic acid (OA), carbohydrate and energy metabolisms [ 13 , 14 ], N, protein and amino acid (AA) metabolisms [ 3 , 10 , 14 ], secondary metabolism, and cell wall biosynthesis [ 14 ]. Low pH-induced alterations of these physiological processes should be reflected in gene expression profiles.…”

“…RNA-Seq has been widely applied to investigate abiotic stress-induced alterations of gene expression in plants, including aluminum (Al) and heavy metal toxicities, as well as nutrient stresses [ 14 , 15 , 16 , 17 , 18 ]. Although the physiological responses of leaves to low pH have been investigated in some detail, less information was available about low pH-responsive genes.…”

“…Although the physiological responses of leaves to low pH have been investigated in some detail, less information was available about low pH-responsive genes. In a study, Zhang et al [ 14 ] used RNA-Seq and metabolomics to investigate low pH effects on gene expression profiles and metabolite abundances in leaves of sweet orange ( Citrus sinensis ) seedlings treated with pH 3.0 and pH 4.8 for 17 weeks and identified 13 upregulated and 87 downregulated genes and nine upregulated and 18 downregulated metabolites in pH 3.0-treated leaves. A total of 44 differentially expressed genes (DEGs) and 14 differentially abundant metabolites (DAMs) were assigned to 29 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including one significantly enriched KEGG pathway [protein processing in endoplasmic reticulum (ko04141)] with a corrected p < 0.05 and eight KEGG pathways, respectively.…”

“…Citrus can be cultivated in soils covering a wide range of pH and are tolerant to acid soils [ 4 ]. Previously, we investigated low pH effects on growth, nutrient and water uptake, carbohydrates, gas exchange, photosynthetic electron transport, and protein expression profiles in leaves; production and detoxification of ROS and methylglyoxal in roots and leaves; and pH-mediated mitigation of copper (Cu) and Al toxicities in sweet orange seedlings [ 3 , 4 , 7 , 11 , 13 , 14 , 19 , 21 , 22 ]. Based on our findings, we used RNA-Seq and targeted metabolomics to investigate low pH-induced alterations in the expression levels of genes and the abundances of OAs and free AAs (FAAs) in sweet orange leaves.…”