An Integrated Analysis of Metabolome, Transcriptome, and Physiology Revealed the Molecular and Physiological Response of Citrus sinensis Roots to Prolonged Nitrogen Deficiency

Abstract

Citrus sinensis seedlings were supplied with a nutrient solution containing 15 (control) or 0 (nitrogen (N) deficiency) mM N for 10 weeks. Extensive metabolic and gene reprogramming occurred in 0 mM N-treated roots (RN0) to cope with N deficiency, including: (a) enhancing the ability to keep phosphate homeostasis by elevating the abundances of metabolites containing phosphorus and the compartmentation of phosphate in plastids, and/or downregulating low-phosphate-inducible genes; (b) improving the ability to keep N homeostasis by lowering the levels of metabolites containing N but not phosphorus, upregulating N compound degradation, the root/shoot ratio, and the expression of genes involved in N uptake, and resulting in transitions from N-rich alkaloids to carbon (C)-rich phenylpropanoids and phenolic compounds (excluding indole alkaloids) and from N-rich amino acids to C-rich carbohydrates and organic acids; (c) upregulating the ability to maintain energy homeostasis by increasing energy production (tricarboxylic acid cycle, glycolysis/gluconeogenesis, oxidative phosphorylation, and ATP biosynthetic process) and decreasing energy utilization for amino acid and protein biosynthesis and new root building; (d) elevating the transmembrane transport of metabolites, thus enhancing the remobilization and recycling of useful compounds; and (e) activating protein processing in the endoplasmic reticulum. RN0 had a higher ability to detoxify reactive oxygen species and aldehydes, thus protecting RN0 against oxidative injury and delaying root senescence.

Trends and Prospects of Genetic and Molecular Research in Plants

“…In plants, the regulatory function of the m 6 A methylation component has been shown to be involved in various elements of RNA processing, such as RNA stability, alternative polyadenylation, and miRNA regulation. The authors also summarized the molecular mechanisms behind m 6 A modifications and recent insights into the diverse roles of m 6 A in RNA regulation.…”

“…In the first, Cho et al [ 5 ] revealed correlations between ncRNAs and target coding RNAs through transcriptome analysis of suspension cells derived from damask rose petals, revealing important biological molecular mechanisms that occur during cell culture. In the second article, through an integrated analysis of the metabolome, transcriptome, and physiology, Lai et al [ 6 ] found that extensive metabolic and genetic reprogramming occurred in N-deficient roots, which not only improved the ability to detoxify reactive oxygen species and aldehydes, but also delayed root aging due to oxidative damage.…”