Histone methyltransferases SlSDG33 and SlSDG34 mediate organ-specific nitrogen responses in tomato

Histone posttranslational modifications play an important role in regulating plant responses to environmental cues, however, few studies have focused on the role of histone lysine methylation in regulating plant responses to nutrient availability, especially in agriculturally important species. Here, we describe the functions of two paralogous histone lysine methyltransferases, SET Domain Group 33 (SDG33) and SDG34, in mediating nitrogen responses in tomato through genetic and transcriptome analyses. Our transcriptome analysis comparing tomato lines demonstrated that SDG33 and SDG34 have overlapping yet distinctly regulated targets in tomato. Importantly, both SDG33 and SDG34 mediate gene regulation in response to changes in nitrogen level, with organ specificity. In roots, SDG33 and SDG34 are required for the regulation of a gene network that includes nitrate transporter NRT1.1, as well as auxin responsive SAUR genes. Consistently, mutations in sdg33 or sdg34 abolish the root growth response to N. In shoots, SDG33 and SDG34 affect the expression of photosynthesis genes and chlorophyll a/b ratio in response to nitrogen. Overall, we show that SDG33 and SDG34 regulate nitrogen responsive gene expression and hence physiological responses to nitrogen nutrients in an organ specific manner in the roots and shoots. This study includes 36 RNA-seq samples, including three genotypes (WT, sdg33, sdg 34) x two conditions (-N and +N) x two tissues (shoots and roots), in three biological replicates