Antagonistic regulation of nitrogen and drought signaling mediated by NIN-like protein 7 transcription factor in Arabidopsis thaliana

Abstract

Plants face the constant challenge of reconciling antagonistic environmental signals, such as nutrient-driven growth and water deficit–induced stress responses. However, the molecular mechanisms that integrate these conflicting pathways remain poorly understood. Through a comprehensive transcriptomic meta-analysis in Arabidopsis thaliana, we show that nitrogen (N) supply and water deficit signaling exhibit overlapping and often opposing gene expression responses. Regulatory network modeling identifies the NIN-LIKE PROTEIN 7 (NLP7) transcription factor (TF) as a central integrator of these convergent transcriptional responses. Through combinatorial water deficit and N supply treatments in wild-type and nlp7 mutant plants, we find that NLP7 accounts for 85% of the transcriptional interaction between these pathways. Chromatin immunoprecipitation and sequencing and a cell TF assay to detect TF regulation genome-wide reveal that NLP7 directly downregulate the expression of TFs such as HB6, NAC6, NAP, and WRKY18, which are central regulators of water deficit–mediated stress signaling. Repression of these secondary TFs has distinct downstream effects on gene expression, influencing shared and water deficit–specific responses. Loss of NLP7 enhances water deficit tolerance, characterized by increased water retention, reduced abscisic acid-mediated stomatal aperture, and altered expression of stress-responsive genes. These findings establish NLP7 as a central hub balancing growth and stress responses, providing insight into how plants integrate competing environmental cues.