The NRT1.1-NLP7 Nexus: An Integrative Signaling Nexus from Nitrate Sensing to Systemic Adaptation and Structure-Guided Engineering

Nitrate functions as both a nutrient and a signaling molecule in plants, initiating genome-wide transcriptional reprogramming and systemic developmental adjustments. Traditionally, plasma membrane nitrate sensing and nuclear transcriptional responses have been considered independent processes linked through linear transduction pathways. However, recent findings reveal that the dual-affinity nitrate transceptor NRT1.1 (NPF6.3) and the transcription factor NLP7 form an integrated signaling nexus—the Nitrate transporter 1.1 (NRT1.1)-NIN-like protein 7 (NLP7) nexus. This review examines the coupling mechanisms, including Ca2+-dependent phosphorylation cascades, nucleocytoplasmic shuttling, and a recently discovered MAPK amplification branch. We further explore the nexus’s conserved and diversified functions across crop species, and propose a three-tier rational design framework for reprogramming nitrate responses to enhance nitrogen use efficiency. By bridging structural biology and synthetic biology, this integrative perspective transitions crop improvement from empirical selection to structure-guided design, offering a roadmap for predictive crop engineering.