In silico evolutionary origin, structural properties, molecular docking, following expression analysis of the nitrate...

Nitrogen (N), which serves as the structural building block of protein, is essential for long-distance transfer from source to sink in plants for proper growth and development. Long-distance N transport occurs through either diffusion-based passive transport or active transport mediated by transporter proteins. In maize, N transporters have a significant impact on long-distance N transport and total N accumulation in seeds. To investigate the critical roles of these transporters in nutrient balance, total N accumulation, and tolerance to abiotic stresses, a series of bioinformatics analyses, following qRT-PCR, and experimental subcellular localization were conducted. Following phylogenetic analysis, maize nitrate transporters (ZmNRTs) shared three different clades (NRT1/PTR, NRT2, and NRT3). Significant differences in molecular weight, as well as multiple beta-strands, multiple alpha helices, and transmembrane helices, were observed in ZmNRTs. The majority of the transporters are found to be localized in the plasma membrane. The transporters showed the highest homolog pairs (63) with S. italica, revealing their similar functional properties. Gene ontology analysis reveals that ZmNRTs play significant role in biological processes, cellular components, and molecular functions. During molecular docking analysis, the lowest binding affinity (ΔG: - 3.7 kcal/mol) in ZmNRT1c4D-Nit might reveal their binding integrity. During protein-protein interaction, significant interaction of 75 transporters among 83 might be due to their cumulative/interactive roles in the same signaling pathways. Significant upregulation of ZmNRT1.1C, ZmNRT1.6A, and ZmNRT1.6B, in node and tassel tissues during qRT-PCR and RNA-Seq experiments might guide their great impact on N transport in vegetative and reproductive tissues. In the same experiments, significant upregulation of ZmNRT1.3 and ZmNRT1c4C under heat stress in root tissue might guide their great role in heat stress tolerance in maize. Altered expression of ZmNRT1.1C and ZmNRT1.1E under salinity stress, and ZmNRT1.3 under drought stress, might guide their great role in the respective stress conditions. Co-expression of transcription factors, LOC778437 with ZmNRT2.4B and ZmNRT2.4C genes might reveal their regulatory effect in high-affinity NO₃ ^- transport and accumulation in maize. Bioinformatics-based prediction following GFP-tagged expression of ZmNRT1.6B protein in plasma membrane might reveal its great role in cellular NO₃ ^- transport through the cellular membrane. These bioinformatics-based structural analyzes, following wet lab-based validation of maize NRTs, might guide the maize biologists in developing NRT-based genetic circuits to improve the N uptake, transport, mobilization, and accumulation in maize following programming-based genetic circuit-enabled synthetic biology approaches.

The online version contains supplementary material available at 10.1007/s12298-025-01669-0.