Shining light on Arabidopsis regulatory networks integrating nitrogen use and photosynthesis

Authors: DE SILVA, KITHMEE - University Of Illinois; COELHO, CAMILA - New York University; GAO, JENNY - New York University; Brooks, Matthew

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/28/2025
Publication Date: 5/13/2025
Citation: De Silva, K., Coelho, C., Gao, J., Brooks, M.D. 2025. Shining light on Arabidopsis regulatory networks integrating nitrogen use and photosynthesis. Plant Journal. https://doi.org/10.1111/tpj.70211.
DOI: https://doi.org/10.1111/tpj.70211

Interpretive Summary: The close relationship between nitrogen assimilation and photosynthetic activity has been recognized and studied at the physiological level for more than 50 years, however relatively little is understood about how these two important plant metabolic pathways are coordinated at a molecular level. To identify transcriptional regulators that integrate nitrogen and photosynthesis, we grew Arabidopsis plants under 12 combined nitrogen and light treatments and measured gene expression which was linked to physiological traits using gene network analysis. We identified two groups of transcription factors, belonging to the bZIP and MYB-related families, which were important for the coordinating genes involved in photosyntheisis in response to light and nitrogen signals. The transcription factors unveiled in this study have the potential to unlock new strategies for enhancing photosynthetic activity and nutrient-use efficiency in plants.

Technical Abstract: Nitrogen and light availability are well-known to influence photosynthesis, having both individual and synergistic effects. However, the regulatory interactions between these signaling pathways, especially the transcription factors (TFs) that perceive and integrate these cues remain to be elucidated. Arabidopsis grown in a matrix of nitrogen and light treatments exhibited distinct physiological and transcriptomic responses. Notably, the effect of nitrogen dose on biomass, nitrogen use efficiency, carbon to nitrogen ratio, and gene expression was highly dependent on light intensity. Genes differentially expressed across the treatments were enriched for photosynthetic processes, including pentose-phosphate cycle, light-harvesting and chlorophyll biosynthesis. A gene regulatory network built on expression data revealed interconnected gene clusters (or “subnetworks”) coordinating photosynthesis, carbon-to-nitrogen balance, and nitrogen uptake. TFs previously linked to either nitrogen or light signaling, now emerge as regulatory hubs in these subnetworks, suggesting an integrated regulatory mechanism. Among these, we identified bZIP and MYB-related family transcription factors as pivotal players in harmonizing photosynthesis, nitrogen assimilation, and light responses. The transcription factors unveiled in this study have the potential to unlock new strategies for enhancing photosynthetic activity and nutrient-use efficiency in plants.