CIPK1‐regulated transcription factor NAM3 coordinates shoot branching and nitrate accumulation in tomato

Nitrate serves as an essential nutrient for plant growth and functions as a signaling molecule that modulates plant growth and development. Shoot branching is known to be responsive to nitrogen levels and associated with the nitrogen use efficiency (NUE), yet the underlying mechanisms remain unclear. Through RNA-seq, we identified NAM3, which encodes a NAC transcription factor, as a gene responsive to low nitrate levels in tomato (Solanum lycopersicum). NAM3 inhibits lateral bud growth by directly promoting the transcription of BRC1. Meanwhile, NAM3 enhances nitrate accumulation through promoting the expression of the nitrate transporter gene NRT1.7. Further genetic analysis showed that NAM3's regulation of shoot branching is independent of the expression of NRT1.7. The Ca²⁺ influx and transcription of CIPK1 are induced in response to the low nitrate level. The CBL3-CIPK1 complex phosphorylates NAM3 at Ser-183, thereby enhancing its protein stability and strengthening the transcriptional activity of NAM3 on BRC1 and NRT1.7. Our findings provide evidence that the CIPK1-regulated NAM3 modulates shoot branching and nitrate accumulation by activating the transcription of BRC1 and NRT1.7 in response to low nitrate levels. The coordination of shoot branching and nitrate accumulation by NAM3 implies that it is a promising genetic modification target for improving NUE.