OsHMGB1 functions as a transcriptional repressor of OsNRT2.2 in rice: Calcium-regulation and additive function with OsCCA1.

Plant nitrogen uptake and utilization are governed by a complex network involving nitrate transporters and signal-responsive genes. Here, we show that the high mobility group box 1 protein OsHMGB1 directly binds to the OsNRT2.2 promoter and functions as a transcriptional repressor, negatively regulating its expression. Knockout of OsHMGB1 upregulates OsNRT2.2 expression, leading to increased nitrate accumulation and enhanced tolerance to low-nitrogen (LN) conditions in rice seedlings. Furthermore, OsHMGB1 expression is significantly reduced in OsCBL1-knockdown (OsCBL1-KD) plants, suggesting its dependence on OsCBL1-mediated signaling. OsHMGB1 acts additively with OsCCA1, a known repressor that binds the OsNRT2.2 promoter, to negatively regulate OsNRT2.2 expression. Notably, sequence variation in the OsHMGB1 promoter between indica and japonica rice varieties correlates with lower expression levels in indica varieties, which are associated with higher nitrogen use efficiency (NUE)-related agronomic traits, specifically, greater grain yield and increased number of effective panicles, in indica varieties compared with japonica. Together, these findings identify OsHMGB1 as a key repressor of OsNRT2.2, associated with OsCBL1-dependent nitrate signaling and act additively with OsCCA1 to enhance LN tolerance, suggesting that OsHMGB1 expression levels correlate with NUE-related traits under LN conditions. This work elucidates a link between calcium signaling and nitrate response in rice.