The NIN-LIKE PROTEIN 7 transcription factor modulates auxin pathways to regulate root cap development in Arabidopsis

The root cap is a small tissue located at the tip of the root with critical functions for root growth. Present in nearly all vascular plants, the root cap protects the root meristem, influences soil penetration, and perceives and transmits environmental signals that are critical for root branching patterns. To perform these functions, the root cap must remain relatively stable in size and must integrate endogenous developmental pathways with environmental signals, yet the mechanism is not clear. We previously showed that low pH conditions altered root cap development, and these changes are mediated by the NIN LIKE PROTEIN 7 (NLP7) transcription factor, a master regulator of nitrate signaling. Here we show that in Arabidopsis NLP7 integrates nitrate signaling with auxin pathways to regulate root cap development. We found that low nitrate conditions promote aberrant release of root cap cells. Nitrate deficiency impacts auxin pathways in the last layer of the root cap, and this is mediated in part by NLP7. Mutations in NLP7 abolish the auxin minimum in the last layer of the root cap and alter root cap expression of the auxin carriers PIN-LIKES 3 (PILS3) and PIN-FORMED 7 (PIN7) as well as transcription factors that regulate PIN expression. Together, our data reveal NLP7 as a link between endogenous auxin pathways and nitrate signaling in the root cap. The nitrate master regulator NLP7, a nitrate sensor, links nitrate signaling with root cap development by modulating auxin pathways and expression of critical transcription factors.

Automated summary

The root cap plays critical roles in root growth, protecting the root meristem and influencing soil penetration, as well as perceiving and transmitting environmental signals for root branching patterns. However, the mechanism by which the root cap integrates endogenous developmental pathways with environmental signals remains unclear. This study demonstrates that the transcription factor NLP7 links nitrate signaling with auxin pathways to regulate root cap development in Arabidopsis. NLP7 is involved in the release of root cap cells under low nitrate conditions and impacts auxin pathways in the last layer of the root cap. Mutations in NLP7 affect the expression of auxin carriers and transcription factors that regulate auxin transport. Overall, NLP7 acts as a key regulator in integrating nitrate signaling and endogenous auxin pathways for root cap development.