The transcription factors, STOP1 and TCP20, are required for root system architecture alterations in response to nitrate deficiency

Nitrate distribution in soils is often heterogeneous. Plants have adapted to this by modifying their root system architecture (RSA). Previous studies showed that NITRATE-TRANSPORTER1.1 (NRT1.1), which also transports auxin, helps inhibit lat-eral root primordia (LRP) emergence in nitrate -poor patches, by preferentially transporting auxin away from the LRP. In this study, we identified the regulatory system for this response involving the transcription factor (TF), SENSITIVE - TO- PROTON-RHIZOTOXICITY1 (STOP1), which is accumulated in the nuclei of LRP cells under nitrate deficiency and directly regulates Arabidopsis NRT1.1 expression. Mutations in STOP1 mimic the root phenotype of the loss - of-function NRT1.1 mutant under nitrate deficiency, com-pared to wild -type plants, including increased LR growth and higher DR5promoter activity (i.e., higher LRP auxin signaling/activity). Nitrate deficiency-induced LR growth inhibition was almost completely reversed when STOP1 and the TF, TEOSINTE-BRANCHED1,-CYCLOIDEA,-PCF-DOMAIN-FAMILY-PROTEIN20 (TCP20), a known activator of NRT1.1 expression, were both mutated. Thus, the STOP1- TCP20 system is required for activation of NRT1.1 expression under nitrate deficiency, leading to reduced LR growth in nitrate -poor regions. We found this STOP1-mediated system is more active as growth media becomes more acidic, which correlates with reductions in soil nitrate as the soil pH becomes more acidic. STOP1 has been shown to be involved in RSA modifications in response to phosphate deficiency and increased potassium uptake, hence, our findings indicate that root growth regulation in response to low availability of the major fertilizer nutrients, nitrogen, phosphorus and potassium, all involve STOP1, which may allow plants to maintain appropriate root growth under the complex and varying soil distribution of nutrients. Significance Nitrate transporter NRT1.1-mediated lateral root (LR) growth inhibition in nitrate -poor soil patches enables plants to focus their LR growth on nitrate -rich soils, which contributes to efficient nitrate acquisition. Here, we show that the transcription factors STOP1 and TCP20 regulate NRT1.1 expression under nitrate deficiency. LR growth inhibition on nitrate-starved medium was almost completely reversed in the stop1tcp20- double- mutant,demonstrating they are required for the nitrate-dependent root architecture modification. Current and previousstudies indicate that STOP1 is involved root growth regulation in response to low availability of the major nutrients, N -P -K (nitrogen, phosphorous deficiency induced by Fe3+ excess, and potassium), with different partners/downstream genes involved, suggesting that STOP1 acts as a hub to integrate root responses to N -P -K under complex soil conditions.