WRKY46 promotes ammonium tolerance in Arabidopsis by repressing NUDX9 and indole‐3‐acetic acid‐conjugating genes and by inhibiting ammonium efflux in the root elongation zone

Summary Ammonium (NH4+) is toxic to root growth in most plants, even at moderate concentrations. Transcriptional regulation is one of the most important mechanisms in the response of plants to NH4+ toxicity, but the nature of the involvement of transcription factors (TFs) in this regulation remains unclear. Here, RNA‐seq analysis was performed on Arabidopsis roots to screen for ammonium‐responsive TFs. WRKY46, the member of the WRKY transcription factor family most responsive to NH4+, was selected. We defined the role of WRKY46 using mutation and overexpression assays, and characterized the regulation of NUDX9 and indole‐3‐acetic acid (IAA)‐conjugating genes by WRKY46 via yeast one‐hybrid and electrophoretic mobility shift assays and chromatin immunoprecipitation‐quantitative real‐time polymerase chain reaction (ChIP‐qPCR). Knockout of WRKY46 increased, while overexpression of WRKY46 decreased, NH4+‐suppression of the primary root. WRKY46 is shown to directly bind to the promoters of the NUDX9 and IAA‐conjugating genes (GH3.1, GH3.6, UGT75D1, UGT84B2) and to inhibit their transcription, thus positively regulating free IAA content and stabilizing protein N‐glycosylation, leading to an inhibition of NH4+ efflux in the root elongation zone (EZ). We identify TF involvement in the regulation of NH4+ efflux in the EZ, and show that WRKY46 inhibits NH4+ efflux by negative regulation of NUDX9 and IAA‐conjugating genes.