Systems approach identifies <scp>TGA</scp>1 and <scp>TGA</scp>4 transcription factors as important regulatory components of the nitrate response of <i><scp>A</scp>rabidopsis thaliana</i> roots

<jats:title>Summary</jats:title><jats:p>Nitrate acts as a potent signal to control global gene expression in <jats:styled-content style="fixed-case">A</jats:styled-content>rabidopsis. Using an integrative bioinformatics approach we identified <jats:styled-content style="fixed-case">TGA</jats:styled-content>1 and <jats:styled-content style="fixed-case">TGA</jats:styled-content>4 as putative regulatory factors that mediate nitrate responses in <jats:styled-content style="fixed-case">A</jats:styled-content>rabidopsis roots. We showed that both <jats:italic><jats:styled-content style="fixed-case">TGA</jats:styled-content>1</jats:italic> and <jats:italic><jats:styled-content style="fixed-case">TGA</jats:styled-content>4</jats:italic> m<jats:styled-content style="fixed-case">RNA</jats:styled-content>s accumulate strongly after nitrate treatments in roots. Global gene expression analysis revealed 97% of the genes with altered expression in <jats:italic>tga1 tga4</jats:italic> double mutant plants respond to nitrate treatments, indicating that these transcription factors have a specific role in nitrate responses in Arabidopsis root organs. We found <jats:styled-content style="fixed-case">TGA</jats:styled-content>1 and <jats:styled-content style="fixed-case">TGA</jats:styled-content>4 regulate the expression of nitrate transporter genes <jats:italic><jats:styled-content style="fixed-case">NRT</jats:styled-content>2.1</jats:italic> and <jats:italic><jats:styled-content style="fixed-case">NRT</jats:styled-content>2.2</jats:italic>. Specific binding of <jats:styled-content style="fixed-case">TGA</jats:styled-content>1 to its cognate <jats:styled-content style="fixed-case">DNA</jats:styled-content> sequence on <jats:italic><jats:styled-content style="fixed-case">NRT</jats:styled-content>2.1</jats:italic> and <jats:italic><jats:styled-content style="fixed-case">NRT</jats:styled-content>2.2</jats:italic> promoters was confirmed by chromatin immunoprecipitation assays. The <jats:italic>tga1 tga4</jats:italic> double mutant plants exhibit nitrate‐dependent lateral and primary root phenotypes. Lateral root initiation is affected in both <jats:italic>tga1 tga4</jats:italic> and <jats:italic>nrt1.2 nrt2.2</jats:italic> double mutants, suggesting <jats:styled-content style="fixed-case">TGA</jats:styled-content>1 and <jats:styled-content style="fixed-case">TGA</jats:styled-content>4 regulate lateral root development at least partly via <jats:styled-content style="fixed-case">NRT</jats:styled-content>2.1 and <jats:styled-content style="fixed-case">NRT</jats:styled-content>2.2. Additional root phenotypes of <jats:italic>tga1 tga4</jats:italic> double mutants indicate that these transcription factors play an important role in root developmental responses to nitrate. These results identify <jats:styled-content style="fixed-case">TGA</jats:styled-content>1 and <jats:styled-content style="fixed-case">TGA</jats:styled-content>4 as important regulatory factors of the nitrate response in <jats:styled-content style="fixed-case">A</jats:styled-content>rabidopsis roots.</jats:p>