Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots

• Published in: The Plant journal : for cell and molecular biology Vol. 80; no. 1; pp. 1 - 13
• Main Authors: Alvarez, José M, Riveras, Eleodoro, Vidal, Elena A, Gras, Diana E, Contreras‐López, Orlando, Tamayo, Karem P, Aceituno, Felipe, Gómez, Isabel, Ruffel, Sandrine, Lejay, Laurence, Jordana, Xavier, Gutiérrez, Rodrigo A
• Format: Journal Article
• Language: English
• Published: England Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology 01-10-2014; Blackwell Publishing Ltd; Wiley
• Subjects: Arabidopsis; Arabidopsis - genetics; Arabidopsis - growth & development; Arabidopsis - metabolism; Arabidopsis thaliana; Basic-Leucine Zipper Transcription Factors - genetics; Basic-Leucine Zipper Transcription Factors - metabolism; bioinformatics; chromatin; Computational Biology; DNA; gene expression; Gene Expression Regulation, Plant; Gene Regulatory Networks; genes; lateral root growth; Life Sciences; messenger RNA; mutants; Mutation; nitrate sensing; nitrate signal; nitrates; Nitrates - metabolism; nucleotide sequences; Phenotype; Plant Roots - genetics; Plant Roots - growth & development; Plant Roots - metabolism; precipitin tests; Promoter Regions, Genetic - genetics; roots; Signal Transduction; TGA1 and TGA4; transcription factors; Transcriptome; Up-Regulation; Vegetal Biology; TGA1 and TGA4; lateral root growth; nitrate sensing; Arabidopsis; nitrate signal
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.12618

Nitrate acts as a potent signal to control global gene expression in Arabidopsis. Using an integrative bioinformatics approach we identified TGA1 and TGA4 as putative regulatory factors that mediate nitrate responses in Arabidopsis roots. We showed that both TGA1 and TGA4 mRNAs accumulate strongly after nitrate treatments in roots. Global gene expression analysis revealed 97% of the genes with altered expression in tga1 tga4 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 TGA1 and TGA4 regulate the expression of nitrate transporter genes NRT2.1 and NRT2.2. Specific binding of TGA1 to its cognate DNA sequence on NRT2.1 and NRT2.2 promoters was confirmed by chromatin immunoprecipitation assays. The tga1 tga4 double mutant plants exhibit nitrate‐dependent lateral and primary root phenotypes. Lateral root initiation is affected in both tga1 tga4 and nrt1.2 nrt2.2 double mutants, suggesting TGA1 and TGA4 regulate lateral root development at least partly via NRT2.1 and NRT2.2. Additional root phenotypes of tga1 tga4 double mutants indicate that these transcription factors play an important role in root developmental responses to nitrate. These results identify TGA1 and TGA4 as important regulatory factors of the nitrate response in Arabidopsis roots.