NIGT1 family proteins exhibit dual mode DNA recognition to regulate nutrient response-associated genes in Arabidopsis

Autoři: Yoshiaki Ueda aff001;  Shohei Nosaki aff003;  Yasuhito Sakuraba aff001;  Takuya Miyakawa aff003;  Takatoshi Kiba aff004;  Masaru Tanokura aff003;  Shuichi Yanagisawa aff001
Působiště autorů: Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan aff001;  Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan aff002;  Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan aff003;  Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan aff004;  Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Japan aff005
Vyšlo v časopise: NIGT1 family proteins exhibit dual mode DNA recognition to regulate nutrient response-associated genes in Arabidopsis. PLoS Genet 16(11): e32767. doi:10.1371/journal.pgen.1009197
Kategorie: Research Article


Fine-tuning of nutrient uptake and response is indispensable for maintenance of nutrient homeostasis in plants, but the details of underlying mechanisms remain to be elucidated. NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1) family proteins are plant-specific transcriptional repressors that function as an important hub in the nutrient signaling network associated with the acquisition and use of nitrogen and phosphorus. Here, by yeast two-hybrid assays, bimolecular fluorescence complementation assays, and biochemical analysis with recombinant proteins, we show that Arabidopsis NIGT1 family proteins form a dimer via the interaction mediated by a coiled-coil domain (CCD) in their N-terminal regions. Electrophoretic mobility shift assays defined that the NIGT1 dimer binds to two different motifs, 5'-GAATATTC-3' and 5'-GATTC-N38-GAATC-3', in target gene promoters. Unlike the dimer of wild-type NIGT1 family proteins, a mutant variant that could not dimerize due to amino acid substitutions within the CCD had lower specificity and affinity to DNA, thereby losing the ability to precisely regulate the expression of target genes. Thus, expressing the wild-type and mutant NIGT1 proteins in the nigt1 quadruple mutant differently modified NIGT1-regulated gene expression and responses towards nitrate and phosphate. These results suggest that the CCD-mediated dimerization confers dual mode DNA recognition to NIGT1 family proteins, which is necessary to make proper controls of their target genes and nutrient responses. Intriguingly, two 5'-GATTC-3' sequences are present in face-to-face orientation within the 5'-GATTC-N38-GAATC-3' sequence or its complementary one, while two 5'-ATTC-3' sequences are present in back-to-back orientation within the 5'-GAATATTC-3' or its complementary one. This finding suggests a unique mode of DNA binding by NIGT1 family proteins and may provide a hint as to why target sequences for some transcription factors cannot be clearly determined.

Klíčová slova:

Arabidopsis thaliana – Dimerization – DNA-binding proteins – Gene expression – Nitrates – Protein interactions – Seedlings – Sequence motif analysis


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