A Nitrate-Inducible GARP Family Gene Encodes an Auto-Repressible Transcriptional Repressor in Rice

Abstract

Nitrogen is the most important macronutrient in plants and its supply induces responses in gene expression, metabolism and developmental processes. However, the molecular mechanisms underlying the nitrogen responses remain poorly understood. Here we show that the supply of nitrate but not ammonium immediately induces the expression of a transcriptional repressor gene in rice, designated NIGT1 (Nitrate-Inducible, GARP-type Transcriptional Repressor 1). The results of DNA-binding site selection experiments and electrophoretic mobility shift assays indicated that NIGT1 binds to DNA containing either of two consensus sequences, GAATC or GAATATTC. In transient reporter assays, NIGT1 was found to repress transcription from the promoters containing the identified NIGT1-binding sequences in vivo. Furthermore, NIGT1 repressed the activity of its own promoter, suggesting an autorepression mechanism. Consistently, nitrate-induced NIGT1 expression was found to be down-regulated after a transient peak during nitrate treatment, and the nitrate-induced expression of NIGT1 decreased in transgenic rice plants in which this gene was constitutively overexpressed. Furthermore, the chlorophyll content that could be a marker of nitrogen utilization was found to be decreased in NIGT1 overexpressors of rice grown with nitrate medium but not with ammonium medium. Thus, we propose NIGT1 as a nitrate-inducible and autorepressible transcriptional repressor that may play a role in the nitrogen response in rice. Taken together with the fact that the NIGT1-binding sites are conserved in promoter sequences of Arabidopsis NIGT1 homologs, our findings imply the presence of a time-dependent complex system for nitrate-responsive transcriptional regulation that is conserved in both monocots and dicots.

Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments

“…G2-like transcription factors are members of the GARP superfamily and are characterized by a conserved domain (GARP) that is a single Myb-related DNA-binding domain (Sawaki et al, 2013). It is interesting to note that there are several connections between the three members of the G2-like transcription factors family, suggesting they respond to nitrate treatments in a coordinated fashion (Figure 5A).…”

“…Recent studies indicate NLPs are also important transcription factors in the nitrate response because they regulate many known nitrate signaling and assimilation genes (Konishi and Yanagisawa, 2013; Marchive et al, 2013). Additional transcription factors known to regulate N responses include members of the LBD family (Rubin et al, 2009); HY5 , which is related to phytochrome-mediated effects on enzymes involved in nitrogen assimilation (Lillo, 2008); and a nitrate-induced NIGT1 member of the GARP family, which has been suggested to be involved in the control of nitrate utilization (Sawaki et al, 2013). Recently, NAC4 was found to be a key regulatory element controlling a nitrate-responsive network and lateral root development in Arabidopsis (Vidal et al, 2013).…”

Ubiquitin ligase EL5 maintains the viability of root meristems by influencing cytokinin-mediated nitrogen effects in rice

“…These results strongly suggest that reduction of EL5 function causes activation of nitrogen signalling despite the absence of a nitrogen source. Recently, transcription factors that regulate nitrogen signalling have been identified in rice and Arabidopsis (LOB, Rubin et al , 2009; Albinsky et al , 2010; NIGT1, Sawaki et al , 2013; NLP6 and NLP7, Castaings et al , 2009; Konishi and Yanagisawa, 2013; Marchive et al , 2013). Expression of genes in the same family as these transcription factor genes was induced in rice roots after nitrite treatment, but in mEL5 their expression levels were elevated prior to nitrite treatment (Fig.…”

Nitrogen-Dependent Regulation of De Novo Cytokinin Biosynthesis in Rice: The Role of Glutamine Metabolism as an Additional Signal

“…This response is rapid and does not require de novo protein synthesis since it is cycloheximide insensitive (Gowri et al 1992, Sakakibara et al 1997, Sakakibara 2003a). Key transcription factors and cis -element sequences for the nitrate-specific response recently have been described (Castaings et al 2009, Konishi and Yanagisawa 2010, Konishi and Yanagisawa 2011, Konishi and Yanagisawa 2013, Sawaki et al 2013). On the other hand, the nitrogen-non-specific response is observed following exogenous application of nitrate, ammonium and various amino acids, and a wide spectrum of genes have been reported to be up- or down-regulated during the response (Hirose et al 1997, Sivasankar et al 1997, Stitt 1999, Stitt et al 2002, Sonoda et al 2003, Tabuchi et al 2007, Konishi and Yanagisawa 2010, Kiba et al 2012).…”