Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade

Abstract

Dynamic reprogramming of gene regulatory networks (GRNs) enables organisms to rapidly respond to environmental perturbation. However, the underlying transient interactions between transcription factors (TFs) and genome-wide targets typically elude biochemical detection. Here, we capture both stable and transient TF-target interactions genome-wide within minutes after controlled TF nuclear import using time-series chromatin immunoprecipitation (ChIP-seq) and/or DNA adenine methyltransferase identification (DamID-seq). The transient TF-target interactions captured uncover the early mode-of-action of NIN-LIKE PROTEIN 7 (NLP7), a master regulator of the nitrogen signaling pathway in plants. These transient NLP7 targets captured in root cells using temporal TF perturbation account for 50% of NLP7-regulated genes not detectably bound by NLP7 in planta. Rapid and transient NLP7 binding activates early nitrogen response TFs, which we validate to amplify the NLP7-initiated transcriptional cascade. Our approaches to capture transient TF-target interactions genomewide can be applied to validate dynamic GRN models for any pathway or organism of interest.

The Arabidopsis Transcription Factor CDF3 Is Involved in Nitrogen Responses and Improves Nitrogen Use Efficiency in Tomato

“…This study also showed that those TFs are connected with additional second layer of TFs, which includes CDF1 (Varala et al, 2018). In addition, it is reported that master factor NLP7 targets multiple TFs including LBD37, LBD38, TGA4, HAP2C, NAC096, and CDF1 using the TARGET system (Alvarez et al, 2020), suggesting that CDF1 is a component of the regulatory network involved in N responses. In addition, we previously reported that tomato and Arabidopsis plants overexpressing the AtCDF3 gene, the closest homolog of CDF1, exhibited changes in primary metabolism, with increased amounts of amino acids like glutamine, asparagine and GABA, and higher sucrose contents (Corrales et al, 2017;Renau-Morata et al, 2017).…”

“…In addition, recent studies point to an involvement of CDF1, the closest CDF3 homolog, in the responses to nitrogen (Varala et al, 2018). Moreover, it is reported that NLP7, a master regulator of the nitrogen signaling pathway, targets multiple TFs including CDF1 (Alvarez et al, 2020), suggesting that CDF1 plays a role in the regulatory network involved in N responses. However, there is still a lack of information regarding the specific roles of CDF1 and CDF3 in N responses.…”

“…Nitrate (NO 3 − ) is the main source of inorganic nitrogen for land plants (Krapp et al, 2014;Vidal et al, 2014). In addition,NO 3 − plays a key function as a signaling molecule in many aspects of plant metabolism and developmental have been identified so far, including NIN Like protein 7, NLP7 (Castaings et al, 2009;Alvarez et al, 2020), NLP8 (Yan et al, 2016); TGA1 and TGA4 (Alvarez et al, 2014(Alvarez et al, , 2019, SPL9 (Krouk et al, 2010), LBD37, LBD38, and LBD39 (Rubin et al, 2009), bZIP1 (Obertello et al, 2010), TCP20 (Guan et al, 2014), and ANR1 (Zhang and Forde, 1998). However, our understanding of the diverse regulatory pathways and the molecular mechanisms by which the different TFs modulate NO 3 − responses is still limited.…”

Evolution of NIN and NIN-like Genes in Relation to Nodule Symbiosis

“…Interestingly, transcriptome analysis of the Arabidopsis nlp7 (from a different orthogroup than NIN ) mutant shows altered expression levels of several genes encoding NF-YA subunits, including AtNF-YA2 and AtNF-YA10 [ 69 , 70 ]. This suggests that (some) NLPs can regulate the expression of NF-Y (A1) .…”

“…This level of induction is comparable to that in Lotus and Medicago [ 49 , 67 ]. In Arabidopsis, LBD16 has been shown to be a direct target of NLP7 [ 70 ]. Therefore, NIN-controlled LBD16 expression most likely is adopted from a non-symbiotic module in which its expression is controlled by NLP, and this module evolved before the occurrence of nodulation.…”