Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate

Abstract

Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type–specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type–specific transcription factor (TF)–target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF–target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.

The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply

“…In addition, NLP2-bound genes showed a significant enrichment in GO terms related to phytohormone metabolism, transport, and transcriptional regulation (Figure 2C). The NLP2-bound genes contributing to this last GO term included several genes encoding TFs that are involved in the transcriptional response to nitrate availability such as HRS1 HOMOLOG1 (HHO1), HHO2, HHO3 (Medici et al, 2015; Maeda et al, 2018; Kiba et al, 2018; Safi et al, 2021), LOB DOMAIN-CONTAINING PROTEIN37, 38 and 39 (Rubin et al, 2009), TGACG SEQUENCE-SPECIFIC BINDING PROTEIN 1 and 4 (Alvarez et al, 2014), and ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR 2 (ABF2) (Contreras-López et al, 2022).…”

“…However, constructs swapping the NLP7 and NLP2 promoter to drive NLP2 or NLP7 transcription only complemented the nlp2 mutant phenotype with the NLP2 coding sequence regardless of the promoter used (Konishi et al, 2021), pointing to a more complex mechanism explaining the specificities of NLP2 and NLP7. Indeed, other TFs such as ABF2 and ABF3 support a highly localized transcriptional response to nitrate in the pericycle, and other cell type–specific TF-target interactions have been predicted (Contreras-López et al, 2022). Taken together, our data strongly indicate that NLP2 co-orchestrates the primary nitrate response together with NLP7, likely in a cell-type-specific manner.…”

Synergistic effects of nitrogen metabolites on auxin regulating plant growth and development

“…This leads to a theory that plant cells needed an availability sensor for . Local availability regulates the expression of nitrate assimilation genes ( Krapp et al., 2014 ), breaks seed dormancy ( Alboresi et al., 2005 ; Liu et al., 2021 ), controls leaf morphogenesis ( Yang et al., 2022 ), stimulates the formation and extension of lateral roots ( Forde and Walch-Liu, 2009 ; Chen et al., 2018 ; Contreras-López et al., 2022 ) and postpones flowering ( Yuan et al., 2016 ; Sanagi et al., 2021 ; Ye et al., 2021 ; Zhang S. et al., 2021 ). Lack of nitrate also affects tomato fruit yield and quality ( Belfry et al., 2017 ) and maize stem internodes development ( Peng et al., 2013 ).…”

Transcriptome Profiling and Chlorophyll Metabolic Pathway Analysis Reveal the Response of Nitraria tangutorum to Increased Nitrogen

“…Nitrogen (N) is an essential macronutrient and key signal throughout the plant life cycle [ 1 , 2 ]. In the genetic evolution of plants, the N element is one of the most considerable limiting factors for plant metabolism, as it is a constituent of a variety of many biomolecules, such as amino acids, proteins, chlorophylls, phytohormones, and nucleic acids [ 3 , 4 , 5 , 6 ].…”