Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor

Abstract

BackgroundIdentifying the target genes of transcription factors is important for unraveling regulatory networks in all types of organisms. Our interest was precisely to uncover the spectrum of loci regulated by a widespread plant transcription factor involved in physiological adaptation to drought, a type of stress that plants have encountered since the colonization of land habitats 400 MYA. The regulator under study, named ASR1, is exclusive to the plant kingdom (albeit absent in Arabidopsis) and known to alleviate the stress caused by restricted water availability. As its target genes are still unknown despite the original cloning of Asr1 cDNA 20 years ago, we examined the tomato genome for specific loci interacting in vivo with this conspicuous protein.ResultsWe performed ChIP followed by high throughput DNA sequencing (ChIP-seq) on leaves from stressed tomato plants, using a high-quality anti-ASR1 antibody. In this way, we unraveled a novel repertoire of target genes, some of which are clearly involved in the response to drought stress. Many of the ASR1-enriched genomic loci we found encode enzymes involved in cell wall synthesis and remodeling as well as channels implicated in water and solute flux, such as aquaporins. In addition, we were able to determine a robust consensus ASR1-binding DNA motif.ConclusionsThe finding of cell wall synthesis and aquaporin genes as targets of ASR1 is consistent with their suggested role in the physiological adaptation of plants to water loss. The results gain insight into the environmental stress-sensing pathways leading to plant tolerance of drought.

ASR1 transcription factor and its role in metabolism

“…17,[33][34][35] Moreover, ASR1 was recently found to interact physically with regulatory regions of genes related to cell wall synthesis and remodeling as well as with channels implicated in water and solute flux, such as aquaporins. 36 These findings support 2 physicochemical studies that suggest that the tomato ASR1 acts as a chaperone-like protein in the cytosol while being unstructured and as a transcription factor in the nucleus after acquiring its quaternary structure. 13,31 However, ASR1 is also expressed under many other physiological conditions, such as tomato and strawberry fruit ripening.…”

Investigation of the ASR family in foxtail millet and the role of ASR1 in drought/oxidative stress tolerance

“…Overexpression of tomato SlASR1 decreased rates of water loss during drought stress in tobacco (Ricardi et al 2014). Overexpressing lily LLA23 or banana MpASR conferred drought tolerance in Arabidopsis (Yang et al 2008;Liu et al 2010).…”

A Key Role for Apoplastic H2O2 in Norway Spruce Phenolic Metabolism

“…10C; Table II). In tomato (Solanum lycopersicum), ASR1 has been found to act as a transcription factor also targeting cell wallrelated genes (Ricardi et al, 2014). In addition, rice (Oryza sativa) ASR1 may directly scavenge H 2 O 2 (Kim et al, 2012).…”