Abstract
SummaryPlants respond actively to changes in their environment. Variations in nutrient availability elicit substantial transcriptional reprogramming, and we aimed to systematically describe these adjustments and identify the regulators responsible. Using gene coexpression analysis based on 13 different nutrient availability anomalies, we defined and analyzed nutrient stress response signatures. We identified known regulators and could predict functions in nutrient responses for transcriptional regulators previously associated with other processes, thus linking development and environmental interaction. Three of the identified transcriptional regulators, PIF4, HY5, and NF-Y, known from their role in light signaling, targeted a substantial part of the network and may participate in remodeling the global Arabidopsis transcriptome in response to variations of nutrient availability. We present gene coexpression and transcriptional regulation networks, which can be used as tools to further explore regulatory events and dependencies even by users with basic informatics skills.
Highlights
Plants are sessile organisms, and when faced with environmental changes, they have to adapt to them, rather than escape
Plants respond to changes in nutrient availability by remodeling their transcriptional program
We show that at least three of them, PIF4, HY5, and the NF-Y complex, coordinate the responses to nutrient availability with the fundamental developmental program of the plant
Summary
When faced with environmental changes, they have to adapt to them, rather than escape. Plants respond to changes in nutrient availability by remodeling their transcriptional program. Challenges, such as iron (Fe), copper (Cu), or phosphate (Pi) deficiency, for example, cause the upregulation of specific genes responsible for the high-affinity uptake of these nutrients (Briat et al, 2015; Brumbarova et al, 2015; Penarrubia et al, 2015). Changes in factors, such as soil pH, might affect plant’s access to more than one nutrient, whereas on the other hand, certain transporters may use more than one nutrient as substrate (Cailliatte et al, 2010; Dubeaux et al, 2018; Korshunova et al, 1999). Instead of resulting in the differential expression of few key genes, changes in nutrient availability elicit complex transcriptional signatures, often revealing interconnections between nutrient stress responses
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