Nitrogen Regulatory Networks

Plant Systems Biology @ The Coruzzi Lab

From predictive network modeling to trait evolution

Click here for a list of published experiments


Nitrogen Regulatory Networks

Predictive modeling of gene networks controlling nitrogen-use and plant development

Our lab uses System Biology approaches to understand the mechanisms controlling nitrogen use efficiency (NUE) in plants.   These studies have uncovered the regulatory mechanisms by which plants assimilate and forage for nitrogen – by sensing and responding to nitrogen signals in their internal and external environments.  To uncover the underlying regulatory mechanisms for nitrogen signaling, we have analyzed genome-wide transcriptome responses to nitrogen treatments.  Our earliest regulatory network modeling of the underlying N-regulatory networks began with the creation of the Arabidopsis multinetwork – a qualitative network model of the genome integrating all data supporting gene, protein, and RNA interactions [1]. By querying this Arabidopsis multinetwork with steady-state transcriptome data from nitrogen-treated plants, the sub-networks derived enabled us to uncover “molecular machines” involved in carbon and nitrogen signaling [1] and a novel role for the master clock gene CCA1 as a transcription factor hub in an organic-N regulatory network – revealing nitrogen-control of the circadian clock [2].  To advance our goal of predictive network modeling, we next used time-series transcriptome data and a machine-learning approach called “State space modeling” to generate a predictive network model for nitrate control of the N-assimilatory pathway [3]. This approach has enabled us to achieve the ultimate goal of systems biology – to predict network states under untested conditions.  These predictions were validated in silico (using left-out data) and experimentally using mutants [3].  Our N-regulatory network studies have also begun to uncover the mechanisms involved in nitrogen control of plant root development enabling plants to forage for nitrogen in their environment. In one approach, we performed cell-specific analysis that enabled us to uncover a role for a miRNA-TF motif involved in the regulation of lateral root outgrowth in response to N-application [4].  Our more recent work in this area involves the use of a “split root” system to uncover the signals involved in plant root growth in response to N-supply and demand – the “nitrogen-economics” of root development [5].  We are continuing to explore the genes underlying N-regulation of root development by exploiting the diversity of root responses to nitrogen in natural variants of Arabidopsis.


[1] Gutiérrez et al (2007) Genome Biol. 8:R7; [2] Gutiérrez et al (2008) Proc. Natl Acad. Sci USA. 105:4939-4944; [3] Krouk et al Genome Biol. 11 (12):R123; [4] Gifford et al (2008) Proc. Natl. Acad. Sci. USA. 105:803-808; [5] Ruffel et al (2011) Proc. Natl. Acad. Sci. USA. 108(45):18524-9