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System biology of nitrogen-carbon-signal integration in the overall Arabidopsis signaling network

Final Report Summary - ATSYSTM-BIOL (System biology of nitrogen-carbon-signal integration in the overall Arabidopsis signaling network.)

As sessile organisms, plants must cope with multiple and combined variations of internal and external signals in their environment. The scientific goals of the ATSYSTBIOL program was to use systems biology approaches to discover, through genome wide bioinformatic analysis, the relationships between nutrient sources (nitrogen and carbon) and hormones in the control of gene network regulation in Arabidopsis. This systems biology perspective aimed at discovering master-hubs regulating and integrating plant metabolic and developmental signals. This programme was divided in three major aims. Aim1 planed to study seven signals combinatorial interactions (NO3-, NH4+, carbon, light, cytokinin, auxin, ABA) on sentinel genes and further studied a subset of it by transcriptome analysis. This approach has also been expanded to the study of the control of the root architecture. Aim2 planed to integrate this data into a comprehensive and integrated model of signals propagation / interactions and try to decipher gene networks involved in signal interaction between the studied signals. This modelling has further been conceptually developed in order to integrate, the phenotypic and transcriptomic data in a unified multivariate model. Aim3 was devoted to the study of specific genes and their role in the control of the studied signals and their interaction.

The ATSYSTBIOL project reached important goals. Indeed, we documented genome wide interaction of nutritional (NO3- and NH4+) and hormonal signaling. This approach demonstrated that we can uncovered a very strong constraining structure that lead to the transcriptional regulation of the genome and a very coordinated action of the combined signals (Krouk et al., 2009). We uncovered the dynamics of NO3- regulation and built a post hoc evaluation of its coordination with hormonal signals (Krouk et al., 2010a). In this same work we:

i) demonstrated the role of SPL9 (an early nitrate regulated transcription factor) in the transcriptional control of NO3- regulated genes; and
ii) developed and published one of the first predictive network modelling in plants (Krouk et al., 2010).

We also identified several candidate genes involved in signal coordination. Globally, the ATSYSTBIOL has been acknowledged in eight original papers in peer-reviewed high impact journals. This Marie Curie project greatly helped my research and my career and provided me the necessary means to reach my goal, i.e. be recruited as a permanent scientist in CNRS in autumn 2011.