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Open Access Research article

Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis

Mariana Obertello13, Gabriel Krouk12, Manpreet S Katari1, Suzan J Runko1 and Gloria M Coruzzi1*

Author Affiliations

1 Center for Genomics and Systems Biology, Department of Biology, New York University. 100 Washington Square East, 1009 Main Building, New York, NY 10003, USA

2 Institut de Biologie Intégrative des Plantes, UMR 5004, Biochimie et Physiologie Moléculaire des Plantes, Agro-M/CNRS/INRA/SupAgro/UM2, Montpellier, France

3 Instituto de Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Vuelta de Obligado 2490 piso 2, C1428ADN Buenos Aires, Argentina

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BMC Systems Biology 2010, 4:111  doi:10.1186/1752-0509-4-111

Published: 12 August 2010

Abstract

Background

Nitrogen and light are two major regulators of plant metabolism and development. While genes involved in the control of each of these signals have begun to be identified, regulators that integrate gene responses to nitrogen and light signals have yet to be determined. Here, we evaluate the role of bZIP1, a transcription factor involved in light and nitrogen sensing, by exposing wild-type (WT) and bZIP1 T-DNA null mutant plants to a combinatorial space of nitrogen (N) and light (L) treatment conditions and performing transcriptome analysis. We use ANOVA analysis combined with clustering and Boolean modeling, to evaluate the role of bZIP1 in mediating L and N signaling genome-wide.

Results

This transcriptome analysis demonstrates that a mutation in the bZIP1 gene can alter the L and/or N-regulation of several gene clusters. More surprisingly, the bZIP1 mutation can also trigger N and/or L regulation of genes that are not normally controlled by these signals in WT plants. This analysis also reveals that bZIP1 can, to a large extent, invert gene regulation (e.g., several genes induced by N in WT plants are repressed by N in the bZIP1 mutant).

Conclusion

These findings demonstrate that the bZIP1 mutation triggers a genome-wide de-regulation in response to L and/or N signals that range from i) a reduction of the L signal effect, to ii) unlocking gene regulation in response to L and N combinations. This systems biology approach demonstrates that bZIP1 tunes L and N signaling relationships genome-wide, and can suppress regulatory mechanisms hypothesized to be needed at different developmental stages and/or environmental conditions.