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RESEARCH PAPERS ON SYSTEMS BIOLOGY/GENOMICS/BIOINFORMATICS

Light- and Carbon-Signaling Pathways. Modeling Circuits of Interactions¹

Department of Biology (K.E.T., L.V.L., G.M.C.), and Department of Computer Science (D.E.S.), New York University, New York, New York 10003

Here, we report the systematic exploration and modeling of interactions between light and sugar signaling. The data set analyzed explores the interactions of sugar (sucrose) with distinct light qualities (white, blue, red, and far-red) used at different fluence rates (low or high) in etiolated seedlings and mature green plants. Boolean logic was used to model the effect of these carbon/light interactions on three target genes involved in nitrogen assimilation: asparagine synthetase (ASN1 and ASN2) and glutamine synthetase (GLN2). This analysis enabled us to assess the effects of carbon on light-induced genes (GLN2/ASN2) versus light-repressed genes (ASN1) in this pathway. New interactions between carbon and blue-light signaling were discovered, and further connections between red/far-red light and carbon were modeled. Overall, light was able to override carbon as a major regulator of ASN1 and GLN2 in etiolated seedlings. By contrast, carbon overrides light as the major regulator of GLN2 and ASN2 in light-grown plants. Specific examples include the following: Carbon attenuated the blue-light induction of GLN2 in etiolated seedlings and also attenuated the white-, blue-, and red-light induction of GLN2 and ASN2 in light-grown plants. By contrast, carbon potentiated far-red-light induction of GLN2 and ASN2 in light-grown plants. Depending on the fluence rate of far-red light, carbon either attenuated or potentiated light repression of ASN1 in light-grown plants. These studies indicate the interaction of carbon with blue, red, and far-red-light signaling and set the stage for further investigation into modeling this complex web of interacting pathways using systems biology approaches.

¹ This work was supported by the Department of Energy (grant no. DEFG02–92–20071 to G.M.C.), the National Science Foundation (grant nos. 11S-9988636 and N2010-0115586 to D.E.S.), and by the National Institutes of Health, National Research Service Award (no. GM63350 to K.E.T.).

^* Corresponding author; e-mail gloria.coruzzi{at}nyu.edu; fax 212–995–4204.

Received February 27, 2003; returned for revision March 8, 2003; accepted March 8, 2003.

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