Journal Article

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

Biochimie et Physiologie Moléculaire des Plantes (BPMP) ; Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Krouk, Gabriel, G.C.: National Institutes of Health (NIH) NIGMS Grant GM032877, DOE Grant DEFG02-92ER20071, and National Science Foundation (NSF) Arabidopsis 2010 Genome Grant MCB- 0929338, Runko, Suzan J, Katari, Manpreet S, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, “Dr. Héctor N. Torres” [Buenos Aires] (INGEBI) ; Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas y Naturales [Buenos Aires] (FCEyN) ; Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Center for Genomics and Systems Biology ;

2010

Overview

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.

• Publisher: CCSD,BioMed Central,BioMed Central Ltd
• Subject: Algorithms / Analysis / Arabidopsis / Arabidopsis - cytology / Arabidopsis - drug effects / Arabidopsis - metabolism / Arabidopsis - radiation effects / Arabidopsis Proteins - genetics / Arabidopsis Proteins - metabolism / Arabidopsis thaliana / Basic-Leucine Zipper Transcription Factors - genetics / Basic-Leucine Zipper Transcription Factors - metabolism / Bioinformatics / Biomedical and Life Sciences / Cell cycle / Cellular and Medical Topics / Computational Biology/Bioinformatics / Data mining / Developmental stages / DNA, Bacterial - genetics / DNA-ligand interactions / Environmental conditions / Gene expression / Gene Expression Regulation, Plant - drug effects / Gene Expression Regulation, Plant - genetics / Gene Expression Regulation, Plant - radiation effects / Genetic aspects / Genome, Plant - genetics / Genomes / Genomics / Grants / Kinases / Leucine / Life Sciences / Light / Models, Biological / Mutation / Nitrogen / Nitrogen - pharmacology / Oligonucleotide Array Sequence Analysis / Physiological / Physiological aspects / Plant growth / Plant metabolism / Proteins / Regulation / Research Article / Signal Transduction - drug effects / Signal Transduction - genetics / Signal Transduction - radiation effects / Simulation and Modeling / Systems Biology / Variance analysis / Vegetal Biology
• ISBN: 0002822586000