A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis

Gabriel Krouk, Daniel Tranchina, Laurence Lejay, Alexis A. Cruikshank, Dennis Shasha, Gloria M. Coruzzi, Rodrigo A. Gutiérrez

Research output: Contribution to journalArticle

Abstract

As sessile organisms, plants must cope with multiple and combined variations of signals in their environment. However, very few reports have studied the genome-wide effects of systematic signal combinations on gene expression. Here, we evaluate a high level of signal integration, by modeling genome-wide expression patterns under a factorial combination of carbon (C), light (L), and nitrogen (N) as binary factors in two organs (O), roots and leaves. Signal management is different between C, N, and L and in shoots and roots. For example, L is the major factor controlling gene expression in leaves. However, in roots there is no obvious prominent signal, and signal interaction is stronger. The major signal interaction events detected genome wide in Arabidopsis roots are deciphered and summarized in a comprehensive conceptual model. Surprisingly, global analysis of gene expression in response to C, N, L, and O revealed that the number of genes controlled by a signal is proportional to the magnitude of the gene expression changes elicited by the signal. These results uncovered a strong constraining structure in plant cell signaling pathways, which prompted us to propose the existence of a "code" of signal integration.

Original languageEnglish (US)
JournalPLoS Computational Biology
Volume5
Issue number3
DOIs
StatePublished - Mar 2009

Fingerprint

Arabidopsis
Systems Analysis
Gene expression
Cues
Genome
genome
Genes
Restriction
Gene Expression
gene expression
Interaction
Cell signaling
Roots
Plant Cells
leaves
Nitrogen
Carbon
Leaves
Light
shoots

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Molecular Biology
  • Computational Theory and Mathematics
  • Ecology
  • Modeling and Simulation
  • Cellular and Molecular Neuroscience

Cite this

A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. / Krouk, Gabriel; Tranchina, Daniel; Lejay, Laurence; Cruikshank, Alexis A.; Shasha, Dennis; Coruzzi, Gloria M.; Gutiérrez, Rodrigo A.

In: PLoS Computational Biology, Vol. 5, No. 3, 03.2009.

Research output: Contribution to journalArticle

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