Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root

Daniela Ristova, Clément Carré, Marjorie Pervent, Anna Medici, Grace Jaeyoon Kim, Domenica Scalia, Sandrine Ruffel, Kenneth Birnbaum, Benoît Lacombe, Wolfgang Busch, Gloria Coruzzi, Gabriel Krouk

Research output: Contribution to journalArticle

Abstract

Plants form the basis of the food webs that sustain animal life. Exogenous factors, such as nutrients and sunlight, and endogenous factors, such as hormones, cooperate to control both the growth and the development of plants. We assessed how Arabidopsis thaliana integrated nutrient and hormone signaling pathways to control root growth and development by investigating the effects of combinatorial treatment with the nutrients nitrate and ammonium; the hormones auxin, cytokinin, and abscisic acid; and all binary combinations of these factors. We monitored and integrated short-term genome-wide changes in gene expression over hours and longterm effects on root development and architecture over several days. Our analysis revealed trends in nutrient and hormonal signal cross-talk and feedback, including responses that exhibited logic gate behavior, which means that they were triggered only when specific combinations of signals were present. From the data, we developed a multivariate network model comprising the signaling molecules, the early gene expression modulation, and the subsequent changes in root phenotypes. This multivariate network model pinpoints several genes that play key roles in the control of root development and may help understand how eukaryotes manage multifactorial signaling inputs.

Original languageEnglish (US)
Article numberrs13
JournalScience Signaling
Volume9
Issue number451
DOIs
StatePublished - Oct 25 2016

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Arabidopsis
Nutrients
Nitrogen
Hormones
Food
Growth and Development
Gene expression
Genes
Gene Expression
Cytokinins
Abscisic Acid
Indoleacetic Acids
Food Chain
Logic gates
Sunlight
Eukaryota
Animals
Modulation
Genome
Phenotype

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root. / Ristova, Daniela; Carré, Clément; Pervent, Marjorie; Medici, Anna; Kim, Grace Jaeyoon; Scalia, Domenica; Ruffel, Sandrine; Birnbaum, Kenneth; Lacombe, Benoît; Busch, Wolfgang; Coruzzi, Gloria; Krouk, Gabriel.

In: Science Signaling, Vol. 9, No. 451, rs13, 25.10.2016.

Research output: Contribution to journalArticle

Ristova, Daniela ; Carré, Clément ; Pervent, Marjorie ; Medici, Anna ; Kim, Grace Jaeyoon ; Scalia, Domenica ; Ruffel, Sandrine ; Birnbaum, Kenneth ; Lacombe, Benoît ; Busch, Wolfgang ; Coruzzi, Gloria ; Krouk, Gabriel. / Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root. In: Science Signaling. 2016 ; Vol. 9, No. 451.
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