Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root.
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 long-term effects on root development and architecture over several days. Our analysis revealed trends in nutrient and hormonal signal crosstalk 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.
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.|Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria.
Daniela
D
Ristova
Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France.|Institut Montpelliérain Alexander Grothendieck, Place Eugene Bataillon, 34090 Montpellier, France.
Clément
C
Carré
Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France.
Marjorie
M
Pervent
Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France.
Anna
A
Medici
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.
Grace Jaeyoon
GJ
Kim
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.
Domenica
D
Scalia
Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France.
Sandrine
S
Ruffel
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.
Kenneth D
KD
Birnbaum
Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France.
Benoît
B
Lacombe
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria.
Wolfgang
W
Busch
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.
Gloria M
GM
Coruzzi
Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France. gkrouk@gmail.com.
Gabriel
G
Krouk
D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D009584:Nitrogen / Q000378:metabolism*; D010937:Plant Growth Regulators / Q000235:genetics / Q000378:metabolism*; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D059467:Transcriptome / Q000502:physiology*
D010937:Plant Growth Regulators; D009584:Nitrogen