Meta-analysis of retrograde signaling in Arabidopsis thaliana reveals a core module of genes embedded in complex cellular signaling networks.
Plastid-to-nucleus signaling is essential for the coordination and adjustment of cellular metabolism in response to environmental and developmental cues of plant cells. A variety of operational retrograde signaling pathways have been described that are thought to be triggered by reactive oxygen species, photosynthesis redox imbalance, tetrapyrrole intermediates, and other metabolic traits. Here we report a meta-analysis based on transcriptome and protein interaction data. Comparing the output of these pathways reveals the commonalities and peculiarities stimulated by six different sources impinging on operational retrograde signaling. Our study provides novel insights into the interplay of these pathways, supporting the existence of an as-yet unknown core response module of genes being regulated under all conditions tested. Our analysis further highlights affiliated regulatory cis-elements and classifies abscisic acid and auxin-based signaling as secondary components involved in the response cascades following a plastidial signal. Our study provides a global analysis of structure and interfaces of different pathways involved in plastid-to-nucleus signaling and a new view on this complex cellular communication network.
Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology (IBIS), Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany.
Christine
C
Gläßer
Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology (IBIS), Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany.
Georg
G
Haberer
Biozentrum der LMU München, Department of Biologie I-Botanik, Großhaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany.
Iris
I
Finkemeier
Friedrich-Schiller-Universität Jena, Institut für Allgemeine Botanik und Pflanzenphysiologie, Dornburger Str. 159, D-07743 Jena, Germany Laboratoire de Physiologie Cellulaire Végétale (LPCV), CEA/CNRS/UJF iRTSV, CEA Grenoble 17, rue des Martyrs, 38054 Grenoble cedex 9, France.
Thomas
T
Pfannschmidt
Biozentrum der LMU München, Department of Biologie I-Botanik, Großhaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany.
Tatjana
T
Kleine
Biozentrum der LMU München, Department of Biologie I-Botanik, Großhaderner Str. 2-4, D-82152 Planegg-Martinsried, Germany.
Dario
D
Leister
Biochemistry and Physiology of Plants, Faculty of Biology, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany.
Karl-Josef
KJ
Dietz
University of Cologne, Botanical Institute, Cologne Biocenter, Zülpicher Str. 47B, D-50674 Cologne, Germany.
Rainer Erich
RE
Häusler
Humboldt-Universität zu Berlin, Institut für Biologie, AG Pflanzenphysiologie, Philippstrasse 13, D-10115 Berlin, Germany.
Bernhard
B
Grimm
Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology (IBIS), Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany kmayer@helmholtz-muenchen.de.
Klaus Franz Xaver
KF
Mayer
D000040:Abscisic Acid / Q000378:metabolism; D017360:Arabidopsis / Q000166:cytology* / Q000235:genetics* / Q000378:metabolism; D050260:Carbohydrate Metabolism; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics; D008969:Molecular Sequence Data; D018087:Plastids / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping; D017382:Reactive Oxygen Species / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D015398:Signal Transduction; D049490:Systems Biology
D035683:MicroRNAs; D017382:Reactive Oxygen Species; D000040:Abscisic Acid
abscisic acid; auxin.; meta-analysis; retrograde signaling