title: Stitching together the Multiple Dimensions of Autophagy Using Metabolomics and Transcriptomics Reveals Impacts on Metabolism, Development, and Plant Responses to the Environment in Arabidopsis.
abstract: Autophagy is a fundamental process in the plant life story, playing a key role in immunity, senescence, nutrient recycling, and adaptation to the environment. Transcriptomics and metabolomics of the rosette leaves of Arabidopsis thaliana autophagy mutants (atg) show that autophagy is essential for cell homeostasis and stress responses and that several metabolic pathways are affected. Depletion of hexoses, quercetins, and anthocyanins parallel the overaccumulation of several amino acids and related compounds, such as glutamate, methionine, glutathione, pipecolate, and 2-aminoadipate. Transcriptomic data show that the pathways for glutathione, methionine, raffinose, galacturonate, and anthocyanin are perturbed. Anthocyanin depletion in atg mutants, which was previously reported as a possible defect in flavonoid trafficking to the vacuole, appears due to the downregulation of the master genes encoding the enzymes and regulatory proteins involved in flavonoid biosynthesis. Overexpression of the PRODUCTION OF ANTHOCYANIN PIGMENT1 transcription factor restores anthocyanin accumulation in vacuoles of atg mutants. Transcriptome analyses reveal connections between autophagy and (1) salicylic acid biosynthesis and response, (2) cytokinin perception, (3) oxidative stress and plant defense, and possible interactions between autophagy and the COP9 signalosome machinery. The metabolic and transcriptomic signatures identified for the autophagy mutants are discussed and show consistencies with the observed phenotypes.
authors.affiliation: Unité Mixte de Recherche 1318, INRA, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France AgroParisTech, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France celine.masclaux@versailles.inra.fr.
authors.forename: Céline
authors.initials: C
authors.lastname: Masclaux-Daubresse
authors.affiliation: Unité Mixte de Recherche 1318, INRA, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France AgroParisTech, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France.
authors.forename: Gilles
authors.initials: G
authors.lastname: Clément
authors.affiliation: Unité Mixte de Recherche 1318, INRA, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France AgroParisTech, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France.
authors.forename: Pauline
authors.initials: P
authors.lastname: Anne
authors.affiliation: Unité Mixte de Recherche 1318, INRA, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France AgroParisTech, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Routaboul
authors.affiliation: Unité Mixte de Recherche 1318, INRA, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France AgroParisTech, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Guiboileau
authors.affiliation: Unité Mixte de Recherche 1318, INRA, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France AgroParisTech, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France.
authors.forename: Fabienne
authors.initials: F
authors.lastname: Soulay
authors.affiliation: RIKEN, Plant Science Center, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Shirasu
authors.affiliation: Unité Mixte de Recherche 1318, INRA, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France AgroParisTech, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France RIKEN, Plant Science Center, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Kohki
authors.initials: K
authors.lastname: Yoshimoto