May 15, 2014

Review: Stitching together the Multiple Dimensions of Autophagy Using Metabolomics and Transcriptomics Reveals Impacts on Metabolism, Development, and Plant Responses to the Environment in Arabidopsis


The Plant Cell tpc.114.124677 


(click here to download the original article)


Céline Masclaux-Daubressea,b,*, Gilles Clémenta,b, Pauline Annea,b, Jean-Marc Routaboula,b, Anne Guiboileaua,b, Fabienne Soulaya,b, Ken Shirasuc and Kohki Yoshimotoa,b,c

* Corresponding author (celine.masclaux@versailles.inra.fr)
a Unité Mixte de Recherche 1318, INRA, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France
b AgroParisTech, Institut Jean-Pierre Bourgin, 78026 Versailles cedex, France
c RIKEN, Plant Science Center, Tsurumi-ku, Yokohama 230-0045, Japan

    Autophagy is a cellular process whereby cytoplasmic materials and organelles are sequestered and  degraded for the purpose of recycling. This conserved process was originally discovered in yeast but also occurs in animals and plants. Chloroplast specific autophagy is known as chlorophagy. This week researchers from the RIKEN plant center in Yokohama as well as investigators from the INRA in Versaillles, France report on metabolomic and transcriptomic analysis of autophagy (atg) mutants. Extensive metabolomic analysis using GCMS of small molecules (amino acids, sugars, and organic acids), LCMS of larger metabolites (anthocynanins and phenylpropanoids), as well as enzyme assays for labile compounds (glutathione) revealed the accumulation of several amino acids, in particular glutamate and methionone, as well as amino acid intermediates (pipecolate and shikimate). These increases were noted in multiple mutant lines and were accompanied by decreases in hexose sugars. Various stress marker metabolites were also detected (raffinose, galacturonate, phytol, pipecolate, and stigmasterols). This established a link between amino acid metabolism and oxidative stress management. Transcriptomic analysis indicated a link between autophagy and cytokinin perception. This work extends our limited knowledge of autophagy in plants and highlights the metabolic pathways that are involved by identifying individual metabolites that accumulate when the genes involved in autophagy are disrupted.

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