V-ATPases and amino acid catabolism are strongly disturbed in the roots of autophagy mutants in Arabidopsis, impacting water use efficiency and tricarboxylic acid metabolism.

Autophagy is essential for homeostasis and nutrient recycling. Its activity increases with aging and in response to deficiencies. The effects of defective autophagy on root metabolism have not yet been described. Addressing this question through root proteome analyses, we found that most V-ATPases were less abundant in the roots of autophagy mutants than in wild type. V-ATPases deficit, associated with lower root water contents and lower nitrate, magnesium, and potassium concentrations, indicated that the disturbance of cellular ion and water management in autophagy mutants was likely related to vacuole function. Isotopic δC analyses and leaf temperature measurements using thermography showed that water deficit in autophagy mutants was not due to excess transpiration, as the conductance of stomata was reduced in mutants compared to wild type. Many proteins related to the catabolism of amino acids and lipids and the tricarboxylic acid (TCA) cycle were over-abundant in atg mutants. The increase in several proteases that paralleled amino acid catabolism suggested that in the absence of autophagic flux, compensatory processes could be established to degrade proteins, recycle amino acids, and fuel TCA. Whether the V-ATPases defect affects energy metabolism and promotes lipid and amino acid catabolism to compensate and fuel TCA remains to be explored. In conclusion, this report establishes for the first time a correlation between autophagy and vacuole function through V-ATPases, particularly with regard to water and ion management. Additionally, this report shows the exacerbation of amino acid catabolism in relation to the stimulation of the TCA cycle in autophagy mutants.