A family of metabolite damage-control phosphatases modulates ROS-induced autophagy and plant stress resilience
Year: 2026
Type: preprint
Abstract: Autophagy is an intracellular recycling pathway with profound impacts on development, growth, and stress tolerance in eukaryotes. Therefore, unravelling signalling mechanisms that modulate the process has broad applicability. Here, we characterised a small organic molecule as an enhancer of autophagy across diverse plant lineages. Through an in vivo photoaffinity proteomics approach in Arabidopsis thaliana seedlings, we identified Domain of Unknown Function 89 (DUF89) proteins as molecular targets. Hereafter, we refer to these proteins as Reactive Metabolite Damage-Control Phosphatases (RMDPs), which are metabolite-repair phosphatases that clear reactive products. The new autophagy modulator is called RMDP inhbitor-1 (RMDPi-1) due to its demonstrated inhibitory effect on AtRMDP1 activity in vitro. Binding was further confirmed through co-incubation that thermostabilised the protein. Crystal structures of AtRMDP1 were obtained via X-ray diffraction, confirming binding of RMDPi-1 in the catalytic site and revealing a flexible region near the binding pocket that was absent in previous models. Molecular docking predicted two possible binding modes consistent with the observed electron density. RMDPi-1 treatment and the phosphatase gene knockout increased autophagic flux in Arabidopsis and Chlamydomonas reinhardtii, establishing a conserved effect. The observed autophagy response is linked to a spike in reactive oxygen species (ROS). AtRMDP knockout also results in higher ROS tolerance and greater biomass in Arabidopsis seedlings. Targeted and untargeted metabolomic experiments revealed that both pharmacological and genetic suppression of RMDP leads to accumulation of glycating agents and phosphate sugars, associating loss of RMDP activity to the ROS stress that induces alternate ROS-scavenging mechanisms, and autophagy. Taken together, our integrated chemical genetics approach reveals enhanced autophagy via inhibition of RMDP family members, which impacts on plant stress tolerance via conserved metabolite damage-control functions.
Authors: Florentine Ballhaus, Viviana Vella, Yong Zou, Glenn R Hicks, Jacob Whittaker, Adrian Suarez Covarrubias, Flavio Ballante, Ali Moazzami, Igor Sabljic, Mary A Nishiotis, Anette Roos, Selvaraju Kanagarajan, Stina Berglund-Fick, Weixing Qian, Gustav Nestor, Peter V Bozhkov, Elena A Minina, Adrian N Dauphinee
Language: English
Subfield: Cell Biology
Domain: Life Sciences
Open Access status: green
Awards: G1677966246, Manipulating autophagy to increase plant productivity, AutoMods: Improving plant fitness and health using chemical genetics, Structure-function understanding of stress granules in plants, SwedNMR - a national NMR research infrastructure, Modulating Autophagy: New Strategies Toward Improved Crop Fitness and Health, Plant autophagy for sustainable agriculture, Chemical Biology Consortium Sweden
OpenAlex ID: W7214791001