Biology subjects

Dauphinee, A. N.

Publications and source records attributed to Dauphinee, A. N..

5 recordsLinked to original sources

bioRxiv2026

A family of metabolite damage-control phosphatases modulates ROS-induced autophagy and plant stress resilience

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.

plant biology↗

bioRxiv2026

Organ identity shapes autophagy dynamics and selectivity in plants

Plants, with their unique evolutionary trajectory and complex physiological adaptations, have developed organ-specific mechanisms to cope with various environmental stresses. Autophagy, an essential catabolic process, plays an important role in maintaining plant growth, immunity, and overall fitness. In this study, we reveal the spatio-temporal dynamics of autophagic responses in Arabidopsis thaliana roots and shoots under different stress conditions, including AZD8055 treatment and carbon and nitrogen depletion. Our findings demonstrate that roots exhibit stronger autophagic activity than shoots under all three conditions, highlighting the unique adaptations of these two organs. Furthermore, we dissect the selectivity of autophagy in targeting organelles, revealing immediate, delayed, and no uptake categories. Additionally, we observe organelles coexisting within autophagic bodies, shedding light on the complexity of cargo selection. This study enhances our understanding of plant specific autophagy dynamics, emphasizing its role in sustaining the source-sink functions and offering insights into plant adaptation to diverse stressors.

plant biology↗

bioRxiv2021

SPIRO-the automated Petri plate imaging platform designed by biologists, for biologists

Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photos of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIROs excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared to manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing and photoblastic response.

plant biology↗

bioRxiv2020

Apoptosis in plants: from semantic appeal to empirical rejection

BackgroundAnimals and plants diverged over one billion years ago and evolved unique mechanisms for many cellular processes, including cell death. One of the most well-studied cell-death programmes in animals, apoptosis, involves gradual cell dismantling and engulfment of cellular fragments, apoptotic bodies, through phagocytosis. However, rigid cell walls prevent plant cell fragmentation and thus apoptosis is not applicable for executing cell death in plants. Furthermore, plants are devoid of the key components of apoptotic machinery, including phagocytosis as well as caspases and Bcl-2 family proteins. Nevertheless, the concept of plant "apoptosis-like programmed cell death" (AL-PCD) is widespread. This is largely due to superficial morphological resemblances between plant cell death and apoptosis; in particular between protoplast shrinkage in plant cells killed by various stimuli and animal cell volume decrease preceding fragmentation into apoptotic bodies. ResultsHere, we provide a comprehensive spatio-temporal analysis of cytological and biochemical events occurring in plant cells subjected to heat shock at 40-55{degrees}C and 85{degrees}C, the experimental conditions typically used to trigger AL-PCD and necrotic cell death, respectively. We show that cell death under both conditions was not accompanied by membrane blebbing or formation of apoptotic bodies, as would be expected during apoptosis. Instead, we observed instant and irreversible permeabilization of the plasma membrane and ATP depletion. These processes did not depend on mitochondrial functionality or the presence of Ca2+ and could not be prevented by an inhibitor of ferroptosis. We further reveal that the lack of protoplast shrinkage at 85{degrees}C, the only striking morphological difference between cell deaths induced by 40-55{degrees}C or 85{degrees}C heat shock, is a consequence of the fixative effect of the high temperature on intracellular contents. ConclusionsWe conclude that heat shock-induced cell death is an energy-independent process best matching definition of necrosis. Although the initial steps of this necrotic cell death could be genetically regulated, classifying it as apoptosis or AL-PCD is a terminological misnomer. Our work supports the viewpoint that apoptosis is not conserved across animal and plant kingdoms and demonstrates the importance of focusing on plant-specific aspects of cell death pathways.

plant biology↗

bioRxiv2019

Chemical screening pipeline for identification of specific plant autophagy modulators

Autophagy is a major catabolic process in eukaryotes with a key role in homeostasis, programmed cell death and aging. In plants, autophagy is also known to regulate agriculturally important traits such as stress resistance, longevity, vegetative biomass and seed yield. Despite its significance, there is still a shortage of reliable tools modulating plant autophagy. Here we describe the first robust pipeline for identification of specific plant autophagy-modulating compounds. Our screening protocol comprises four phases: (i) high-throughput screening of chemical compounds in cell cultures of Nicotiana tabacum; (ii) confirmation of the identified hits in planta using Arabidopsis thaliana; (iii) further characterization of the effect using conventional molecular biology methods; (iv) verification of chemical specificity on autophagy in planta. The methods detailed here streamline identification of specific plant autophagy modulators and aid in unravelling the molecular mechanisms of plant autophagy.

plant biology↗