A revised assay for monitoring autophagic flux in Arabidopsis thaliana reveals involvement of AUTOPHAGY-RELATED9 in autophagy

Origin of the Autophagosomal Membrane in Plants

During autophagy, cargo molecules destined for degradation are sequestrated into a double-membrane structure called autophagosome, which subsequently fuses with the vacuole. An isolation membrane structure (also called the phagophore) initiates from the platform termed PAS (phagophore assembly site or preautophagosomal structure), which then elongates and expands to become the completed autophagosome. The origin of the membrane for autophagosome formation has been extensively investigated but remains an enigma in the field of autophagy. In yeast and mammalian cells multiple membrane sources have been suggested to contribute to autophagosome formation at different steps, from initiation through expansion and maturation. Recent studies in plants have provided a significant advance in our understanding of the conserved role of autophagy and the underlying mechanism for autophagosome formation. Here, we will discuss and evaluate these new findings on autophagosome formation in plants, with a particular focus on the origin of plant autophagosomal membranes.

Physiological Functions of the COPI Complex in Higher Plants

COPI vesicles are essential to the retrograde transport of proteins in the early secretory pathway. The COPI coatomer complex consists of seven subunits, termed α-, β-, β'-, γ-, δ-, ε-, and ζ-COP, in yeast and mammals. Plant genomes have homologs of these subunits, but the essentiality of their cellular functions has hampered the functional characterization of the subunit genes in plants. Here we have employed virus-induced gene silencing (VIGS) and dexamethasone (DEX)-inducible RNAi of the COPI subunit genes to study the in vivo functions of the COPI coatomer complex in plants. The β'-, γ-, and δ-COP subunits localized to the Golgi as GFP-fusion proteins and interacted with each other in the Golgi. Silencing of β'-, γ-, and δ-COP by VIGS resulted in growth arrest and acute plant death in Nicotiana benthamiana, with the affected leaf cells exhibiting morphological markers of programmed cell death. Depletion of the COPI subunits resulted in disruption of the Golgi structure and accumulation of autolysosome-like structures in earlier stages of gene silencing. In tobacco BY-2 cells, DEX-inducible RNAi of β'-COP caused aberrant cell plate formation during cytokinesis. Collectively, these results suggest that COPI vesicles are essential to plant growth and survival by maintaining the Golgi apparatus and modulating cell plate formation.

Methods for analysis of autophagy in plants

The plant vacuole is a major site for the breakdown and recycling of cellular macromolecules. Cytoplasmic components destined for degradation are delivered to the vacuole in vesicles termed autophagosomes, and the breakdown products are transported back into the cytosol for reuse, with the overall process termed autophagy. In plants, autophagy is required for nutrient remobilization and recycling during senescence and nutrient deficiency, for clearance of protein aggregates and damaged organelles during environmental stress, for pathogen defense, and for general cellular maintenance under normal growth conditions. There is growing interest in autophagy in plants due to the wide range of processes in which it functions. While much of the work thus far has used the model plant Arabidopsis thaliana, autophagy is now under investigation in a number of other plants, particularly in economically important crop species. Here, I discuss methods for assessing autophagy activity in plant cells. Microscopic and biochemical assays are described, along with ways to distinguish the steady-state number of autophagosomes from flux through the autophagic pathway. Some deficiencies still exist in plant autophagy analysis, and there is a particular need for more accurate methods of quantifying autophagic flux in plants.