An Arabidopsis Rab18 GTPase promotes autophagy by tethering ATG18a to the ER in response to nutrient starvation

How coat proteins shape autophagy in plant cells

Autophagy is a membrane trafficking pathway through which eukaryotic cells target their own cytoplasmic constituents for degradation in the lytic compartment. Proper biogenesis of autophagic organelles requires a conserved set of autophagy-related (ATG) proteins and their interacting factors, such as signalling phospholipid phosphatidylinositol 3-phosphate (PI3P) and coat complex II (COPII). The COPII machinery, which was originally identified as a membrane coat involved in the formation of vesicles budding from the endoplasmic reticulum, contributes to the initiation of autophagic membrane formation in yeast, metazoan, and plant cells; however, the exact mechanisms remain elusive. Recent studies using the plant model species Arabidopsis thaliana have revealed that plant-specific PI3P effectors are involved in autophagy. The PI3P effector FYVE2 interacts with the conserved PI3P effector ATG18 and with COPII components, indicating an additional role for the COPII machinery in the later stages of autophagosome biogenesis. In this Update, we examined recent research on plant autophagosome biogenesis and proposed working models on the functions of the COPII machinery in autophagy, including its potential roles in stabilizing membrane curvature and sealing the phagophore.

The potential role of vesicle transport-related small GTPases rabs in abiotic stress responses

Rab GTPases are a class of small GTP-binding proteins, play crucial roles in the membrane transport machinery with in eukaryotic cells. They dynamically regulate the precise targeting and tethering of transport vesicles to specific compartments by transitioning between active and inactive states. In plants, Rab GTPases are classified into eight distinct subfamilies: Rab1/D, Rab2/B, Rab5/F, Rab6/H, Rab7/G, Rab8/E, Rab11/A, and Rab18/C. Their functional specificity is often attributed to their cellular localization. This paper reviews provides a comprehensive review of the pivotal roles played by Rab GTPases in plant intracellular transport and their significant contributions to abiotic stress responses. Additionally, it critically examines the identified activators and effectors associated with these proteins. In the context of abiotic stress, Rab GTPases play a crucial role in regulating vesicle transport and secretion, thereby enhancing plant adaptability and survival under adverse conditions such as drought, salt stress, and low temperatures. By mediating these intricate processes, Rab GTPases actively contribute to maintaining cellular homeostasis and improving stress resilience - factors that are indispensable for sustainable agricultural development and ecosystem stability.

Genome-Wide and Transcriptome Analysis of Autophagy-Related ATG Gene Family and Their Response to Low-Nitrogen Stress in Sugar Beet

Sugar beet (Beta vulgaris L.) is a significant global crop for sugar production, with nitrogen playing a crucial role in its growth, development, and sugar yield. Autophagy facilitates nutrient reabsorption and recycling under nutrient stress by degrading intracellular components, thereby enhancing plant nitrogen use efficiency. However, research on the autophagy response to low-nitrogen stress in sugar beet remains limited. In this study, 29 members of the ATG gene family were identified, with genes within the same subfamily displaying similar gene structures and conserved domains. These ATG genes in sugar beet contain various hormone and stress-response elements. Transcriptome data and qRT-PCR analysis further revealed that the expression levels of ATG4, ATG8b, ATG18a, TOR, NBR1, ATI, ATG8a, ATG12, and VTI12a were significantly upregulated under low-nitrogen stress, with most genes showing high expression levels across different tissues. These ATG genes are thus likely involved in regulating autophagy in response to low-nitrogen conditions. The observed increase in autophagosome numbers further supports the induction of autophagy by low-nitrogen stress. These nine genes can be considered key candidates for further research on nitrogen-sensitive autophagy in the sugar beet ATG gene family. This study provides a comprehensive analysis of the structure and biological functions of ATG genes in sugar beet, offering genetic resources for future efforts to improve sugar beet varieties through genetic engineering. Such efforts could focus on regulating autophagy to enhance nitrogen use efficiency and develop new germplasm.

A Nitrogen-specific Interactome Analysis Sheds Light on the Role of the SnRK1 and TOR Kinases in Plant Nitrogen Signaling

Nitrogen (N) is of utmost importance for plant growth and development. Multiple studies have shown that N signaling is tightly coupled with carbon (C) levels, but the interplay between C/N metabolism and growth remains largely an enigma. Nonetheless, the protein kinases Sucrose Non-fermenting 1 (SNF1)-Related Kinase 1 (SnRK1) and Target Of Rapamycin (TOR), two ancient central metabolic regulators, are emerging as key integrators that link C/N status with growth. Despite their pivotal importance, the exact mechanisms behind the sensing of N status and its integration with C availability to drive metabolic decisions are largely unknown. Especially for SnRK1, it is not clear how this kinase responds to altered N levels. Therefore, we first monitored N-dependent SnRK1 kinase activity with an in vivo Separation of Phase-based Activity Reporter of Kinase (SPARK) sensor, revealing a contrasting N-dependency in Arabidopsis thaliana (Arabidopsis) shoot and root tissues. Next, using affinity purification (AP) and proximity labeling (PL) coupled to mass spectrometry (MS) experiments, we constructed a comprehensive SnRK1 and TOR interactome in Arabidopsis cell cultures during N-starved and N-repleted growth conditions. To broaden our understanding of the N-specificity of the TOR/SnRK1 signaling events, the resulting network was compared to corresponding C-related networks, identifying a large number of novel, N-specific interactors. Moreover, through integration of N-dependent transcriptome and phosphoproteome data, we were able to pinpoint additional N-dependent network components, highlighting for instance SnRK1 regulatory proteins that might function at the crosstalk of C/N signaling. Finally, confirmation of known and identification of novel SnRK1 interactors, such as Inositol-Requiring 1 (IRE1A) and the RAB GTPase RAB18, indicate that SnRK1, present at the ER, is involved in N signaling and autophagy induction.

Autophagosome biogenesis and organelle homeostasis in plant cells

Autophagy is one of the major highly inducible degradation processes in response to plant developmental and environmental signals. In response to different stimuli, cellular materials, including proteins and organelles, can be sequestered into a double membrane autophagosome structure either selectively or nonselectively. The formation of an autophagosome as well as its delivery into the vacuole involves complex and dynamic membrane processes. The identification and characterization of the conserved autophagy-related (ATG) proteins and their related regulators have greatly advanced our understanding of the molecular mechanism underlying autophagosome biogenesis and function in plant cells. Autophagosome biogenesis is tightly regulated by the coordination of multiple ATG and non-ATG proteins and by selective cargo recruitment. This review updates our current knowledge of autophagosome biogenesis, with special emphasis on the core molecular machinery that drives autophagosome formation and autophagosome-organelle interactions under abiotic stress conditions.

RABC1, an Arabidopsis RAB18 regulates binding and subsequent detachment of autophagosomes from the ER in autophagy

Macroautophagy/autophagy is a strategy cells use to cope with detrimental conditions, e.g. nutrient deficiency. Phagophores, the precursors to autophagosomes, are initiated and expanded on the endoplasmic reticulum (ER). However, how phagophores and completed autophagosomes are linked to the ER remains incompletely understood. We recently unveiled a RAB GTPase-based linkage between the two structures. RABC1 is a plant member of RABC/RAB18 GTPases. Our biochemical and microscopy data indicated that RABC1 promotes autophagy in response to nutrient starvation, but not under ER stress. Under nutrient-starvation conditions, active RABC1 interacts with ATG18a on the ER, controlling the association of ATG18a to the ER. Subsequently, active RABC1 is turned off allowing expanded phagophores or autophagosomes to detach from the ER. Our work identifies a RAB GTPase-mediated autophagy process in plant cells, opening a door for improving crop productivity in the changing environment.