Transcriptional and post-translational regulation of plant autophagy

Abstract

In response to changing environmental conditions, plants activate cellular responses to enable them to adapt. One such response is autophagy, in which cellular components, for example proteins and organelles, are delivered to the vacuole for degradation. Autophagy is activated by a wide range of conditions, and the regulatory pathways controlling this activation are now being elucidated. However, key aspects of how these factors may function together to properly modulate autophagy in response to specific internal or external signals are yet to be discovered. In this review we discuss mechanisms for regulation of autophagy in response to environmental stress and disruptions in cell homeostasis. These pathways include post-translational modification of proteins required for autophagy activation and progression, control of protein stability of the autophagy machinery, and transcriptional regulation, resulting in changes in transcription of genes involved in autophagy. In particular, we highlight potential connections between the roles of key regulators and explore gaps in research, the filling of which can further our understanding of the autophagy regulatory network in plants.

Keywords: ATG; autophagy; gene expression; persulfidation; phosphorylation; post-translational modification; starvation; stress; transcription factors; ubiquitination.

Fig. 1.

Post-translational modifications (PTMs) of core ATG proteins in plants. During autophagy, the core ATG proteins form distinct functional groups that can be divided into the ATG1/ATG13 kinase complex, PI3K complex, ATG2–ATG18–ATG9 complex, and the ATG conjugation machinery. Post-translational modifications such as phosphorylation, persulfidation, ubiquitination, and lipidation occur in the early steps of autophagy and dictate the function, dynamics, and stability of these proteins. Stress triggers the ATG1/ATG13 kinase complex to initiate phagophore formation. The PI3K complex decorates the phagophore with PI3P to facilitate vesicle nucleation while the ATG2–ATG9–ATG18 complex provides lipids and membranes to promote phagophore expansion. The ATG8 and ATG12 conjugation systems together facilitate ATG8 lipidation to promote autophagosome maturation. The completed autophagosome fuses with the vacuole to deposit the cargo for degradation and recycling. ‘P’ refers to phosphorylation known to be regulated by the indicated upstream kinase and ‘Ph’ refers to phosphorylation validated through phosphoproteomics by Mergner et al. (2020) and Montes et al. (2022).

Fig. 2.

Regulatory pathways that modulate plant autophagy in response to stress conditions. Autophagy is induced by different stress conditions via TORC-dependent (red arrow) and TORC-independent pathways (black arrow). Nutrient starvation, salt, and osmotic stress activate SnRK1, which inhibits TORC expression and activity. TORC can suppress autophagy through the inhibition of the ATG1/ATG13 complex (red arrow). SnRK1 can directly phosphorylate and activate the ATG1/ATG13 complex, leading to autophagy induction. Upon long-term carbon starvation, SnRK1 phosphorylates ATG6 to activate autophagy, which is independent of TORC (black arrow). Endoplasmic reticulum stress and oxidative stress activate autophagy through SnRK1-mediated phosphorylation of ATG1, independent of TORC repression (black arrow). Endoplasmic reticulum stress-induced autophagy is also regulated by INOSITOL REQUIRING 1A/B (IRE1A/B), but its relationship with SnRK1 is unknown (black dashed arrow). Phosphate deficiency activates autophagy through the endoplasmic reticulum stress-mediated pathway (green arrow). TAP46 (a regulatory subunit of PP2A) is phosphorylated by TORC, acts as a downstream effector of TOR signaling, and negatively regulates autophagy (beige arrow). All the stress-induced autophagy pathways require SnRK1 activity. Upon osmotic stress, ABA-activated SnRK2 phosphorylates RAPTOR and inhibits TORC activity. In the absence of stress, TORC phosphorylates the PYL ABA receptors (blue arrow). Whether or not SnRK2 kinase and PP2C protein phosphatase are involved in autophagy regulation through TORC inhibition is still unknown (blue dashed arrow).

Fig. 3.

Model of the role of transcriptional regulators of plant autophagy. (A) Under nutrient-rich conditions, HY5 and SOC1 translocate to the nucleus where they repress ATG expression to maintain autophagy at a low basal level. (B) Under nutrient starvation, HY5 and SOC1 protein abundance are reduced, which negatively regulates their transcriptional activities. In Arabidopsis, positive regulators such as TGA9 and ATAF1 up-regulate several ATG genes to promote autophagy and enhance starvation tolerance. Negative regulators such as LUX and TOC1 down-regulate ATG expression to fine-tune the level of autophagy and prevent autophagy-induced cell death. In tomato plants, BR induces the translocation of BZR1 into the nucleus where it activates ATG expression in response to starvation. (C) WRKY transcription factors positively regulate ATG expression to facilitate autophagy-mediated resistance to pathogen infection in various plant species. (D) To promote leaf senescence, WRKY53, in complex with PWR and HDA9, represses ATG9 expression. (E) Several transcription factors positively regulate ATG expression in response to different abiotic stresses such as heat (WRKY33, HSFA1a), drought (HSFA1a, ERF5), cold (BZR1), and osmotic stress (TGA9). Solid lines indicate direct transcriptional regulation with experimental evidence. Dashed lines indicate direct transcriptional regulation requiring experimental validation. BR, brassinosteroid; ETH, ethylene; Foc, Fusarium oxysporum f. sp. cubense; Xam, Xanthomonas axonopodis pv. manihotis.

Fig. 4.

Proposed model of potential connections between transcriptional and post-translational regulation of autophagy. (A) Under optimal growth conditions, the activity of positive regulators of autophagy (e.g. ATAF1, SnRK1) is inhibited while negative regulators are activated. Negative upstream regulators, such as TORC, can control ATG protein abundance by suppressing the transcriptional activation of ATG expression through post-translational modifications of transcriptional regulators. In addition, these negative upstream regulators may inhibit the stability and function of ATG proteins in the cytosol and thereby keep autophagy at a low basal level. (B) In stress conditions, the activity of negative regulators (e.g. SOC1, HY5, TORC, SINAT1/2) is inhibited while positive regulators (e.g. TGA9, HSFA1a, SnRK1) are activated. Positive upstream regulators (e.g. SnRK1) can enhance ATG protein abundance by promoting the transcriptional activation of ATG expression. Upstream regulators can also promote the stability and function of ATG proteins in the cytosol leading to increased autophagic activity. Black lines with arrow heads indicate activation while black lines with bars indicate repression. Solid black lines indicate activation or repression with experimental evidence whereas dashed black lines indicate lack of experimental evidence. Red arrows pointing down indicate decreased autophagy while red arrows pointing up indicate increased autophagy.