Arabidopsis SINAT Proteins Control Autophagy by Mediating Ubiquitylation and Degradation of ATG13

Abstract

In eukaryotes, autophagy maintains cellular homeostasis by recycling cytoplasmic components. The autophagy-related proteins (ATGs) ATG1 and ATG13 form a protein kinase complex that regulates autophagosome formation; however, mechanisms regulating ATG1 and ATG13 remain poorly understood. Here, we show that, under different nutrient conditions, the RING-type E3 ligases SEVEN IN ABSENTIA OF ARABIDOPSIS THALIANA1 (SINAT1), SINAT2, and SINAT6 control ATG1 and ATG13 stability and autophagy dynamics by modulating ATG13 ubiquitylation in Arabidopsis (Arabidopsis thaliana). During prolonged starvation and recovery, ATG1 and ATG13 were degraded through the 26S proteasome pathway. TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR1a (TRAF1a) and TRAF1b interacted in planta with ATG13a and ATG13b and required SINAT1 and SINAT2 to ubiquitylate and degrade ATG13s in vivo. Moreover, lysines K607 and K609 of ATG13a protein contributed to K48-linked ubiquitylation and destabilization, and suppression of autophagy. Under starvation conditions, SINAT6 competitively interacted with ATG13 and induced autophagosome biogenesis. Furthermore, under starvation conditions, ATG1 promoted TRAF1a protein stability in vivo, suggesting feedback regulation of autophagy. Consistent with ATGs functioning in autophagy, the atg1a atg1b atg1c triple knockout mutants exhibited premature leaf senescence, hypersensitivity to nutrient starvation, and reduction in TRAF1a stability. Therefore, these findings demonstrate that SINAT family proteins facilitate ATG13 ubiquitylation and stability and thus regulate autophagy.

Genome-Wide Identification of Apple Ubiquitin SINA E3 Ligase and Functional Characterization of MdSINA2

“…We found that the MdSINA2 degraded in the dark, and it became insensitive to light after its RING domain had been destroyed. Based on this result and those of previous studies (Qi et al, 2017;Qi et al, 2020), we speculate that the degradation of MdSINA2 in the dark may stem from the lack of energy available under dark conditions.…”

“…In addition, some of these genes had a higher expression level at 24 h, implying that MdSINAs were involved in ABA response and may act as important regulators of drought resistance as has been described previously. Recently, studies have shown that SINAT1/2/6 are involved in starvation-induced autophagy in Arabidopsis (Nolan et al, 2017;Qi et al, 2017;Qi et al, 2020). To further characterize the potential roles of MdSINA genes in nutrient starvation, the expression levels of MdSINAs were examined under carbon-and nitrogen-starvation conditions.…”

Role of Autophagy in Male Reproductive Processes in Land Plants

“…In A. thaliana, the expression of core ATG genes is spatiotemporally regulated, and the transcription factor TGA9 has been shown to positively regulate ATG8 expression and autophagic activity (Slavikova et al, 2005;Rose et al, 2006;Wang et al, 2019). Post-transcriptional regulation has also been reported in A. thaliana, which is exemplified by that the TOR and SnRK1 complexes catalyze phosphorylation of and SINAT proteins mediate ubiquitylation of the ATG1 complex responding to the nutrient status (Chen et al, 2017;Huang et al, 2019;Van Leene et al, 2019;Qi et al, 2020). It would be useful to explore whether these regulations have a role in male reproduction in plants.…”

Interplay between the Ubiquitin Proteasome System and Ubiquitin-Mediated Autophagy in Plants

“…Under starvation conditions, the levels of phosphorylated ATG1a and ATG13a drop dramatically, but this turnover is abolished when the ATG system is inhibited, indicating that the ATG1-ATG13 complex is degraded by autophagy [ 55 ]. Recent studies revealed that the stability of the ATG1-ATG13 complex is modulated by the ubiquitination pathway [ 56 ]. In Arabidopsis wild-type plants, ATG1a and ATG13a accumulate under carbon or nitrogen starvation, but are significantly reduced under prolonged starvation treatment.…”

“…Although ATG1 protein levels are also significantly reduced during prolonged starvation treatment, the mechanism of ATG1 degradation is still elusive. It was shown that the stability of TRAF1 can be regulated by ATG1, indicating feedback regulation between the ATG1-ATG13 kinase complex and TRAF1 proteins [ 56 , 57 ].…”