Autophagy is a major degradation process of cytoplasmic components in eukaryotes, and executes both bulk and selective degradation of targeted cargos. A set of autophagy-related (ATG) proteins participate in various stages of the autophagic process. Among ATGs, ubiquitin-like protein ATG8 plays a central role in autophagy. The ATG8 protein is conjugated to the membrane lipid phosphatidylethanolamine in a ubiquitin-like conjugation reaction that is essential for autophagosome formation. In addition, ATG8 interacts with various adaptor/receptor proteins to recruit specific cargos for degradation by selective autophagy. The ATG8-interacting proteins usually contain the ATG8-interacting motif (AIM) or the ubiquitin-interacting motif (UIM) for ATG8 binding. Unlike a single ATG8 gene in yeast, multiple ATG8 orthologs have been identified in the plant kingdom. The large diversity within the ATG8 family may explain the various functions of selective autophagy in plants. Here, we discuss and summarize the current view of the structure and function of ATG8 proteins in plants.

Autophagy is a highly conserved process of degradation of cytoplasmic constituents in eukaryotes. It is involved in the growth and development of plants, as well as in biotic and abiotic stress response. Although autophagy-related (ATG) genes have been identified and characterized in many plant species, little is known about this process in Medicago truncatula. In this study, 39 ATGs were identified, and their gene structures and conserved domains were systematically characterized in M. truncatula. Many cis-elements, related to hormone and stress responsiveness, were identified in the promoters of MtATGs. Phylogenetic and interaction network analyses suggested that the function of MtATGs is evolutionarily conserved in Arabidopsis and M. truncatula. The expression of MtATGs, at varied levels, was detected in all examined tissues. In addition, most of the MtATGs were highly induced during seed development and drought stress, which indicates that autophagy plays an important role in seed development and responses to drought stress in M. truncatula. In conclusion, this study gives a comprehensive overview of MtATGs and provides important clues for further functional analysis of autophagy in M. truncatula.

Autophagy is an evolutionarily conserved degradation pathway in eukaryotes; it plays a critical role in nutritional stress tolerance. The circadian clock is an endogenous timekeeping system that generates biological rhythms to adapt to daily changes in the environment. Accumulating evidence indicates that the circadian clock and autophagy are intimately interwoven in animals. However, the role of the circadian clock in regulating autophagy has been poorly elucidated in plants. Here, we show that autophagy exhibits a robust circadian rhythm in both light/dark cycle (LD) and in constant light (LL) inArabidopsis. However, autophagy rhythm showed a different pattern with a phase‐advance shift and a lower amplitude in LL compared to LD. Moreover, mutation of the transcription factorLUX ARRHYTHMO(LUX) removed autophagy rhythm in LL and led to an enhanced amplitude in LD. LUX represses expression of the core autophagy genesATG2,ATG8a, andATG11by directly binding to their promoters. Phenotypic analysis revealed thatLUXis responsible for improved resistance of plants to carbon starvation, which is dependent on moderate autophagy activity. Comprehensive transcriptomic analysis revealed that the autophagy rhythm is ubiquitous in plants. Taken together, our findings demonstrate that the LUX‐mediated circadian clock regulates plant autophagy rhythms.

The plant circadian clock operates through interlocked transcriptional-translational feedback loops (TTFLs), comprising circadian-regulated transcriptional activators and repressors at the core oscillator. These transcription factors (TFs) not only regulate the timing of gene expression within the oscillator but also orchestrate downstream transcriptomic regulation in output pathways by directly binding to the promoters of key genes. To date, most plant transcription factors identified in these loops are transcriptional repressors, supporting a clock model dominated by repressive interactions. However, some studies have revealed the presence of transcriptional activators in newly identified feedback loops. Interestingly, some transcription factors can function as both activators and repressors of circadian-regulated genes, offering new insights into the clock's regulatory mechanisms. This review revisits the longstanding question of transcriptional activation and repression in core oscillator genes, offering a conceptual framework to advance understanding of their roles, particularly in the regulation of clock output pathways.