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Abudu et al. report that mitochondrial β-barrel biogenesis protein SAMM50 recruits ATG8 proteins through an LIR motif and interacts with p62/SQSTM1 to mediate basal piecemeal mitophagy of SAM and MICOS components. Upon metabolic switch to oxidative phosphorylation, SAMM50 and p62 cooperate to mediate efficient mitophagy., Mitophagy is the degradation of surplus or damaged mitochondria by autophagy. In addition to programmed and stress-induced mitophagy, basal mitophagy processes exert organelle quality control. Here, we show that the sorting and assembly machinery (SAM) complex protein SAMM50 interacts directly with ATG8 family proteins and p62/SQSTM1 to act as a receptor for a basal mitophagy of components of the SAM and mitochondrial contact site and cristae organizing system (MICOS) complexes. SAMM50 regulates mitochondrial architecture by controlling formation and assembly of the MICOS complex decisive for normal cristae morphology and exerts quality control of MICOS components. To this end, SAMM50 recruits ATG8 family proteins through a canonical LIR motif and interacts with p62/SQSTM1 to mediate basal mitophagy of SAM and MICOS components. Upon metabolic switch to oxidative phosphorylation, SAMM50 and p62 cooperate to mediate efficient mitophagy.

Summary Autophagy is the degradation of cytoplasmic material through the lysosomal pathway. One of the most studied autophagy-related proteins is LC3. Despite growing evidence that LC3 is enriched in the nucleus, its nuclear role is poorly understood. Here, we show that Drosophila Atg8a protein, homologous to mammalian LC3, interacts with the transcription factor Sequoia in a LIR motif-dependent manner. We show that Sequoia depletion induces autophagy in nutrient-rich conditions through the enhanced expression of autophagy genes. We show that Atg8a interacts with YL-1, a component of a nuclear acetyltransferase complex, and that it is acetylated in nutrient-rich conditions. We also show that Atg8a interacts with the deacetylase Sir2, which deacetylates Atg8a during starvation to activate autophagy. Our results suggest a mechanism of regulation of the expression of autophagy genes by Atg8a, which is linked to its acetylation status and its interaction with Sequoia, YL-1, and Sir2., Graphical Abstract, Highlights • Transcription factor Sequoia is a negative regulator of autophagy • Sequoia interacts with Atg8a via a LIR motif • Atg8a interacts with YL-1, a subunit of a nuclear acetyltransferase complex • Sir2 interacts with and deacetylates Atg8a during starvation, Jacomin et al. show that Atg8a interacts with transcription factor Sequoia. Depletion of Sequoia induces autophagy through enhanced expression of autophagy genes. Atg8a also interacts with YL-1, a component of a nuclear acetyltransferase complex, and deacetylase Sir2. Sir2 deacetylates Atg8a during starvation to activate autophagy.

SUMMARYAutophagy is a fundamental, evolutionarily conserved, process in which cytoplasmic material is degraded through the lysosomal pathway [1–7]. One of the most important and well-studied autophagy-related proteins is LC3 [Microtubule-associated protein 1 light chain 3, (called Atg8 in yeast and Drosophila)], which participates in autophagosome formation and autophagy cargo selection in the cytoplasm, and is one of the most widely utilized markers of autophagy [8, 9]. Despite growing evidence that LC3 is enriched in the nucleus, little is known about the mechanisms involved in targeting LC3 to the nucleus and the nuclear components it interacts with [10–13]. Here we show that Drosophila Atg8a protein, homologous to mammalian LC3 and yeast Atg8, interacts with the transcription factor Sequoia in a LIR-motif dependent manner. We show that Sequoia depletion induces autophagy in nutrient rich conditions through enhanced expression of autophagy genes. We also show that Atg8a interacts with YL-1, a component of a nuclear acetyltransferase complex, and is acetylated at position K46. Additionally, we show that Atg8a interacts with the deacetylase Sir2, which deacetylates Atg8a during starvation in order to activate autophagy. Our results suggest a mechanism of regulation of expression of autophagy genes by Atg8a, which is linked to its acetylation status and its interaction with Sequoia, YL-1 and Sir2.

Autophagy is a process in which cytoplasmic material is degraded through the lysosomal pathway. One of the most studied autophagy-related proteins is LC3, which participates in autophagosome formation and autophagy cargo selection in the cytoplasm. Despite growing evidence that LC3 is enriched in the nucleus, little is known about the nuclear components it interacts with. Here we show that Drosophila Atg8a protein, homologous to mammalian LC3, interacts with the transcription factor Sequoia in a LIR-motif dependent manner. We show that Sequoia depletion induces autophagy in nutrient rich conditions through enhanced expression of autophagy genes. We show that Atg8a interacts with YL-1, a component of a nuclear acetyltransferase complex and that it is acetylated in nutrient rich conditions. We also show that Atg8a interacts with the deacetylase Sir2, which deacetylates Atg8a during starvation in order to activate autophagy. Our results suggest a mechanism of regulation of expression of autophagy genes by Atg8a, which is linked to its acetylation status and its interaction with Sequoia, YL-1 and Sir2.

Transmission Electron Microscopy (TEM) provides high resolution and accuracy at the subcellular level for observing and investigating cellular structures. This is essential for understanding a large variety of cellular processes. In this chapter, we describe a detailed protocol for preparing Drosophila follicles in order to be used as a specimen for transmission electron microscopy.

Transmission Electron Microscopy (TEM) provides high resolution and accuracy at the subcellular level for observing and investigating cellular structures. This is essential for understanding a large variety of cellular processes. In this chapter, we describe a detailed protocol for preparing Drosophila follicles in order to be used as a specimen for transmission electron microscopy.