Selective Autophagy of Mitochondria on a Ubiquitin-Endoplasmic-Reticulum Platform

摘要

class="head no_bottom_margin" id="sec1title">IntroductionAutophagy is a conserved pathway for nutrient supply during periods of starvation, classified as non-selective autophagy, or for degradation of intracellular large structures that are pathogenic or have become damaged, classified as selective autophagy (, , ). In both pathways, a novel double membrane organelle termed autophagosome is formed in the cytosol that then engulfs its cargo for eventual delivery to the lysosomes and degradation (, ). For non-selective autophagy, the cargo is total cytosol, and its degradation in the lysosomes generates nutrients essential during starvation (, ). In contrast, specific elimination of large membrane structures—damaged mitochondria, endoplasmic reticulum (ER) fragments, or bacterial pathogens—is the purview of selective autophagy and constitutes an essential quality control system (, , , ).The pathway of autophagosome formation in response to starvation is now well understood, although the exact origin of the autophagosomal membrane is still a matter of debate (, ). For autophagosomes that originate from within PI3P-enriched regions of the ER termed omegasomes, the pathway starts by inactivation of the protein kinase complex mTORC1 and the concomitant activation of the autophagy-specific ULK protein kinase complex composed of the protein kinase ULK1 (or its homolog ULK2) and the adaptors FIP200, ATG13, and ATG101 (, ). Activated ULK complex translocates to tubulovesicular regions of the ER marked by ATG9 vesicles, and these sites attract the lipid kinase complex termed VPS34 complex I, which produces PI3P and forms omegasomes (href="#bib71" rid="bib71" class=" bibr popnode">Walker et al., 2008, href="#bib30" rid="bib30" class=" bibr popnode">Karanasios et al., 2016). PI3P within the omegasome membrane attracts members of the WIPI family of proteins that in turn bind to the protein ATG16 and mediate the covalent modification of the LC3 and GABARAP proteins with phosphatidylethanolamine, which is an important requirement for the formation of autophagosomes (href="#bib76" rid="bib76" class=" bibr popnode">Wilson et al., 2014, href="#bib85" rid="bib85" class=" bibr popnode">Yu et al., 2018).The process of selective autophagy requires a set of proteins connecting the targeted cargo to the autophagic machinery and a signal on the cargo to mark it for sequestration (href="#bib25" rid="bib25" class=" bibr popnode">Johansen and Lamark, 2011, href="#bib60" rid="bib60" class=" bibr popnode">Rogov et al., 2014). Selective autophagy receptors are responsible for bridging cargo with the forming autophagosome. In yeast, they include Atg32 for mitochondrial autophagy (mitophagy, href="#bib54" rid="bib54" class=" bibr popnode">Okamoto et al., 2009, href="#bib27" rid="bib27" class=" bibr popnode">Kanki et al., 2009), Atg36 and Atg30 for autophagy of peroxisomes (pexophagy, href="#bib47" rid="bib47" class=" bibr popnode">Motley et al., 2012, href="#bib50" rid="bib50" class=" bibr popnode">Nazarko et al., 2014), Atg39 and Atg40 for autophagy of ER membranes (href="#bib44" rid="bib44" class=" bibr popnode">Mochida et al., 2015), and Atg19/Atg34 for the Cvt pathway (href="#bib63" rid="bib63" class=" bibr popnode">Scott et al., 2001, href="#bib66" rid="bib66" class=" bibr popnode">Suzuki et al., 2010, href="#bib73" rid="bib73" class=" bibr popnode">Watanabe et al., 2010). Equivalent and homologous proteins exist for mammals and for many types of cargo (href="#bib31" rid="bib31" class=" bibr popnode">Khaminets et al., 2016). Receptors interact with the autophagic machinery via LC3 and GABARAP-interacting regions that bridge autophagosomal membranes with targeted cargo, and such a simple bi-valent interaction could, in principle, enable engulfment (href="#bib6" rid="bib6" class=" bibr popnode">Birgisdottir et al., 2013). However, the autophagic machinery must also be involved in this process since it is responsible for generating lipidated LC3 and GABARAP residing on autophagosomal membranes. The current work aims to identify the dynamics and hierarchical coordination between the autophagic machinery and the selective autophagy receptors.The pathway of mitophagy has been extensively studied since it was first described (href="#bib38" rid="bib38" class=" bibr popnode">Lemasters, 2005). The “eat me” signals on damaged mitochondria initiating this process (href="#bib56" rid="bib56" class=" bibr popnode">Randow and Youle, 2014) can be divided into ubiquitin-dependent and ubiquitin-independent (href="#bib31" rid="bib31" class=" bibr popnode">Khaminets et al., 2016, href="#bib79" rid="bib79" class=" bibr popnode">Yamano et al., 2016). The former rely on ubiquitination of mitochondrial outer membrane proteins in response to damage that is then recognized by mitophagy receptors for recruitment of the LC3 and GABARAP proteins (href="#bib11" rid="bib11" class=" bibr popnode">Dikic, 2017, href="#bib35" rid="bib35" class=" bibr popnode">Kwon and Ciechanover, 2017). A paradigm is the mitophagy pathway regulated by the PINK1 and Parkin proteins (href="#bib49" rid="bib49" class=" bibr popnode">Narendra et al., 2008, href="#bib51" rid="bib51" class=" bibr popnode">Nguyen et al., 2016) where several receptors such as optineurin, NDP-52, Tax1BP1, and p62 translocate to damaged mitochondria (href="#bib37" rid="bib37" class=" bibr popnode">Lazarou et al., 2015). Mitophagy “eat me” signals independent of ubiquitination rely on specific mitochondrial proteins acting as mitophagy receptors (href="#bib31" rid="bib31" class=" bibr popnode">Khaminets et al., 2016, href="#bib58" rid="bib58" class=" bibr popnode">Roberts et al., 2016).Although mitophagy plays an essential role for mitochondrial homeostasis in vivo, the exact signals that trigger it at the organismal level are still relatively obscure (href="#bib74" rid="bib74" class=" bibr popnode">Whitworth and Pallanck, 2017, href="#bib59" rid="bib59" class=" bibr popnode">Rodger et al., 2018). In contrast, at least 14 different pharmacological agents induce mitophagy in tissue culture cells (href="#bib17" rid="bib17" class=" bibr popnode">Georgakopoulos et al., 2017). Taking advantage of our experimental models previously used to follow the dynamics of non-selective autophagy in mammalian cells, we have now examined the dynamics of mitophagy including the origin of the membrane used for mitophagy and the coordination between autophagy and mitophagy machineries during the engulfment step.