2. The types of Autophagy
Thus far, there are three main types of autophagy, macroautophagy, microautophagy and Chaperone mediated autophagy, which are mediated by the autophagy-related genes and their associated enzymes. Macroautophagy (referred to throughout this article as autophagy), is the main pathway which is primarily used to eradicate damaged cell organelles or unused proteins and divided into canonical and non-canonical autophagy. In this article, we focus on the research progress of macroautophagy.
a. Canonical Autophagy
Canonical autophagy, also considered as a nonselective process, is the highly conserved process by which eukaryotic cells scavenge their own cytoplasmic contents by sequestration into a phagophore and then fusion with a lysosome for degradation.
mTOR is the key regulator of the molecular mechanisms of canonical autophagy. autophagy-inducing stimus (such as nutrient deprivation, stress, hypoxia) triggers the activation of AMPK, whose kinase activity inhibits mTOR, and then activates the pre-initiation complex, composed of ULK1/2, ATG13, ATG101 and FIP200. This complex then activates the PI3K complex(VPS34, Beclin 1 and ATG14). The PI3K complex produces phosphatidylinositol 3-phosphate (PI3P), which acts as recruitment messenger for the downstream two ubiquitin-like conjugation systems. One of ubiquitin-like conjugation systems is responsible for the formation of a supramolecular protein complex containing ATG5, ATG12 and autophagy-related 16-like 1 (ATG16L1), including autophagy-related 7 (ATG7) and ATG10. another composes of ATG3, ATG4 and ATG7, promotes the cleavage of members of the Atg8 protein family, including human LC3, and their conjugation to phosphatidylethanolamine (PE). The activity and coordination of these two systems facilitate the expansion and sealing of the autophagosome, as well as the lipidation and embedding of LC3-PE into the autophagosomal membrane.
b. Non-canonical Autophagy
On the contrary, non-canonical autophagy is considered a specific process that selectively targets to internal cellular substrates. The selective autophagy is the autophagy of oragenelles, such as ribophagy, pexophagy, lipophagy, chlorophagy, ]mitophagy and others.
Currently, mitophagy is a representive of selective autophagy, which can be regulated by serveral different mechanisms depending on the physiological context. Here are two different menchanisms to regulate mitophagy.
One key regulator is Parkin. Upon damage or depolarization, the mitochondrial kinase PteN-induced kinase 1 (PiNK1) becomes stabilized and recruits the Ub E3 protein ligase Parkin. PiNK1 and Parkin assemble phosphorylated Ub (pUb) chains on several proteins of the outer mitochondrial membrane via a feedforward mechanism. These proteins of the outer mitochondrial membrane in turn recruit cargo receptors such as calcium-binding and coiled-coil domaincontaining protein 2 (NDP52) and optineurin (OPtN). In this process, free Ub is phosphorylated by PiNK1, and Parkin attaches polyUb to the mitochondrial surface and the ubiquitin-like (uBl) domain of Parkin. these phosphorylation events enhance both the ubiquitin ligase activity of Parkin and its retention time on damaged mitochondria.
Another player in mitophagy is taNKbinding kinase 1 (tBK1), which promotes coupling of the cargo to the phagophore via phosphorylating ub-binding domains and LIRs of several cargo receptors, thereby increasing their affinity for pub and LC3, respectively. Notably, mitophagy can also occur in a ub-independent manner via mitochondrial proteins such as BCL2/adenovirus E1B protein-interacting protein 3-like (NiX), FuN14 domain-containing protein 1 (FuNDC1) and BCL2/adenovirus E1B protein-interacting protein 3 (BNiP3), which possess an LC3-interacting region (LIR) and therefore function as direct cargo receptors. they are typically regulated by stress-dependent phosphorylation. Finally, lipids, including phospholipids, such as cardiolipin and ceramide, have been shown to mediate mitophagy. in neuronal cells, cardiolipin is located at the inner membrane of healthy mitochondria, but upon mitochondrial damage, it is externalized and presented on the mitochondrial surface, where it is recognized by LC3.
4. Autophagy and Disease
The field of autophagy research has developed rapidly since the first description of the process in the 1960s and the identification of autophagy genes in the 1990s. Autophagy is now increasingly studied at the level of organismal pathophysiology and is being connected to the medical sciences.
a. Autophagy and cancer
Autophagy is an important process during cancer progression, but the exact roles of autophagy are strongly context-dependent in cancer cells. It is thought that autophagy prevents cancer development. In theory, high autophagic activity is believed to be cytoprotective and to suppress cancer initiation. However, once cancer is established, increased autophagic flux often enables tumour cell survival and growth. In pre-malignant lesions, much evidence suggests that enhancers of autophagy might prevent cancer development. Conversely, in advanced cancers, both enhancing autophagy and inhibiting it have been suggested as therapeutic strategies. Thus, there is an important question in cancer therapy: should we try to enhance autophagy or should we try to inhibit it? In another word, autophagy has opposing, context-dependent roles in cancer, and interventions to both stimulate and inhibit autophagy have been proposed as cancer therapies.
b. Autophagy in inflammation and immunity
Numerous studies reveal that autophagy is involved in a variety of immune functions, such as inflammatory cytokine secretion, lymphocyte development, control of inflammation, antigen presentation and removal of intracellular bacteria. Emerging evidences demonstrate that autophagy play a crucial role in these functions through the susceptibility of autophagy-deficient animals.
Mechanistically, autophagy extensively crosstalks with inflammatory signalling cascades, including multiple context-specific and bidirectional interactions with the IKK–NF-κB pathway. Autophagy is induced by NF-κB via transactivating Beclin 1. Moreover, in the presence of various physiological and pharmacological stress stimuli, the IKK complex can induce autophagy. However, the NF-κB pathway may also inhibit autophagy, for instance, in the context of tumour necrosis factor-α (TNFα)-induced cell death and in macrophages infected by Escherichia coli. Furthermore, in several cell lines, TNFα-driven NF-κB activation requires a functional autophagy pathway. Autophagy can also suppress NF-kB signalling by the autophagic degradation of active IKKβ, mediated either by KEAP1 (Kelch-like ECH-associated protein 1) or by the E3 ubiquitin-protein ligase RO52 (also known as TRIM21).
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