The Overview of Autophagy

1. What is Autophagy?

Autophagy is a highly conserved adaptive process through which eukaryotic cells deliver dispensable or potentially dangerous cytoplasmic material to lysosomes for degradation under various conditions of cellular stress, including deprivation, growth factor depletion, infection, low energy and hypoxia. The main function of autophagy is to provide nutrients for vital cellular functions during fasting and other forms of stress, and is crucial to the maintenance of organismal homeostasis in both physiological and pathological situations[1][2].

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[3][4][5]. 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[6].

Canonical Autophagy

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[7], pexophagy[8], lipophagy[9], chlorophagy[10], ]mitophagy[11] 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.

Non-canonical Autophagy

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[12][13].

3. Core autophagy proteins of the autophagic pathway

Autophagy is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components. This progress is consist of six stages, including induction, phagophore nucleation, phagophore expansion, autophagosome formation, lysosome fusion, and component degradation. The core proteins of that stages are shown in the table 1 in details.

Table 1. Key autophagic factors and their regulation

Protein Function Mechanisms of regulation
Initiation and phagophore nucleation
ULK1 and ATG1 Serine/threonine kinase; initiates autophagy by phosphorylating components of the autophagy machinery Stress and nutrients (via mTORC1, AMPK and LKB1); TFEB and several miRNAs
FIP200 Component of ULK complex (possibly scaffolding function) ULK1 and miRNAs
ATG13 Adaptor mediating the interaction between ULK1 and FIP200; enhances ULK1 kinase activity ULK1, mTORC1 and AMPK
ATG101 Component of ULK complex; recruitment of downstream ATG proteins ULK1
VPS34 Catalytic component of PI3KC3–C1; generates PI3P in the phagophore and stabilizes the ULK complex AMPK, ULK1 and p300 (acetylation)
Beclin 1 Promotes formation of PI3KC3–C1 and regulates the lipid kinase VPS34 Activation: AMPK, ULK1, MAPKAPK2, MAPKAPK3, DAPK and UVRAG; inhibition: BCL-2, AKT and EGFR
ATG14 PI3KC3–C1 targeting to the PAS and expanding phagophore PIPKIγI5 and mTORC1
ATG9 Delivery of membrane material to the phagophore ULK1 complex
WIPI2 PI3P-binding protein that recruits ATG12-ATG5-ATG16L to the phagophore; retrieval of ATG9 from early autophagosomal membranes TFEB (positive transcription regulator) and ZKSCAN3 (negative transcription regulator)
Phagophore expansion
ATG4 Cysteine protease that processes pro-ATG8s; also, deconjugation of lipidated LC3 and ATG8s ULK1 and ROS
ATG7 E1-like enzyme; activation of ATG8; conjugation of ATG12 to ATG5 miRNAs
ATG3 E2-like enzyme; conjugation of activated ATG8s to membranal PE miRNAs
ATG10 E2-like enzyme that conjugates ATG12 to ATG5 miRNAs
ATG12~ATG5ATG16L E3-like complex that couples ATG8s to PE CSNK2
PE-conjugated ATG8s Scaffold for assembly of the ULK1 complex; supports membrane tethering and hemifusion events for phagophore expansion ULK1, PKA, ATG4 and mTOR
ATG9 Delivery of membrane material to the phagophore ULK1
Autophagosome formation
Ubiquitin Cargo labelling PINK (phosphorylation)
Cardiolipin and ceramide Cargo labelling Phosphorylation
p62 Autophagy receptor ULK1 and TBK1
OPTN Autophagy receptor TBK1
NBR1 Autophagy receptor TBK1
NDP52 Autophagy receptor TBK1
PE-conjugated LC3 Interaction with autophagy receptors; also phagophore expansion and sealing ULK1, PKA, ATG4 and mTOR
LC3s and GABARAPs Unclear Unclear; might involve phosphorylation and acetylation events
ATG4 Removal of ATG8s from the surface of the autophagosome Unknown
PE-conjugated LC3s and GABARAPs Linking the autophagosome to microtubulebased kinesin motor Unclear; might involve phosphorylation and acetylation events
Fusion with the lysosome
PE-conjugated LC3s and GABARAPs Mediates autophagosome–lysosome fusion upon phosphorylation through PLEKHM1 and HOPS STK3 and STK4
ATG14 Promotes SNARE-driven membrane fusion Unknown
Rab GTPase RAB7 Unclear Unknown

*Note: this content of the table 1 is driven from Ivan Dikic[14]

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[15]. 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[16][17]. In pre-malignant lesions, much evidence suggests that enhancers of autophagy might prevent cancer development[18]. Conversely, in advanced cancers, both enhancing autophagy and inhibiting it have been suggested as therapeutic strategies[19][20]. 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[21][22][23][24] and removal of intracellular bacteria[25][26][27]. Emerging evidences demonstrate that autophagy play a crucial role in these functions through the susceptibility of autophagy-deficient animals[28][29].

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[28]. 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)[30][31][32].


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Cite this article

CUSABIO team. The Overview of Autophagy.


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