Selective autophagy of intracellular organelles: recent research advances

Abstract

Macroautophagy (hereafter called autophagy) is a highly conserved physiological process that degrades over-abundant or damaged organelles, large protein aggregates and invading pathogens via the lysosomal system (the vacuole in plants and yeast). Autophagy is generally induced by stress, such as oxygen-, energy- or amino acid-deprivation, irradiation, drugs, etc. In addition to non-selective bulk degradation, autophagy also occurs in a selective manner, recycling specific organelles, such as mitochondria, peroxisomes, ribosomes, endoplasmic reticulum (ER), lysosomes, nuclei, proteasomes and lipid droplets (LDs). This capability makes selective autophagy a major process in maintaining cellular homeostasis. The dysfunction of selective autophagy is implicated in neurodegenerative diseases (NDDs), tumorigenesis, metabolic disorders, heart failure, etc. Considering the importance of selective autophagy in cell biology, we systemically review the recent advances in our understanding of this process and its regulatory mechanisms. We emphasize the 'cargo-ligand-receptor' model in selective autophagy for specific organelles or cellular components in yeast and mammals, with a focus on mitophagy and ER-phagy, which are finely described as types of selective autophagy. Additionally, we highlight unanswered questions in the field, helping readers focus on the research blind spots that need to be broken.

Keywords: ER-phagy; autophagy receptor; lipophagy; lysophagy; mitophagy; nucleophagy; pexophagy; proteaphagy; ribophagy; selective autophagy.

Figure 1

Timeline of key discoveries in selective autophagy. This timeline depicts a selection of important discoveries in different selective autophagy processes. However, not all important discoveries are included due to space limitations.

Figure 2

Proposed models for different mammalian mitophagy pathways. The diagram shows two classical mitophagy pathways: (1) mitophagy receptors/adapters-mediated mitophagy and (2) PINK1/Parkin-induced mitophagy. (1) Under hypoxic conditions, FUNDC1, BNIP3 and NIX recruits autophagosomes to mitochondria by direct interaction with LC3 through its LIR domains. Upon mitophagy induction, Ambra1 mediates HUWE1 translocation from cytosol to mitochondria, leading to the degradation of MFN2. This event is necessary for Ambra1-induced mitophagy. Additionally, the phosphorylation status of S1014 on Ambra1 by IKKα kinase enables the interaction between Ambra1 and LC3 during mitophagy. PHB2 is a newly identified inner mitochondrial protein that is crucial for targeting mitochondria for autophagic degradation. Externalization of CL to the OMM in response to mitochondrial damage serves as a recognition signal for selective autophagic clearance of dysfunctional mitochondria. CL interacts with LC3 and functions as a mitophagy receptor in cortical neurons of mammals. Ceramide has been identified as a selective receptor for mitophagy by binding directly to LC3. FKBP8, an OMM protein, is a novel mitophagy receptor, inducing the degradation of damaged mitochondria via the interaction with LC3. NDP52 and OPTN function as the bridge connecting UPS and autophagy, since they can bind both ubiquitin and LC3/GABARAP. NBR1, a functional homolog of P62, is dispensable for Parkin-mediated mitophagy regardless of the presence or absence of P62. TBK1-mediated phosphorylation promotes the recruitment of OPTN, NDP52, and P62 to depolarized mitochondria. (2) According to PINK1/Parkin-induced mitophagy, mitochondrial stress leads to mitochondrial damage, which is followed by PINK1-mediated translocation of Parkin from the cytosol to depolarized mitochondrion. Parkin then ubiquitinates outer mitochondrial membrane proteins, which further recruit P62 to the damaged mitochondrion and trigger selective mitophagy. Additionally, PINK1 becomes highly activated through cross-phosphorylation. Parkin and mitochondrial ubiquitin chains are phosphorylated by PINK1. The spatial conformation of phosphorylated Parkin is changed, which leads to the binding of phosphorylated Ub. After this stage, Parkin becomes fully active, and thus the ubiquitin-bound Parkin may transiently associate with mitochondria and interact with substrate proteins. This process compromises the integrity of the outer mitochondrial membrane, thus leading to mitophagy.

Figure 3

ER-phagy: an important process for ER quality control. (A) Eight mammalian ER-phagy receptors have been identified: FAM134B, SEC62, RTN3, CCPG1, ATL3, TEX264, TRIM13 and CALCOCO1. FAM134B, clustered at the edges of ER cisternae, binds to LC3 and GABARAP to facilitate ER-phagy. SEC62, an ER membrane protein, also works as an autophagy receptor. It is activated during the recovery from ER stresses to deliver selected portions of the ER to autolysosomes for clearance. RTN3, another specific receptor, is responsible for the degradation of ER tubules. CCPG1 directly binds to LC3 and FIP200 via a LIR motif and a FIP200-interacting region (FIR) motif, respectively. ATL3 is a receptor for selective turnover of tubular ER by autophagy upon starvation. It specifically binds to GABARAP. TEX264 is an ER-phagy receptor characterized by a single transmembrane domain and a LIR motif, and is the major contributor to ER-phagy in mammals. TRIM13 has been identified to be an ER-associated receptor of P62 in ER-phagy. The interaction between TRIM13, Beclin-1 and VPS34 is indispensable for ER membrane curvature and autophagosome biogenesis. Moreover, K63-linked Ub on TRIM13 promotes ER-phagy. CALCOCO1 directly binds to Atg8 proteins through LIR and UIR motifs. ER-phagy mediated by CALCOCO1 requires interaction with VAPs on the ER membrane. (B) Atg39 and Atg40 are ER-phagy receptors in yeast. Atg39 induces autophagic sequestration of part of the nucleus. However, Atg40 is enriched in the cortical and cytoplasmic ER, and induces these ER subdomains into autophagosomes.

Figure 4

Proteaphagy: selective autophagy of inactive proteasomes. (A) Selective pathway: upon proteasome inactivation by MG132, 26S proteasomes are ubiquitinated in an Hsp42-dependent manner and shepherded to expanding autophagosome membranes by the selective proteaphagy receptors Cue5 in yeast or RPN10 in Arabidopsis. RPN10 recognizes Atg8, an ubiquitin-like modifier that decorates the autophagosome membrane, via the C-terminal ubiquitin-interacting motifs (UIMs) of RPN10. Cue5 can simultaneously bind ubiquitin and Atg8. In mammals, the proteasome subunits RPN1, RPN10, and RPN13 are poly-ubiquitinated upon amino acid starvation, which facilitates their recognition by P62. By simultaneous interaction with LC3, P62 delivers inactive 26S proteasomes to the expanding phagophore for eventual turnover by autophagy, a process that requires the TOR kinase. (B) Nonselective pathway: nitrogen starvation induces proteaphagy in yeast in a way that does not depend on RUNP10. During this process, 26S proteasomes dissociate into core particle (CP) and regulatory particle (RP) sub-complexes. The CP and RP then coalesce into cytoplasmic foci in a Snx4/41/42-dependent manner. Autophagy of CP (but not RP) also depends on the deubiquitinating enzyme Ubp3/Bre5. In contrast, during carbon starvation, proteasomes are reversibly sorted to avoid autophagic degradation. This process requires Blm10 for the CP, Spg5 and the C-terminus of Rpn11 for the RP, and the Nat3/Mdm20 complex for both.

Figure 5

Models of ribophagy in yeast and mammals. (A) Ribosomes contain 40S and 60S ribosomal subunits that are selectively recruited to the phagophore. In yeast, upon the ubiquitination of 60S subunit, Rkr1/Ltn1 decreases during selective ribosome degradation under nutrient starvation. The mechanism for recruitment of 60S to the phagophore involves de-ubiquitination via the Ubp3-Bre5 complex, whereas the mechanism for 40S recruitment remains unclear. Recently, Cdc48 and Ufd3 were identified to be new partners of Ubp3. Cdc48 acts as a major factor of the ubiquitin and proteasome system, while Ufd3 functions as an ubiquitin-binding cofactor of Cdc48. Recently, the 60S ribosomal protein Rpl25 has been identified as a substrate of Ubp3 and Ltn1. Ubiquitylation of Rpl25 prevents 60S ribophagy. Upon starvation, Ubp3-mediated de-ubiquitination of Rpl25 accelerates the selective autophagy of 60S ribosomal subunits. However, in non-selective ribosome degradation, the expression of TORC1 is down-regulated after the onset of nutrient starvation, which leads to dephosphorylation of six residues in the C-terminus of Sch9. Sch9 negatively regulates Rim15 via phosphorylation. Rim15 is also regulated by protein kinase A (PKA) and Pho85. (B) In mammals, under nutrient-deprivation conditions, NUFIP1 and its binding partner ZNHIT3 redistribute from the nucleus to autophagosomes, lysosomes and ribosomes upon mTORC1 inhibition. NUFIP1 binds to LC3B and delivers ribosome to autolysosomes. Current evidence suggests that NUFIP1 is a mammalian ribophagy receptor.

Figure 6

Pexophagy in yeast and mammals. (A) In yeast, Atg37 positively regulates the formation of RPC. Atg30 selectively degrades peroxisomes in a Pex3 and Atg37 dependent manner, by recruiting Atg8 and Atg11 to the RPC. Moreover, Atg30 is phosphorylated by Hrr25 kinase, and this phosphorylation can be regulated by Pex3 and Atg37, negatively and positively, respectively. Since Atg37 also functions as an Ac binding protein, Ac might regulate the Atg30-Atg37 interaction, hence affects the recruitment of Atg11 to the pexophagic RPC. (B) Pexophagy in mammals. Under normal conditions, a low PEX2 expression level is maintained via the mTORC1-mediated proteasome pathway. (1) Increased PEX2 during starvation conditions leads to the ubiquitination of PEX5 and PMP70, and ultimately induces pexophagy in an NBR1-dependent manner. On the other hand, USP30 counteracts PEX2 by deubiquitinating its substrates to prevent pexophagy. (2) ATM serine/threonine kinase is the first responder to peroxisomal ROS. The activated ATM kinase activates TSC2, and the activated TSC2 suppresses mTORC1. (3) ATM also phosphorylates PEX5 at Ser141, which triggers ubiquitination of PEX5 at Lys209. Ubiquitinated PEX5 is then bound by P62/NBR1 to induce pexophagy in response to ROS. The dashed box represents ubiquitin-dependent recognition of peroxisomes for pexophagy. The pexophagy target is PEX5 mono-ubiquitinated on Cys11. After cargo delivery, PEX1 and PEX6 (anchored on peroxisomes via PEX26) will remove ubiquitinated PEX5 from the peroxisomal membrane. ACBD5 is the only pexophagy-specific protein known to date. ACBD5 might be involved in the recruitment of pexophagy-specific receptors or adapters.

Figure 7

Lipophagy: connecting autophagy and lipid metabolism. Lipid droplets (LDs) are selectively removed by autophagy to generate free fatty acids (FFAs). The LD coat proteins PLIN2 and PLIN3 are degraded through the coordinated action of Hsc70 and the LAMP-2A receptor by CMA. ATGL and PNPLA8 function as selective autophagy receptors for lipophagy to promote LD catabolism and the oxidation of hydrolyzed FFAs. ATG14, which contains a PE-biding region, interacts with ULK1 and LC3 to induce lipophagy resulting in release of FFAs. The released FFAs continually undergo mitochondrial β-oxidation. ER stress induced by metformin or nutrient restriction activates the expression of AMPK. AMPK then inhibits mTORC1, which triggers autophagy by inducing the formation of the autophagy initiation complex (ULK1, ATG13, FIP200, ATG101). Upon nutrient deprivation, the expression of Rab7 (a small GTPase) increases. Rab7 promotes LDs breakdown via an interaction with its downstream effector RILP. DNM2, a large GTPase, regulates lipophagy at the level of autolysosome reformation due to its role in the budding of membrane tubules.

Figure 8

Lysophagy: clearance of damaged lysosomes by autophagy. When lysosomal membranes are damaged or even under normal conditions, lysophagy factors such as UBE2QL1, SCF^FBXO27, LRSAM1 and TRIM16 are recruited to ubiquitinate lysosomal membrane proteins. Ubiquitinated proteins then recruit autophagy adapters (such as TAXBP1, SQSTM1, VCP and PLAA), leading to induction of lysophagy. Galectin-3 (which normally localizes in the cytoplasm and nucleus) can also be recruited to disrupted lysosomes, and the TRIM16-galectin-3 complex acts as a platform for assembly of autophagic initiation proteins that in turn induce phagophore formation. In contrast, galectin-8 directly binds the autophagic receptor NDP52 independently of ubiquitin, which recruits LC3-positive phagophores to mediate lysophagy.

Figure 9

Nucleophagy: selective degradation of genetic material. Nucleophagy can be divided into macronucleophagy and micronucleophagy. Piecemeal micronucleophagy, also known as PMN, involves the direct engulfment of nuclear components by the vacuole, independent of autophagosome formation. (A) In yeast, PMN occurs under nutrient-rich and early nitrogen starvation conditions. PMN is characterized by the formation of nucleus-vacuole (NV) junctions involving Nvj1 and Vac8. The nuclear membrane protrudes toward the vacuole, and then becomes isolated from the nucleus and fuses with the vacuole for enzymatic degradation. (B) Under prolonged (>20 h) nitrogen starvation, late nucleophagy (LN) occurs without formation of NV junctions. (C) Macronucleophagy is the degradation of the nucleus and nuclear materials by auto-lysosomes (or vacuole in yeast). In yeast, the nucleophagy receptor Atg39 localizes to the nuclear envelope and interacts with Atg11 to cause the sequestration of nuclear envelope-derived double-membrane vesicles. Under various stresses, the nucleus and nuclear materials are degraded via macronucleophagy. The substrates of Atg39-dependent nucleophagy include the nuclear envelope proteins Hmg1 and Src1 and the nucleolar protein Nop1.

Figure 10

Xenophagy: specialized elimination of intracellular pathogens. Xenophagy utilizes autophagy receptors (P62, NDP52, OPTN, NBR1 and TAX1BP1) to selectively bring the ubiquitin-coated bacteria to autophagosome, through their interaction with LC3.