Selective Autophagy Receptors in Neuronal Health and Disease

Journal Pre-proof Selective autophagy receptors in neuronal health and disease Owen Conway, Hafize Aysin Akpinar, Vladimir Rogov, Vladimir Kirkin PII:

S0022-2836(19)30609-6

DOI:

https://doi.org/10.1016/j.jmb.2019.10.013

Reference:

YJMBI 66299

To appear in:

Journal of Molecular Biology

Received Date: 16 August 2019 Revised Date:

27 September 2019

Accepted Date: 10 October 2019

Please cite this article as: O. Conway, H.A. Akpinar, V. Rogov, V. Kirkin, Selective autophagy receptors in neuronal health and disease, Journal of Molecular Biology, https://doi.org/10.1016/j.jmb.2019.10.013. This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. © 2019 Elsevier Ltd. All rights reserved.

A. Neuronal selective autophagy

Axon terminal

Schwann cell CDC48-phagy

Myelinophagy

● UBXN7?

● Unknown

Proteaphagy ● Unknown

Pexophagy ● NBR1

Proteasome

Dendrite

Axonal AP transport

ER-phagy ● FAM134 ● Sec62 ● RTN3

● CCPG1 ● ATL3 ● TEX264

Aggrephagy

Protein aggregate

● p62/SQSTM1 ● NBR1 ● TAX1BP1 ● NDP52 ● OPTN

● TOLLIP ● ALFY ● TRIM5 ● ATG16L1

Nucleus

ER

Mitochondrion Ferritinophagy

P

● NCOA4

AP

Mitophagy

AL

● OPTN ● NDP52 ● NIPSNAP1/2 ● AMBRA1 ● NIX

Glycophagy ● STBD1 Ribosome Ribophagy ● NUFIP1 Granulophagy ● p62/SQSTM1

Stress granule

Lipid droplet Lipophagy ● ATGL ● HSL

● BNIP3 ● FUNDC1 ● BCL2L13 ● FKBP8 ● PHB2

Selective autophagy receptors in neuronal health and disease

Owen Conway1, Hafize Aysin Akpinar1, Vladimir Rogov2, and Vladimir Kirkin1*

1

Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London

SM2 5NG, UK 2

Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance,

Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany

*Correspondence to [email protected]

Keywords: aggregates; LC3/GABARAPs, neurodegeneration, SAR, selective autophagy

Abbreviations ATG, autophagy-related (gene or protein); AD, Alzheimer’s disease; ALS, amyotrophic lateral sclerosis; CMA, chaperone-mediated autophagy; CMT1A and CMT2A, CharcotMarie-Tooth disease type 1A and 2A; CNS, central nervous system; FIR, FIP200-interacting region; FTD, frontotemporal dementia; HD, Huntingtin’s disease; HSAN I and HSAN II, hereditary sensory and autonomic neuropathy type I and II; HSP, hereditary spastic paraplegia; LD, lipid droplet; LDS, LIR docking site; LIR, LC3-interacting region; NDD, neurodegenerative disease; NFT, neurofibrillary tangle; PBD, peroxisome biogenesis disorder; PD, Parkinson’s disease; RCDP, rhizomelic chondrodysplasia punctata; RNP, ribonucleoprotein; SAR, selective autophagy receptor; SCA3, spinocerebellar ataxia type 3; SG, stress granule; SLR, p62/SQSTM1-like receptor; UBL, ubiquitin-like protein; UDS, UIM docking site; UPR, unfolded protein response

1

2

Abstract Neurons are electrically excitable, post-mitotic cells that perform sensory, relaying, and motor functions. Because of their unique morphological and functional specialization, cells of this type are sensitive to the stress caused by accumulation of misfolded proteins or damaged organelles. Autophagy is the fundamental mechanism that ensures sequestration of cytosolic material and its subsequent degradation in lysosomes of eukaryotic cells, thereby providing cell-autonomous nutrients and removing harmful cargos. Strikingly, mice and flies lacking functional autophagy develop early-onset progressive neurodegeneration. Like in human neurodegenerative diseases (NDDs) – Alzheimer’s disease, Parkinson’s disease, frontotemporal dementia, Huntingtin’s disease, and amyotrophic lateral sclerosis – characteristic protein aggregates observed in autophagy-deficient neurons in the animal models are indicators of the ongoing neuronal pathology. A number of selective autophagy receptors (SARs) have been characterized that interact both with the cargo and components of the autophagic machinery, thus providing the molecular basis for selective degradation of sizable cytosolic components. Interference with autophagy in experimental models, but also during the pathological vagaries in neurons, will thus have far-reaching consequences for a range of selective autophagy pathways critical for the normal functioning of the nervous system. Here, we review the key principles behind the selective autophagy and discuss how the SARs may be involved in the pathogenesis of NDDs. Using recently published examples, we also examine the emerging role of less well studied selective autophagy pathways in neuronal health and disease. We conclude by discussing targeting selective autophagy as an emerging therapeutic modality in NDDs.

1. Introduction Neurons are highly specialized, post-mitotic cells capable of transmitting electrical impulses, thereby performing their characteristic sensory, relaying, and motor functions. Together with the supporting glia, neurons are organized in the nervous tissue to constitute the nervous system governing all key functions of the human body. Normal functioning of 3

neurons depends on their ability to cope with different forms of stress, e.g., oxidative, metabolic, proteotoxic, and others. However, due to their unique functional and morphological specialization, i.e. presence of slender cellular projections (long axons and shorter branched dendrites, Figure 1A) that transmit electrical impulses over significant distances, and their notorious inability to divide, mature neurons are particularly vulnerable to the accumulation of misfolded proteins and damaged mitochondria. These interfere with intracellular trafficking and serve as a source of reactive oxygen species (ROS), inflicting persistent stress on affected neurons. Amongst other cellular responses, persistent stress can activate programmed cell death [1], leading to the loss of specific types of neurons, as observed in human neurodegenerative diseases (NDDs). Dysregulation of stress responses has been observed in aging neurons [2], which might explain the greatly increased incidence of NDDs, such as Alzheimer’s disease (AD) and Parkinson’s disease (PD), in the elderly [3, 4]. Major NDDs have been linked to accumulation of aberrant proteinaceous inclusions in neurons, glial cells, and the extracellular space (Table 1): e.g., β-amyloid peptide (Aβ) plaques and Tau-positive neurofibrillary tangles (NFTs) in AD (reviewed in [5]); α-synuclein-positive Lewy bodies in PD (reviewed in [6]); Tau-, TDP-43-, and FUS-positive aggregates in frontotemporal dementia (FTD; reviewed in [7-9]); aggregates of a mutant form of huntingtin (HTT) in Huntington’s disease (HD; reviewed in [10]); and inclusions containing various proteins, such as TDP-43, UBQLN2, SOD1, as well as the dipeptide aggregates derived from the non-canonical translation of mutated C9ORF72 in amyotrophic lateral sclerosis (ALS; reviewed in [7, 11, 12]). Besides proteins, accumulation of aberrant RNA species in ALS (reviewed in [13]), as well as glycogen complexes in Lafora disease (reviewed in [14]), is a hallmark of unhealthy neurons. One of the major stress-response pathways activated as a reaction to a wide range of stress cues is autophagy (reviewed in [15-17]). It was originally described as an evolutionarily conserved response to starvation, whereby the inhibition of master metabolic

4

kinase mTOR by amino acid deficiency or treatment with rapamycin leads to the release of constant inhibition of the autophagy-specific Atg1/ULK1 kinase complex by mTOR. During autophagy, random cytoplasmic components become confined in double-membrane vesicles, autophagosomes, which fuse with endosomes or lysosomes causing degradation of autophagosomal contents by lysosomal resident hydrolases. This is followed by the release of nutrients into the cytosol for recycling in metabolic reactions. This mode of autophagy, also known as macroautophagy, is different from the direct acquisition of cytoplasmic material by the endosome or the lysosome via the invagination of their membrane (referred to as microautophagy, reviewed in [18]) and chaperone-mediated autophagy (CMA), whereby proteins with a KFERQ-like amino acid sequence motif are transported across the lysosomal membrane via the concerted action of lysosomal receptor LAMP2A and chaperone HSC70 (reviewed in [19]). Assembly of the functional unit of macroautophagy (henceforth, simply autophagy), the autophagosome, is controlled by five core autophagy-related (ATG) protein complexes conserved from yeasts to humans (reviewed in [15-17]): (1) Atg1/ULK1 complex, consisting of homologous Ser/Thr kinases, ULK1 and ULK2, and the scaffolding proteins ATG13, FIP200/RB1CC1, and ATG101; (2) class III phosphatidylinositol 3-kinase (PI3K) complex, comprising

lipid

kinase

VPS34

and

scaffolding

subunits

VPS15,

Beclin-1,

and

ATG14/Barkor; (3) phosphatidyl-3-phosphate (PI3P)-binding Atg2/Atg18 complex, with ATG2A, ATG2B, and WIPI1-4 proteins; (4) ubiquitin-like conjugation machinery, consisting of E1 enzyme ATG7, E2 enzymes ATG10 and ATG3, and E3 complex ATG12ATG5:ATG16L1 required for covalent conjugation of ubiquitin-like proteins (UBLs), members of the Atg8/LC3/GABARAP family, to the lipid phosphatidylethanolamine (PE) enriched in autophagosomal membranes (of note, like in the ubiquitylation pathway, cysteine proteases from the ATG4 family process immature LC3/GABARAP proteins to expose their C-terminal Gly and enable formation of an amide bond with the amino group of the substrate PE; ATG4s also cleave the LC3/GABARAP-PE bond to release free forms of LC3/GABARAPs from autophagic membranes back into the cytosol); and (5) transmembrane proteins ATG9A 5

and ATG9B that supply additional lipid membrane to the growing autophagic membrane, known as the phagophore. Recently, it was shown that components of the Atg2/Atg18 complex directly participate in the transfer of lipids from the endoplasmic reticulum (ER) to the phagophore [20], where Atg2 is a novel glycerophospholipid-binding protein [21]. A key discovery in the field of autophagy was that autophagosomes can form selectively around specific cargos: protein aggregates, mitochondria, peroxisomes, or cytosolic bacteria (reviewed in [22-24]). Formation of the selective autophagosome is triggered by a modification of the cargo and oligomerization of selective autophagy receptor proteins (SARs). An SAR is defined by its ability to associate simultaneously with both the substrate and components of the ATG machinery represented by Atg8/LC3/GABARAPs (Figure 2A-C) and Atg11/FIP200 (reviewed in [24, 25]). There is a growing number of selective autophagy pathways and receptors, with many of them playing roles in neuronal autophagy (Figure 1A-D). Of clinical importance is the finding that mutations in several SARs are linked to the ALS/FTD disease spectrum (Figure 2C, reviewed in [26]), suggesting a causative relationship between dysfunctional selective autophagy and the observed perturbations in sick neurons. The critical role of autophagy in maintaining neuronal homeostasis was first demonstrated in animal models of autophagy deficiency (reviewed in [27, 28]). Mice with disruption of Atg genes, Atg5 [29-31] and Atg7 [32-34], specifically in the brain cells develop early-onset neurodegeneration characterized by accumulation of ubiquitin-positive protein aggregates and inclusions in autophagy-deficient neurons and selective loss of sensitive neurons, e.g., the demise of cerebellar Purkinje and hippocampal pyramidal cells in both Atg5- [30] and Atg7-null [34] mice. Of note, axonal swellings precede progressive dystrophy and degeneration of axons [31, 32], which is suggestive of a pathological link between defective axon trafficking in the autophagy-deficient neurons and their subsequent functional failure. Similarly, inactivation of autophagy in Drosophila led to accumulation of ubiquitinpositive protein inclusions in neurons and pronounced neurodegeneration of the retina and

6

brain, underscoring the evolutionarily conserved role of autophagy in ensuring neuronal homeostasis (reviewed in [35]). Given the growing appreciation of the link between different forms of autophagy and neuronal health and disease, gaining detailed understanding of mechanisms underlying the diverse selective autophagy pathways is crucial for developing new strategies in ameliorating and curing human NDDs. Here, we review key principles behind the selective autophagy and discuss how SARs can be involved in the pathogenesis of NDDs. Using recently published examples, we examine the emerging role of less well studied selective autophagy pathways in neuronal homeostasis. We also provide a perspective for targeting selective autophagy in NDDs.

2. General principles of selective autophagy A number of cargos relevant for neuronal biology are recognized and sequestered by autophagosomes selectively (Figure 1A). The current list includes physiological and pathological protein aggerates (aggrephagy), mitochondria (mitophagy), parts of the ER (ER-phagy, also known as reticulophagy), peroxisomes (pexophagy), RNA-containing stress granules

(granulophagy),

intracellular

pathogens

(xenophagy),

iron-binding

ferritin

(ferritinophagy), lipid complexes (lipophagy), lysosomes (lysophagy), myelin (myelinophagy), parts of the nucleus (nucleophagy), the proteasome (proteaphagy), the Cdc48 protein complex (Cdc48-phagy), and ribosomes (ribophagy). Their recognition depends on a number of SARs (Figure 1A-D) reviewed in [22-24, 36]). Below, we briefly review the structure and function of the most important SARs.

2.1 Ubiquitin-dependent SARs Several types of cargo, including protein aggregates, mitochondria, and intracellular bacteria, are modified through conjugation of polyubiquitin chains to a Lys residue or the Nterminus of the constituent proteins. This ‘eat-me’ signal (reviewed in [37]) is recognized by the ubiquitin-binding subset of the SARs that includes the prototype SAR, p62/SQSTM1 7

(Figure 1B and Figure 2A), and the p62/SQSTM1-like receptor proteins (SLRs): NBR1 (Figure 1A), optineurin (OPTN, Figure 1B and Figure 2B), NDP52 (also known as CALCOCO2; Figure 1B), TAX1BP1 (Figure 1B), and TOLLIP/Cue5 (Figure 1B). p62/SQSTM1 and NBR1 were first described as signaling adaptors, as they bind a plethora of signaling proteins, but more recently linked to autophagy (reviewed in [38]). They are homologous proteins that both harbor C-terminal ubiquitin-associated (UBA) domains, which interact with ubiquitin chains. Binding of p62/SQSTM1 to ubiquitin can be considerably enhanced by phosphorylation of Ser403 within its UBA domain by CK2 [39] and TBK1 [40] kinases. p62/SQSTM1 and NBR1 bind each other via their respective N-terminal PB1 domains; while p62/SQSTM1’s PB1 domain is also capable of extensive homooligomerization [41]. NBR1 dimerizes via the coiled-coil (CC) domains, which may further contribute to oligomerization of p62/SQSTM1:NBR1 complexes. The intermediate regions of p62/SQSTM1 and NBR1 contain short linear LC3-interacting regions (LIRs) that mediate binding of the SARs to the LC3/GABARAP proteins and are critical for aggrephagy [42, 43]. Both p62/SQSTM1 and NBR1 are enriched in ubiquitin-positive pathological protein inclusions, such as Mallory bodies in liver cells and Lewy bodies in neurons [42, 44, 45]. Recently, it was established that p62/SQSTM1 also interacts with FIP200, thus capable of recruiting the ULK1 complex to the ubiquitylated cargo. The FIP200-interacting region (FIR) was mapped to encompass the LIR, posing the question on the compatibility of the interactions amongst p62/SQSTM1, LC3/GABARAPs, and FIP200 [46]. It is presently unknown if NBR1 directly interacts with FIP200. Also, both p62/SQSTM1 and NBR1 contain ZZ-type zinc finger domains, whose function begins to be revealed. Remarkably, p62/SQSTM1 uses this domain to bind N-arginylated proteins [47] and RNA [48], stimulating p62/SQSTM1 oligomerization and autophagic cargo receptor function. NBR1 has functions independent of p62/SQSTM1. It binds lipid membranes via a juxta-UBA (JUBA or J) domain, which is required for pexophagy, whereas p62/SQSTM1 seems to be redundant in this process [49]. On the other hand, p62/SQSTM1 plays a critical role in the activation of the transcription factor NRF2, which is a master regulator of 8

detoxification and oxidative stress response (reviewed in [50, 51]). By binding to E3 ligase Keap1 via its Keap1-interacting region (KIR), p62/SQSTM1 outcompetes NRF2 allowing its stabilization, dimerization and nuclear localization required for gene transcription. A positive feedback loop leads to an enhanced transcription of the SQSTM1 gene, which has an NRF2-binding site in its promoter, during the oxidative stress response [52]. Interestingly, oxidation of Cys residues C-terminal to the PB1 domain stimulates p62/SQSTM1 oligomerization, thus contributing to p62/SQSTM1 activation during this form of stress [53]. OPTN is a signaling adaptor linked to inflammation (reviewed in [54]). As an SLR, it is critically involved in aggrephagy and is a major component of pathological inclusions, such as Lewy bodies [55]. It binds ubiquitin via the C-terminal UBAN and ZF domains, interacts with LC3/GABARAPs via a LIR, and is capable of self-oligomerization via its CC domains. Unlike p62/SQSTM1 and NBR1, the LIR in OPTN requires activation by TBK1, which phosphorylates OPTN on Ser177 and increases its affinity to LC3/GABARAP by approximately 10-fold. This regulation was shown to be critical in the context of Salmonella clearance from the cytoplasm of infected cells [56] but might be equally important for the role of OPTN in aggrephagy. Also, binding of OPTN to ubiquitin is regulated by the TBK1mediated phosphorylation of its UBAN domain [57]. OPTN has been recognized as a major SAR for ubiquitin-driven mitophagy [58, 59], where it is thought to amplify recruitment of LC3/GABARAPs and ULK1 to the cargo [60]. OPTN was also suggested to promote autophagosome formation by employing the Atg5-Atg12:Atg16L1 complex [61]. NDP52 and TAX1BP1 are a pair of homologous SLRs, which have first been characterized in the context of ubiquitin-driven xenophagy [62, 63]. They possess C-terminal zinc finger (ZF) domains with which they bind ubiquitin and N-terminal SKICH domains with a poorly defined function. Recently, it was shown that the SKICH domain of NDP52 interacts with FIP200 and is thus capable of recruiting the ULK1 complex to the ubiquitylated mitochondria and bacteria [64, 65]. The atypical LIR of NDP52 binds the LC3C member of the LC3/GABARAP family, which was shown to be critical for restriction of Salmonella [66]. Both NDP52 and TAX1BP1 may contain additional canonical LIRs, whose function is less 9

well understood [67]. An association of NDP52 or TAX1BP1 with protein aggregates has not been formally reported; however, together with OPTN, NDP52 has been proposed to be the major SAR for ubiquitin-dependent mitophagy [58, 59]. TOLLIP is the last aggrephagy-specific SAR based on its partial homology with the yeast Cue5, which binds ubiquitin via an N-terminal CUE domain and is able to oligomerize [68]. Unlike Cue5, human TOLLIP has a C-terminal CUE domain and the N-terminal PI3Pbinding C2 domain with an unclear role in autophagy. Based on its protein-protein and protein-lipid interaction profiles, TOLLIP had initially been described as an adaptor protein involved in innate immunity and intracellular trafficking (reviewed in [69]). However, more recently, it was also found to play a role in protein aggregation [68, 70]. TOLLIP interacts with LC3/GABARAPs via its two putative LIRs and is required for efficient clearing of HTT aggregates in human cells. Additional components of the ubiquitin-dependent selective autophagy are being uncovered. Thus, the core component of the E3 ligase complex for LC3/GABARAPs, ATG16L1, binds ubiquitin via its C-terminal WD40 domain, which is critical for restriction of Salmonella infection [71]. ATG16L1 interacts with FIP200 and thus facilitates recruitment of the ULK1 complex to the cargo [71-73]. On the other hand, the PI3P-binding protein WIPI2 also directly binds ATG16L1, further amplifying the autophagosome biogenesis process [74]. It is not clear whether Atg16L1’s binding to ubiquitin is directly required for other ubiquitindependent selective autophagy processes, such as aggrephagy and mitophagy. The giant multi-modular protein ALFY/ WDFY3 does not directly bind ubiquitin but is intimately involved in the protection of cells from protein aggregates. By interacting with PI3P, p62/SQSTM1, ATG5, and LC3/GABARAPs, ALFY mediates clearance of mutated HTT, thereby protecting neurons from polyglutamine (polyQ)-expanded HTT aggregates, as shown in primary rat cortical neurons and Drosophila eye model [75, 76]. Other factors impacting ubiquitin-regulated selective autophagy include the large protein the non-canonical histone deacetylase HDAC6, which participates in the transport of

10

aggregated proteins along the microtubules [77], and the UBL-UBA proteasomal adaptors ubiquilins (UBQLNs), which will be discussed below [78].

2.2 Ubiquitin-independent SARs Physiological elimination of membrane-bound organelles, such as mitochondria, lipid droplets (LDs), parts of the ER and the nucleus, involves a growing number of SARs that are displayed on their surface (Figure 1C). Mitochondrial outer-membrane proteins, NIX (also known as BNIP3L) and BNIP3, are classified as BH3-only proteins. Early studies indicated that NIX and BNIP3 might act as pro-apoptotic factors, due to the BH3 domain-mediated depolarization of the mitochondrial membrane and opening of the mitochondrial permeability transition pore (MPTP) (reviewed in [79]). Indeed, NIX overexpression caused apoptosis in rat pheochromocytoma PC12 cells [80], and also BNIP3 expression was associated with delayed neuronal death following an ischemic stroke in mice [81]. More recent work however highlighted the role of NIX and BNIP3 in selective autophagy due to the presence of conserved LIRs with which they can recruit LC3/GABARAPs to mitochondria and mediate their selective degradation during mitochondrial membrane depolarization [82, 83]. NIX is induced as part of a developmental program during reticulocyte maturation [84], whereas BNIP3 expression is enhanced by hypoxia [85], which highlights different physiological contexts of the SAR-mediated mitophagy. Interestingly, another mitochondrial pro-apoptotic protein BCL2L13 [86], which contains BH1-4 domains, was found to mediate mitophagy. BH domains are important for the mitochondrial fragmentation that precedes the engulfment of mitochondria by autophagosomes, while BCL2L13’s LIR motif is responsible for the delivery of mitochondria to the lysosome, which is mediated by its binding to LC3/GABARAP proteins [87]. Additional mitophagy receptors include FUNDC1, a hypoxia-inducible protein that interacts with LC3/GABARAPs via an N-terminal LIR [88], and FKBP8, an outer membrane mitochondrial protein, which normally functions as a peptidyl-prolyl cis-trans isomerase 11

(PPIase) and requires calmodulin binding for its activity (reviewed in [89]). The N-terminal LIR of FKBP8 preferentially binds LC3A and mediates FKBP8-induced mitophagy. Unlike other mitophagy SARs, FKBP8 escapes from mitochondria onto the ER prior to their degradation [90]. Of note, mitochondria are typically fragmented prior to the engulfment by the autophagosomes, and all of the aforementioned SARs for mitophagy are capable of mitochondrial fragmentation upon their overexpression. Also, largely unstructured protein Ambra1 (Figure 1C) was found to play a role in mitophagy. It normally interacts with Beclin1 and thus positively regulates autophagy, while deficiency in Ambra1 in the mouse leads to severe defects in the neural tube development [91]. A study however found that Ambra1 is partially localized to mitochondria and can interact with LC3/GABARAPs via a LIR during mitochondrial membrane permeabilization, thus establishing Ambra1 as a mitophagy SAR [92]. There are a number of additional LIR-containing proteins that are harbored within the mitochondria but become accessible to LC3/GABARAP proteins upon membrane permeabilization. One such protein is the inner-mitochondrial membrane protein PHB2, which becomes exposed upon the proteasome-mediated rupture of the outer mitochondrial membrane during the ubiquitin-driven mitophagy [93]. NIPSNAP1 and NIPSNAP2 are two mitochondrial proteins that harbor LIRs and become exposed on the outer mitochondrial membrane following the loss of the membrane potential. NIPSNAP1/2 are required for ubiquitin-driven mitophagy, and their deficiency leads to parkinsonism in zebrafish larvae [94]. The ER is represented by an interconnected network of membrane tubules and flattened discs that are continuous with the outer nuclear membrane. Turnover of the ER membranes by selective autophagy had been well documented in mammalian cells (reviewed in [95]), and a growing number of ER-resident SARs have been identified (Figure 1 D).The first of them, FAM134B (also known as RETREG1), is a four-transmembrane domain protein that binds LC3/GABARAPs via its C-terminal LIR. It is both necessary and sufficient for the fragmentation and degradation of the ER membrane, while FAM134B 12

mutations that cause production of a truncated version of the receptor and are associated with sensory neuropathy in humans were unable to support ER-phagy [96]. Interestingly, the ER-resident lectin chaperone calnexin acts as a co-receptor for FAM134B in that it recognizes misfolded procollagen in the ER lumen and delivers it into the selective autophagosome via binding to FAM134B [97]. FAM134B may also act by alternative mechanisms to deliver misfolded ER-resident proteins to the lysosome, as shown for aggregated alpha1-antitrypsin Z, which occurs without capturing ER membranes in an autophagosome [98]. Reticulon-3 (RTN3) is another four-pass ER resident, which is specific to the ER tubules. Its unique role in the selective turnover of the tubular ER compartment is mediated by six LIRs situated in the N-terminal part of the protein, facing the cytosol. Binding of RTN3 to LC3/GABARAPs is essential for the fragmentation of ER tubules and their degradation in the lysosome [99]. The other ER-phagy SAR, Sec62, is a constituent of the translocon complex regulating protein import in the ER, with two transmembrane domains and a LIR in the C-terminus. It is critical for ER-phagy that occurs upon the recovery of cells from the ER stress [100]. CCPG1 spans the membrane only once and is an unusual SAR in that, in addition to a LIR, it also harbors two FIRs, whereby it recruits FIP200 along with the ULK1 signaling complex to the ER membrane during the unfolded protein response (UPR), which also induces the expression of the CCPG1 gene [101]. TEX264 is a recently discovered single-pass SAR for ER-phagy that has a C-terminal LIR. It functions during amino acid starvation, and its LIR-containing, long unstructured region was shown to be required for bridging the gap between the ER and the autophagosomal membranes [102, 103]. Atlastin-3 (ATL3) is the last known ER-specific SAR. It is found in the tubular ER, where it spans the membrane two times and contains two LIRs within its GTPase domain. As the GTPase activity of ATL3 is required for the fusion of ER membranes, it is possible that the LC3/GABARAP binding, and hence autophagy, opposes the ER membrane expansion driven by ATL3 [104].

13

Like in mitophagy, fragmentation of the ER membrane may be the prerequisite for efficient ER-phagy (reviewed in [95]. Both FAM134B and RTN3 contain reticulon-homology domains (RHDs), which represent tandem helical hairpin structures mediating insertion of the protein into the ER membrane from the cytosolic face [105]. The RHDs insert asymmetrically into the ER membrane, pushing the outer leaflet of the lipid bilayer apart. Oligomerization or clustering of the SARs have therefore the potential to drive curvature [106] and even fracture the ER membrane. Ongoing research is focused on the mechanisms of how ER-specific SAR oligomerization can be regulated. LDs are fat storage organelles made up of a neutral lipid core and a shell of phospholipids and associated proteins. They originate from the ER and, when the lipids are needed, are turned over by cytoplasmic lipases and autophagy (reviewed in [107]). Autophagic degradation of LDs (lipophagy) is selective and relies on SARs that are only beginning to be characterized (reviewed in [108]). Cytosolic lipase ATGL contains a LIR within its Patatin domain and is suggested to act as an SAR for lipophagy [109]. Additional SARs for less well characterized selective autophagy pathways, which are relevant for neuronal biology, include NCOA4 for ferritinophagy [110, 111], STBD1 for glycophagy [112], and NUFIP1 for ribophagy [113].

2.3 Protein-protein interactions that drive selective autophagosome formation Recognition of the cargo by an SAR is followed by a signaling cascade that results in confinement of the cargo:SAR complex inside an autophagosome. Extensive research has highlighted key protein-protein interactions that are responsible for the conveyance of the ‘eat-me’ signal to the phagophore (reviewed in [24, 25]). Upon binding to substrate proteins, the SARs, via their oligomerization domains, are able to cluster to make large SAR scaffolding complexes and enhance the affinity of downstream protein-protein interactions. This was clearly demonstrated for p62/SQSTM1, which undergoes liquid-liquid phase separation (LLPS) and forms membrane-less droplets in the cytosol [114, 115]. In the case of membrane-associated SARs, such as those 14

responsible for ER-phagy, SAR clustering leads to changes in membrane curvature [106] and, likely, an enhanced interaction with ATG proteins. Studies using LIR-less FAM134B and RTN3 demonstrated that the effect of SARs on membrane curvature depends on their binding to the LC3/GABARAP proteins [96, 99]. Post-translational modifications of SARs, such as phosphorylation of p62/SQSTM1 and NDP52 by TBK1, significantly enhance the cargo:SAR complex formation [40, 64, 65, 116]. The multi-modular structure of SAR proteins revealed one key evolutionarily conserved feature – all of them (more than 30 in human cells) interact with members of the Atg8/LC3/GABARAP protein family (Figure 2C). The LIR in p62/SQSTM1 was the first sequence shown to bind LC3/GABARAPs [43, 117, 118]. In this short linear motif with the consensus Θ-X-X-Γ (where Θ is an aromatic (W/F/Y), Γ is a hydrophobic (L/I/V), and X can be any amino acid), the conserved aromatic residue binds deeply within the hydrophobic pocket 1 (HP1) formed by the unique N‐terminal extensions of LC3/GABARAPs and by hydrophobic residues within their core UBL domain. The second conserved (aliphatic) hydrophobic residue of the LIR binds in the HP2 on LC3/GABARAP made up by amino acids within the UBL core. The core LIR sequence is often preceded by a short stretch of negatively charged residues, which engage in ionic interactions with the positively charged Lys/Arg

residues

of

LC3/GABARAPs,

thus

significantly

strengthening

the

LIR:LC3/GABARAP complex. The HP1 and the HP2 of LC3/GABARAPs together form the so-called LIR docking site (LDS) employed by the majority of the known SARs. Very recently, it was shown that LC3/GABARAPs possess an additional interaction surface that may be exploited by a new class of SARs, such as UBXN7, which is the putative SAR for degradation of the hexameric AAA+-type ATPase Cdc48/VCP/p97 [119]. UBXN7 contains a ubiquitin-interacting motif (UIM) which binds into the UIM docking site (UDS) situated on the opposite side of the UBL globule of LC3/GABARAP proteins. Further studies are required to define exact structural characteristics of this interaction. Engagement of LC3/GABARAP proteins by an SAR is thought to recruit nascent phagophores, which carry covalently attached LC3/GABARAPs, to the cargo:SAR complex. 15

On the other hand, LIRs within NDP52 and OPTN were shown to be required for an efficient recruitment of the ULK1 complex to the mitochondria during mitophagy [60]. This is based on the observation that components of the ULK1 complex interact with LC3/GABARAPs [120-122], which is required for ULK1 activation [123] and efficient autophagosome formation [122]. Also, components of the VPS34 complex are recruited by LC3/GABARAPs to the nascent phagophore [124], corroborating the role of LC3/GABARAPs as determinants of the autophagosome biogenesis. FIP200 is another key component in the selective autophagosome formation cascade. It acts as a cargo-specific adaptor within the ULK1 complex – the role it shares with the Atg11 protein in yeasts [125, 126]. A growing number of human SARs, namely ATG16L1 [71], CCPG1 [101], p62/SQSTM1 [46], and NDP52 [64, 65], contain FIRs with which they recruit FIP200 and the associated ULK1 to the cargo. In the case of NDP52, its interaction with FIP200 may be assisted by the TBK1-binding adaptor Sintbad [65]. The timing and sequence of the binding events between SARs and FIP200 vs. LC3/GABARAPs are poorly understood. For instance, the FIR in p62/SQSTM1 encompasses the LIR and cannot bind both FIP200 and LC3/GABARAPs simultaneously [46]. In contrast, CCPG1 has well-spaced FIRs and the LIR, compatible with the concurrent engagement of both FIP200 and LC3/GABARAPs. HTT was proposed as another Atg11-like protein in human cells. It binds ULK1, GABARAPs, and p62/SQSTM1, thereby mimicking FIP200 in its function [127, 128]. Importantly, loss of HTT in Drosophila and mice inhibits autophagy and leads to the accumulation of p62/SQSTM1 [127], which may explain selective autophagy defects observed in HD neurons [129]. The current model for the cargo-induced formation of the selective autophagosome suggests that the cargo:SAR complex engages sufficient numbers of LC3/GABARAP and FIP200 proteins, which recruit further key signaling complexes, such as ULK1 and VPS34, thus orchestrating the nucleation and expansion of the phagophore in the close proximity to the cargo [24, 25]. ATG9A and ATG9B are inserted into the membrane of small Golgiderived vesicles that can transport lipid to the site of the growing phagophore. ULK1 activity 16

is crucial for ATG9 trafficking [130], and, at least in yeast, Atg11 directly binds Atg9 deemed to be critical for the selective autophagy in this eukaryote [131]. In yeast, Atg9 also recruits the lipid-binding protein Atg2 to the growing phagophore, further contributing to its expansion [20].

3. Roles of SARs in different types of selective autophagy with links to NDDs 3.1 Aggrephagy Major NDDs, including AD, PD, HD, and ALS/FTD, are characterized by the formation of intracellular aggregates and/or extracellular plaques (Table 1). The aggregates are thought to be the end product of protein misfolding and oligomerization, which can be a natural propensity of some proteins, enhanced under conditions of stress (e.g., Aβ in AD [132] and wild-type SOD1 in ALS [133]), or a result of mutations that cause local unfolding and formation of sticky surfaces engaging in β-sheet formation, such as the polyQ expansion of HTT in HD (reviewed in [10]) and mutant α-synuclein in PD (reviewed in [6]). Chaperones of the heat shock protein family keep misfolded proteins in check (reviewed in [134]): HSP90 chaperones stabilize misfolded proteins and prevent their ubiquitylation, while HSP70 proteins couple misfolding to the ubiquitylation machinery via the E3 ligase CHIP [135]. Once the proteins are ubiquitylated, they can be degraded by one of the two conserved protein degradation systems: the ubiquitin-proteasome system (UPS) or autophagy. If the degradation machinery is overwhelmed, misfolded proteins are stored in inclusion bodies or aggresomes; the latter being large proteinaceous structures associated with the microtubule organizing center (MTOC). The presence of pathological aggregates in NDDs thus suggests an ongoing protein misfolding that overwhelms the degradation capacity of neurons. Whereas polyubiquitin tags of certain composition (e.g., Lys48-linked as well as more recently characterized Lys11-linked and other linkages and topologies of polyubiquitin chains) are recognized as a key signal for the UPS-mediated protein degradation (reviewed in [136]), autophagy/aggrephagy SARs may not be that specific to a certain type of

17

polyubiquitin. Indeed, brains and livers of autophagy-deficient mice accumulate Lys48- and Lys63-linked polyubiquitin chains with an equal abundance, arguing against a specific type of polyubiquitin arrangement serving as an autophagy signal [137]. On the other hand, protein oligomerization has been strongly linked to induction of selective autophagy. Studies in yeasts revealed that strains deficient in the UPS activity (deletion of the UBL-UBA adaptor Dsk2) accumulated mostly soluble proteins, while those lacking aggrephagy (deletion of the TOLLIP homolog Cue5) amassed insoluble protein aggregates [138]. Mammalian genome encodes a number of the UBL-UBA family adaptors for the UPS, known as ubiquilins (UBQLN genes). UBQLN1, UBQLN2, and UBQLN4 were associated with autophagy regulation, whereby UBQLN4 was suggested to interact with LC3/GABARAP directly [78, 139, 140]. Mutations in UBQLN2 underlie cases of dominantly inherited and chromosome Xlinked ALS and ALS/dementia [141, 142]. This suggests an as-yet-unappreciated level of crosstalk between the UPS and aggrephagy. Aggrephagy, as implied by the term, is the prime mechanism for clearing protein aggregates. The ubiquitin-binding, aggrephagy-specific SARs (also known as SLRs) are found enriched in the NDD-linked protein aggregates. Thus, p62/SQSTM1 is detected in ADassociated NFTs and Lewy bodies in the brains of PD patients [44, 45]; it is also enriched in protein inclusions in neurons and glia of ALS/FTD patients [143-145]. Similarly, OPTN [55] and NDP52 [146] are found together with phosphorylated Tau in animal models of AD and cortical brain samples of patients with AD. Also, NBR1 is localized in Lewy bodies and glial cytoplasmic inclusions in α-synucleinopathies [147]. But is the primary role of the SLRs found in the pathological aggregates to mediate their degradation by autophagy? This idea may be supported by the study in SQSTM1-null mice whose brains

contain

hyperphosphorylated Tau and NFTs and which develop age-dependent neurodegeneration [148]. Also, loss of SQSTM1 in zebrafish and the p62/SQSTM1 homolog Ref(2)p in Drosophila leads to an abnormal locomotor phenotypes, indicating neurodegeneration [149, 150]. On the other hand, forced expression of p62/SQSTM1 in mouse brains led to a

18

decreased Aβ and plaque load and an improved cognitive function in APP/PS1 mice, which was dependent on the LIR of p62/SQSTM1, suggesting the aggrephagy-promoting role in this model [151]. Yet, seminal studies revealed that p62/SQSTM1 and NBR1 also act as a molecular glue that keeps protein aggregates together; so that down-regulation of one of these proteins prevented formation of puromycin-induced protein aggregates in HeLa cells [42]and loss of p62/SQSTM1 markedly attenuated formation of ubiquitin-positive protein aggregates in neurons and hepatocytes of autophagy-deficient Atg7-null mice [152]. Thus, at least some of the SLRs, most prominently p62/SQSTM1 and NBR1, may determine the molecular architecture of the pathological aggregate, in part, by promoting their LLPS [114]. As aggregates are thought to represent a repository of toxic misfolded protein, rather than possessing toxic properties per se, removal of the glue (knockout of p62/SQSTM1 and/or NBR1), and hence reduction in the aggregate formation, is not expected to ameliorate the toxicity of the misfolded protein species. Indeed, deletion of SQSTM1 in autophagy-deficient Atg7-null mice did not rescue the neurodegeneration phenotype in the mice despite the strong reduction in the number and size of ubiquitin-positive aggregates in their neurons [152]. Similarly, SQSTM1 deficiency enhanced α-synuclein pathology in mice, which could in part be compensated by an increased NBR1 expression [153]. In the same vein, formation of α-synuclein aggregates was repressed in the cells with an NBR1 knockdown [147]. Unlike p62/SQSTM1 and NBR1, other SLRs have not been described to ‘organize’ protein aggregates and may instead be critically important for the autophagy-mediated degradation of misfolded protein species. Thus, depletion of OPTN was shown to increase the number of SOD1 G93C and HTT Q103 aggregates in HeLa cells and cause motor axonopathy in zebrafish [154]. Similarly, TOLLIP was shown to promote Aβ and α-synuclein clearance and protect neurons of the cerebral cortex, hippocampus, and cerebellum from cell death in the high-fat diet-fed ApoE-null mouse model of AD [155].

19

Accumulation of p62/SQSTM1 in autophagy-deficient neurons or as a consequence of trapping in protein aggregates will lead to the activation of the NRF2 pathway (reviewed in [50, 51]). One of the markers for the pathway activation is an increased phosphorylation of p62/SQSTM1 on Ser349 within its KIR sequence, which allows p62/SQSTM1 to gain higher affinity to Keap1, preventing it from forming a complex with NRF2 and thereby leading to NRF2 stabilization [156]. It was shown that pSer349-positive p62/SQSTM1 is enriched and co-localizes with phosphorylated Tau in the brains of AD patients [157], which can be construed as an indicator for ongoing oxidative stress response in AD neurons. Importantly, p62/SQSTM1 expression is itself under control of NRF2, which constitutes a positive feedback mechanism as shown using mouse embryonic fibroblasts (MEFs) [52]. The promoter of NDP52 also contains NRF2-binding sites, so that NDP52 expression is strongly induced during oxidative stress. In the brains of Nrf2 knockout mice, decreased levels of NDP52 were accompanied by an increase in phosphorylated and insoluble Tau [158]. Thus, aggrephagy SARs by means of inducing the NRF2 signaling also serve as sensors of ongoing oxidative stress. Depending on its interaction partner, NDP52 has different mechanisms of selective autophagy induction. Consistent with the hypothesis of prion-like propagation of Aβ and Tau, Tau assemblies enter the cells via clathrin-independent endocytosis and are released into the cells by damaging endomembranes. The ‘danger receptor’ lectin Galectin-8 induces aggrephagy by recruiting NDP52 to Tau aggregates in AD neurons [159]. In contrast, a direct interaction between the SKICH domain of NDP52 and Tau was also suggested. The dependence of NDP52 aggrephagy on its SKICH domain was shown by overexpressing NDP52 in murine cortical cells CN1.4, which decreased the levels of phosphorylated tau only when SKICH domain was intact. The likely in-vivo interaction between NDP52 and phospho-Tau was also corroborated by colocalization in cortical samples of AD cases [158]. There are a number of ALS/FTD-associated mutations described in OPTN and p62/SQSTM1 (reviewed in [26]). Most of the ALS-linked mutations in OPTN result in decreased protein expression or activity, with some of them (e.g., D474N and E478G, 20

Figure 2C) disrupting the ubiquitin-binding domain of OPTN UBAN, which may explain the insufficiency in clearing mutant HTT and TDP-43 aggregates by OPTN mutants in Neuro-2a mouse neuroblastoma cells [160]. Similarly, several rare mutations within the UBA domain of p62/SQSTM1 have been described to double the risk for FTD susceptibility. Mutated p62/SQSTM1 was associated with neuronal and glial phospho-TDP-43 pathology in patients with FTD [161]. This is in contrast with the p62/SQSTM1 mutations underlying Paget’s disease of bone (PDB) that all cluster around the UBA domain [162]. More frequent ALS/FTD-linked mutations target other parts of p62/SQSTM1. For example, the L341V mutation affects the LIR reducing the affinity to LC3B by 3-fold and affecting p62/SQSTM1 degradation in motor neuron-like cells NSC-34, produced by fusing motor neuro-rich, embryonic mouse spinal cord cells with mouse neuroblastoma [163]. In contrast, the KIR mutants, P348L, G351A, and G427R exhibit reduced binding to Keap1, thus interfering with NRF2 activation and oxidative stress response in both non-neuronal HEK293T cells and neurons [164, 165]. As neurons are largely non-dividing cells, it seems that even a subtle detrimental effect on the cell’s capacity to withstand oxidative stress can lead, with enough time given, to accumulation of the cellular damage and eventually demise of sensitive types of neurons. ALS/FTD-linked mutations in the disaggregase Cdc48/VCP/p97 lead to the accumulation of p62/SQSTM1 and OPTN, which suggests that Cdc48/VCP/p97 may be an important factor in the turnover of higher-order oligomers of the SLRs by the UPS and/or autophagy [166]. In addition, interference with the SAR activation by post-translational modifications will have a similar effect as a mutation that disrupts the function of the SAR. TBK1 is an important kinase that activates both OPTN and p62/SQSTM1 and mutations that diminish TBK1 function are strongly linked to ALS [167, 168]. Considering HTT as a likely Atg11 homolog and selective autophagy adaptor, aggregates made by the polyQ-expanded forms of HTT may have loss- or gain-of-function properties in aggrephagy and actively modify SAR signaling. On the other hand, many of the SLRs, including p62/SQSTM1, OPTN, and TOLLIP, have been shown to promote 21

degradation of mutated HTT [68, 70, 154, 160, 169]. Therefore, the relationship between HTT aggregates and aggrephagy SARs may go beyond a simple substrate:receptor paradigm. It is important to keep in mind that aggrephagy SARs also play roles as signaling adaptors, so that disruption of their functions, e.g. by disease-linked mutations, can have serious implications not connected to the autophagy pathways. A recent example is the discovery of the role for OPTN in suppressing RIPK1 signaling, thus limiting inflammation and necroptosis in murine neurons [170].

3.2 Mitophagy Mitochondria are highly dynamic and metabolically active organelles whose quality control is important to prevent oxidative damage to neurons. The advent of elegant mouse models in which mitochondria are labelled with autophagy reporters (e.g., mCherry-GFPFIS1, known as mito-QC mice, made by Ganley’s group in Dundee, UK [171]), allows monitoring mitophagy in vivo. Using the mito-QC reporter mice, it could be shown that somata of the Purkinje neurons undergo pronounced mitochondrial turnover [172], which is consistent with the severe degeneration seen in this type of neurons if autophagy is disabled, such as in autophagy-deficient Atg5-null mice [30]. Altered mitochondrial morphology and biochemical dysfunction are recognized features of many NDDs, including AD, PD, HD, and ALS. Also, deregulation of the mitochondrial network assembly has been strongly linked to neurodegeneration, as illustrated by the causative mutations in the mitochondrial fusion genes, OPA1 and MFN2, in the autosomal dominant optic atrophy and axonal Charcot-Marie-Tooth disease type 2A (CMT2A) (reviewed in [173]). The number and quality of mitochondria are regulated by selective autophagy and mediated by mitophagy-specific SARs as introduced above. Ubiquitin is involved in the degradation of mitochondria in response to the loss of the mitochondrial membrane potential. Parkin, encoded by the gene PARK2, is an E3 ligase mutated in familial cases of PD [174]. It is recruited to damaged mitochondria and mediates 22

their degradation by mitophagy [175]. As deciphered by the work of several groups, the mitochondrial kinase PINK1, encoded by another PD-associated gene [176], is stabilized in the outer mitochondrial membrane of depolarized mitochondria where it phosphorylates both the UBL domain of Parkin and ubiquitin [177-183]. Following the phosphorylation, ubiquitin interacts with Parkin releasing its autoinhibition and allowing ubiquitylation of outer membrane mitochondrial proteins (reviewed in [184]). A comprehensive analysis of the Parkin-dependent ubiquitinome of mitochondria has been published [185, 186]. Parkinmediated ubiquitylation also mediates proteasome-dependent degradation of proteins within the outer mitochondrial membrane [187, 188] and may lead to its rupture [188], allowing access to the mitochondrial inner space by small cytosolic proteins, such as LC3/GABARAPs. Major research efforts went into deciphering the mechanisms of PINK1/Parkin- and ubiquitin-mediated mitophagy, highly relevant for PD, given that mutations in PINK1 and PARK2 are prominent in the familial cases of PD (reviewed in [189]). Also, in Drosophila, disruption of Pink1 and park led to abrogation of age-dependent mitophagy and neurodegeneration [190]. Mutant PINK1 and/or Parkin are believed to fail to engage in ubiquitylation of proteins residing in the outer mitochondrial membrane and thus stop recruiting SLRs, OPTN and NDP52, critical for Parkin-mediated mitophagy [58, 59]. Similarly, mutations in OPTN and TBK1 (which stimulates OPTN activity), may explain reduced mitophagy in ALS [59, 191]. The role of p62/SQSTM1 in mitophagy has been controversial, with some reports claiming its requirement for efficient mitochondrial degradation [192-194] and others suggesting its redundancy [58, 195]. However, in Drosophila, the p62/SQSTM1 homolog Ref(2)p was required for mitophagy [150]. NIPSNAP1/2 are required for Parkin-mediated mitophagy and bind multiple SARs, including p62/SQSTM1, NBR1, NDP52, TAX1BP1 and ALFY, which may explain p62/SQSTM1’s redundancy in mitophagy [94]. Unlike p62/SQSTM1, NBR1 may not be essential for PINK1/Parkin-mediated mitochondrial

23

degradation [196]. The effect of ALS-associated p62/SQSTM1 mutations on neuronal mitophagy has not been studied to date. Mitochondrial dysfunction has been linked to accumulation of Aβ in AD, and, here, stimulation of PINK1/Parkin-mediated mitophagy by gene-mediated PINK1 overexpression or using chemical activators could reverse neurodegeneration in in-vivo models of AD [197, 198]. Of note, upon PINK1 overexpression, recruitment of OPTN and NDP52 to damaged mitochondria was evident [198]. On the other hand, PINK1 interacts with α-synuclein and abrogates α-synuclein-induced neurotoxicity by activating autophagy in an uncharacterized fashion, providing a complementary mechanism to amelioration of proteinopathy during PINK1 overexpression [199]. A growing list of examples indicates that ubiquitin-dependent mitophagy can be regulated by E3 ligases other than Parkin. Thus, in the livers of the mice lacking mitochondrial fission (Drp1-null mice), p62/SQSTM1 promotes mitochondrial ubiquitination by recruiting Keap1 and Rbx1, two subunits of Cullin 3-based E3 ligase complex to mitochondria [200]. Also, Ambra1 recruits the E3 ligase HUWE1 to mitochondria, which ubiquitylates MFN2, thus causing its proteasomal degradation and promoting mitochondrial fission and mitophagy [201]. The potential role of ubiquitin-independent SARs in neurodegeneration has been largely neglected based on the lack of evidence that mitophagy-specific, but ubiquitinindependent, SARs, such as NIX, BNIP3, FUNDC1, BCL2L13, and FKBP8, are mutated in NDDs. Using the mitophagy reporter mouse models, it could however be demonstrated that a large proportion of basal mitochondrial turnover in neurons takes place also in the absence of PINK1. This was observed for mesencephalic dopaminergic neurons implicated in PD and microglia [172]. Thus, it appears that PINK1/Parkin/ubiquitin-independent SARs and mitophagy may compensate for the loss of Parkin or PINK1 function in neurons [202].

3.3 Pexophagy

24

Peroxisomes are single membrane-bound organelles in which β-oxidation of fatty acids, reduction of ROS, and synthesis of ether phospholipids, plasmalogens, take place. These functions are critical for neuronal homeostasis, as evidenced by a range of neurological disorders caused by the lack of functional peroxisomes. The peroxisome biogenesis disorders (PBDs) are caused by defects in peroxin (PEX) genes and comprise a broad spectrum of neurological symptoms, summarized as Zellweger spectrum and rhizomelic chondrodysplasia punctata (RCDP) type 1 disorders (reviewed in [203]). Peroxisomal deficit was also linked to AD [203] and ALS [204]. Upon amino acid starvation, peroxisomes undergo ubiquitylation on transmembrane peroxins, PEX5 and PMP70, mediated by the E3 ligase PEX2 [205]. NBR1 is a major pexophagy receptor in mammalian cells, while p62/SQSTM1 is required for the clustering of peroxisomes prior to their engulfment by autophagosomes [49, 206]. The role of other SARs in mammalian pexophagy has not been studied. Given the critical role of peroxisomes in the brain, including axon myelination, peroxisomal quality control mediated by selective autophagy should be tightly regulated. Future studies will reveal links between pexophagy and NDDs.

3.4 ER-phagy Increased production of misfolded protein species, which is the hallmark of major NDDs, will be intimately linked to the ER stress in neurons (reviewed in [207]). Besides UPR, ER-phagy serves as a mechanism to reduce the ER stress by degrading parts of the ER containing misfolded proteins. As discussed above, a plethora of SARs orchestrates ERphagy. Illustrating the importance of the permanent turnover of the ER by autophagy for neuronal homeostasis, mutations in FAM134B cause hereditary sensory and autonomic neuropathy type II (HSAN II) [208, 209]. Studies using FAM134B knockdown in primary dorsal root ganglion neurons demonstrated structural alterations in the ER-proximal part of the Golgi apparatus and induction of apoptosis [208], whereas FAM134B knockout mice 25

revealed expansion of the ER and degeneration of sensory neurons [96]. Another ER-phagy SAR, RTN3, has long been associated with AD on the basis of it being a negative regulator of β-secretase (BACE1) that initiates Aβ production [210-212]. Its role in AD and other NDDs will have to be revisited in the light of its newly discovered function in the turnover of the tubular ER [99]. Finally, GTPases atlastins that mediate fusion of ER membranes are also responsible for the degradation of the tubular ER during starvation [213]. Mutations in ATL3 (Y192C and P338R) that reduce its interaction with LC3/GABARAPs are causatively associated with hereditary sensory and autonomic neuropathy type I (HSAN I), in which neuronal ER-phagy is impaired [104]. This clinical finding again underscores the crucial role of physiological ER-phagy in maintaining ER homeostasis and neuronal health.

3.5 Granulophagy and ribophagy Stress granules (SGs) and processing (P) bodies are cytoplasmic aggregates of nontranslating mRNAs in complex with proteins. These ribonucleoprotein complexes (mRNPs) form by LLPS and are implicated in the regulation of mRNA translation and decay. As the name suggests and unlike the P bodies, SGs arise in response to various forms of stress to store stalled mRNA translation initiation complexes (reviewed in [214]). This phenomenon is similar to the inclusion bodies and aggresomes that store misfolded proteins. Mutant TDP-43 and FUS proteins, associated with ALS/FTD, have been described to segregate into SGs based on their ability to bind RNA [215-217]. Of special interest is the relationship between C9ORF72, whose pathogenicity has been linked to both toxic RNA species and di-peptides produced by unconventional translation (reviewed in [11]), and the SG formation. Thus, downregulation of C9ORF72 abolishes the production of SGs, negatively impacts the expression of SG-associated proteins TIA-1 and HuR, and accelerates cell death [218]; while Arg-rich (GR/PR) dipeptides derived from C9ORF72 promote the LLPS, which results in enhanced SG formation [219]. Autophagy has been proposed as a major mechanism for turnover of SGs. Interestingly, deletion of Cdc48/VCP potently inhibits granulophagy in both yeast and 26

mammalian cells, which may provide a link between inactivating VCP mutations and the observed accumulation of SGs in ALS/FTD [220]. On the other hand, UBQLN2 regulates SGs by maintaining FUS solubility and suppressing the LLPS of FUS-RNA complexes during oxidative stress [221]. p62/SQSTM1 is the candidate SAR for granulophagy based on its ability to bind RNA via its ZZ domain [48]. Also, both C9ORF72 and p62/SQSTM1 were shown to associate with SG components and contribute to their clearance. Mechanistically, p62/SQSTM1 was proposed to be recruited to SG proteins with symmetrically dimethylated Arg residues via the Tudor domain-containing protein SMN [222]. Of interest, p62/SQSTM1’s ZZ domain also directly interacts with arginylated proteins [47], which may provide another docking site within the SG-forming proteins for the SAR recruitment. Thus, an arginylated form of calreticulin was shown to localize to SGs [223]. Ribosomes are also affected in NDDs, and abnormal C9ORF72-derived poly(GR) dipeptide-repeat proteins were shown to localize with ribosomal subunits and the translation initiation factor eIF3η in brains of mice and patients with C9ORF72-associated ALS/FTD. These poly(GR) dipeptides interfere with normal protein translation causing permanent ribosomal dysfunction [224]. Selective degradation of ribosomes stalled by poly(GR) dipeptides could provide a way out for the poly(GR) dipeptide-stressed neurons in ALS, and a ribophagy SAR was reported as NUFIP1 [113]. NUFIP1 also localises to SGs [225], so that a tight interplay between ribophagy and granulophagy can be expected and remains to be explored.

3.6 Lipophagy Neurons have high energy demands which they cover through continuous supply of glucose from peripheral organs, such as the liver. Storage of fatty acids in LDs is not typical of neurons, and indeed LDs in neurons were identified only in rare instances (reviewed in [226]). It is believed that in pathological situations neurons increase their lipid storage capacity, as observed in animal models of HD [129] and ALS [227]. Importantly, large LDs 27

accumulate in neurons of mice that lack the lipid hydrolases DDHD2, which leads to the accumulation of triacylglycerols (TAGs) and causes hereditary spastic paraplegia (HSP) [228]. This data reveals certain LD flux in neurons that is held in check under normal circumstances. Accumulation of LDs was associated with neurotoxicity, and activation of lipophagy was shown to reduce dihydroceramide-related neurodegeneration in Drosophila [229]. Besides the CMA [230], selective autophagy of LDs mediated by SARs, such as ATGL, may be a major mechanism of degradation of complex lipids and mobilization of fatty acids [109]. However, much additional work is required to determine if and how ATGL, or related lipophagy SARs, are implicated in NDDs.

3.7 Ferritinophagy Iron is an important enzyme cofactor participating in redox reactions required for normal cell metabolism. However, excessive accumulation of iron leads to oxidative stress and cell death. Iron deposits in affected regions of the brain were reported in AD, PD, and HD (reviewed in [231]), which may also suggest a more general defect in autophagy as autophagy-deficient

mice

accumulate

the

iron

storage

protein

ferritin

alongside

p62/SQSTM1 [232]. Cells can readily utilize iron during iron deficiency via autophagic targeting of ferritin into the lysosomes where iron is extracted and recycled [233]. The SAR, NCOA4, is strongly implicated in ferritinophagy, and its role in neuron health and disease remains to be explored (reviewed in [234]).

3.8 Glycophagy Neurons store negligible amounts of glycogen (reviewed in [235]). However, glycogen accumulation has been observed in neuronal pathologies, with the most prominent example being Lafora disease, a progressive autosomal recessive NDD associated with epileptic seizures (reviewed in [14]). Interestingly, accumulation of glycogen, manifested as 28

polyglucosan inclusions, was shown to impair autophagy in affected neurons [236], which can contribute to the neuronal degeneration phenotype observed in the Lafora disease. Conversely, mutant HTT reportedly promotes glycogen synthesis in neurons by activating glycogen synthase [237]. However, under the experimental settings, overexpressed glycogen synthase was proposed to rather activate autophagy and protect neurons, which contradicts earlier observations of the suppressed selective autophagy in HD [129]. STBD1 is the suggested SAR for glycophagy [112]. However, its role in neuronal biology has not been addressed to date. It is tempting to speculate that overexpression of STBD1 might provide a strategy to stimulate glycophagy and thus ameliorate neurodegeneration seen in Lafora disease.

3.9 Myelinophagy Degradation of myelin is important during Wallerian degeneration of axons required for the nerve repair process but is also a prominent feature in demyelinating diseases, such as Charcot-Marie-Tooth disease type 1A (CMT1A) (reviewed in [238]). Gomez-Sanchez et al described dependence of the myelin degradation in Schwann cells on the core ATG proteins and coined the term myelinophagy [239]. It remains to be established whether this emerging selective autophagy pathway is mediated by a specialized SAR and whether its manipulation can be used to exploit myelinophagy therapeutically.

3.10 Lysophagy Neurons contain a number of other organelles and structures whose regulated degradation is important for homeostasis. Thus, accumulation of damaged lysosomes can be associated with induction of necroptosis in neurons of the central nervous system (CNS) [240]. The damage to the endo-lysosomal membrane system can be afflicted by oxidative stress or by protein aggregates that interact with membranes, such as α-synuclein assemblies (reviewed in [241]). Damaged lysosomal membranes can be recognized by lectins of the galectin family, e.g. Galectin-8 [242], and E3 ligases, such as FBXO27 [243], 29

which mediate ubiquitylation or membrane-associated proteins. While no specific SAR has been proposed to mediate lysophagy, members of the SLR family, e.g. p62/SQSTM1, as well as ATG16L1 may play a role in the process. Also, the ubiquitin-associated ATPase Cdc48/p97/VCP has been implicated in lysophagy [244]. Inhibition of autophagy in neurons affected in NDDs with the concomitant damage to lysosomes by accumulating protein aggregates could significantly amplify the pathogenesis mechanisms that lead to neuronal cell death.

3.11 Proteaphagy and Cdc48-phagy Both key components of the UPS, the proteasome and the ATPase Cdc48/p97/VCP, have been shown to undergo selective degradation by autophagy [119, 245]. The role of these processes in neuronal homeostasis is expected to be highly relevant but has not been explored. Pathological protein aggregates, including Aβ, α-synuclein, and mutant HTT have been shown to clog the proteasome and interfere with the degradation of other protein substrates [246]. The same property was ascribed to the p62/SQSTM1 aggregates that accumulate during autophagy inhibition and perturb cell signalling mediated by the UPS [247]. Therefore, elimination of stalled proteasomes could be an important task in the neurons with protein aggregates. Stalling of Cdc48/p97/VCP may also lead to aggregation and interference with the clearance of multiple ubiquitylated cargos. Therefore, a great amount of work is required to understand the significance of proteaphagy and Cdc48-phagy in neuronal homeostasis and pathology.

4. Potential therapeutic approaches exploiting SARs and selective autophagy Accumulation of protein aggregates, stress granules, and damaged organelles in neurons suggests a fundamental defect in autophagy underlying the pathogenesis of NDDs. Multiple mechanisms have been proposed to explain lower levels of autophagy, including interference of the mutated proteasomal adaptors and SARs with the cargo recognition, 30

altered dynamics in the endocytic pathway, defective formation of autophagosomes, and lysosomal deficiency (reviewed in [28]). The ability of rapamycin and its analogs to ameliorate neurodegeneration in animal models of AD, PD, FTD, and HD suggests that the lysosomal damage is not a global phenomenon in NDDs, so that autophagy activation may be a viable therapeutic option. Similar benefits in NDD models were demonstrated with mTOR-independent autophagy inducers, such as trehalose, metformin, and cyclic AMP/inositol triphosphate modulators: rimeldine, clonidine, minoxidil, and verapamil (reviewed in [28]). Targeting the selective autophagy represents an untapped resource in the field of NDD. As with the general autophagy, an important prerequisite for productive selective autophagy is the normal function of lysosomes which must be capable of digesting complex substrates, such as protein aggregates, ribonucleoprotein complexes, multibranched polysaccharides, or complete mitochondria. Burgeoning research on the mechanisms of selective autophagy suggests several ways of how to enhance the recognition of a cargo by the core autophagy machinery and expedite its engulfment by a selective autophagosome. One approach could be an increased labeling of the substrate by ubiquitin, which has emerged as a major ‘eat-me’ signal in autophagy (reviewed in [37]). Similar to the PROTACs (reviewed in [248]), small molecules that bind both the autophagic cargo and an E3 ligase, like VHL, Keap1, or Parkin, would be worth developing and testing in NDD models. An enhanced presentation of ubiquitin may stimulate higher rates of SAR binding with the resulting higher efficiency in autophagosome formation. An alternative approach could be a forced display of SARs directly on the cargo, e.g., by engineering SARs with higher affinity to the mutant forms of proteins or designing of binders, e.g., DARPINs (reviewed in [249]), that would bridge SARs with the cargo structures. Delivery of engineered peptides and proteins into the CNS presents a considerable challenge. However, the advent of novel brain delivery technologies may allow this type of drugs in NDD already in the near future (reviewed in [250]).

31

Post-translational modifications of SARs, with the best studied examples of p62/SQSTM1 and OPTN phosphorylation, stimulate selective autophagy by dramatically enhancing the affinity of the SARs to the cargo [39, 40, 57] and/or LC3/GABARAP proteins [56, 59, 251]. Activators of TBK1 and/or ULK1/2 kinases might therefore be an interesting modality to enhance natural activity of the SARs and stimulate selective autophagy in NDDs. Examples of small-molecule kinase activators are not numerous but available (reviewed in [252]) and should instill optimism in this disease area. Another class of selective autophagy inducers could be compounds that promoting SAR clustering, thus enhancing their affinity to the ATG machinery, i.e. LC3/GABARAPs and Atg11-like proteins. The small molecule XIE-62-1004 was shown to promote autophagy by interacting with the ZZ domain of p62/SQSTM1 and fostering its oligomerization [47]. A caution should be exercised in those cases where SAR clustering will lead to SLR aggregation without promoting the autophagosome formation. This could lead to an enhanced load of protein aggregates and would be counterproductive. It is difficult to predict the toxicity profile of selective autophagy inducers, which will depend on their mode of action. Small molecules will need to be screened for off-target effects in established assay cascades. On the other hand, peptides and proteins targeting the autophagic machinery to the cargo are predicted to undergo degradation together with the cargo they usher into the lysosome, hopefully limiting the possible side-effects of their build-up in the cell. The important prerequisite for both high-efficacy and low-toxicity profiles of the selective autophagy inducers is the uncompromised function of the lysosomes, unless another clearance mechanism can be used. Autophagy has been proposed as a mechanism for unconventional secretion of proteins that lack a signal peptide (reviewed in [253]). It is therefore important to explore whether the activation of selective autophagy will simultaneously increase the extracellular load of amyloids.

5. Conclusions and perspectives 32

Selective autophagy has been recognized as a powerful mechanism that leads to clearance of a large number of bulky substrates known to accumulate in neurons of patients with NDDs. The SARs form an important component of the cargo degradation system in that they bind to both the cargo and the core autophagy machinery, represented by Atg8/LC3/GABARAP and Atg11-like proteins, thereby defining the specificity of the selective autophagosome machinery. Recent studies revealed that mutations in the components of the cargo:SAR recognition system can lead to neurodegeneration, which matches the neurological defects observed in models with a deficiency in general autophagy. The fact that SLRs oligomerize and participate in aggregate formation, besides their role in protein clearance, makes the analysis of the disease-associated mutations in these proteins less straightforward. Lack of aggregates may not be equal to the absence of toxic misfolded protein species, which needs to be taken into consideration when studying or exploiting the SLRs. A relatively high degree of redundancy in the SAR system suggests the importance of the pathway but also makes the study of the system more challenging. Work in the lower organisms with less developed SAR repertoire will help decipher the key features of the SAR-mediated autophagosome formation. Detailed understanding of the selective autophagy mechanisms will allow harnessing the power of this unique degradation system for therapeutic purposes. Development of compounds that could enhance cargo recognition or physically bridge the autophagic machinery with the cargo by linking SARs to its surface will revolutionize the therapeutic area of NDDs and provide hope for millions of people worldwide.

Acknowledgements VK is supported by the CRUK program grant C2739/A22897 and by a Marie SkłodowskaCurie ETN grant under the European Union’s Horizon 2020 Research and Innovation Program (Grant Agreement No 765912). VR is supported by the SFB 1177 “Molecular and Functional Characterization of Selective Autophagy”. We apologize to those authors whose 33

work could not be cited here due to the space limitation. We would also like to thank Carl Conway, for the excellent contribution to the professional graphical design of Figure 1.

34

Figure legends Figure 1. Types of selective autophagy and SARs relevant for neuronal biology. (A) Neuronal selective autophagy. A neuron showing the different types of selective autophagy and the organelles or sub-cellular structures that are targeted for degradation. Relevant SARs are listed. (B), (C), and (D) Overview of aggrephagy, mitophagy, and ER-phagy SARs, respectively. The domain architecture of specific SARs is highlighted. Abbreviations: BH(14), Bcl2 homology domain (1-4); C2, C2 domain; BEACH, Beige and Chediak-Higashi domain; CaM, Calmodulin-binding domain; Cargo, unspecified cargo-binding domain; CC, coiled-coil domain; DABB1/2, Dimeric A/B barrel domain-containing protein 1/2; FIR, FIP200-inreacting region; FYVE, Fab1, YOTB, Vac1, and EEA1 domain; J, juxta UBA domain; LIR, LC3-interacting region; PB1, Phox and Bem1 domain; PPIase, Peptidyl-prolyl cis-trans isomerase domain; PH, pleckstrin homology domain; RING, really interesting new gene domain; SKICH, SKIP carboxyl homology domain; SPRY, splA and ryanodine homology domain; TM, transmembrane domain; UBAN, ubiquitin binding in ABIN and NEMO domain; UBA, ubiquitin-associated domain; WD40, tryptophan-aspartic acid dipeptide 40 domain; ZF, zinc finger domain; ZZ, ZZ-type zinc finger domain.

Figure 2. p62/SQSTM1 and OPTN – two key SARs associated with NDDs. (A) Structural organization of p62/SQSTM1 and its interactions. Upper panel: a schematic representation of p62/SQSTM1 domains and motifs, with a short legend in (B). The p62/SQSTM1 regions responsible for various interactions are given as lines with indicated interaction partners. Lower panel: a summary of the known structural features of p62/SQSTM1. Each domain/motif (named left) is represented as a monomeric unit, in complex with the corresponding interaction partner, and in a physiological oligomeric state. The partners or oligomeric mates are colored magenta. All structures are shown as ribbon diagrams, in which positions of some NDD-associated mutations are label red. PDB IDs for each structure are indicated. (B) Structural organization of OPTN and its interactions. Upper panel: a schematic representation of OPTN domains and motifs. The OPTN regions 35

responsible for various interactions are given as lines with indicated interaction partners. Lower panel: summary of the known structural features of OPTN. Graphical representation is the same as for p62/SQSTM1. Note that the single helices represented for the monomeric state in the coiled-coil regions are rather improbable. They usually form various types of helical bundles shown for oligomeric states. (C) Structural details of LIR:LC3/GABARAP interactions and the effect of NDD-related mutations on the interactions between specific SARs domain and their interaction partners. Upper panel: structure of p62/SQSTM1 LIR motif in complex with LC3B represents the basic principles of LIR:LC3/GABARAP interactions. LC3B is shown as a surface (magenta) with the two hydrophobic pockets (HP1 and HP2, schematically rendered by the dashed lines) on it. The linear p62/SQSTM1 LIR motif (gray) is shown as backbone sticks with pivotal residues W338 and L341 sidechains (sticks and mesh) placed in the HP1 and HP2, respectively. Structural consequences of NDD-related mutations within the ubiquitin binding domains of p62/SQSTM1 (upper panel) and OPTN (lower panel) on the ubiquitin interaction. G425R mutation in p62/SQSTM1’s UBA domain will lead to a set of steric clashes in the tight intermolecular contacts between sidechains of p62/SQSTM1 G425 (red, spheres for sidechain) and ubiquitin V70 and L71 (blue). These clashes disrupt UBA-mediated ubiquitin binding and prevent p62/SQSTM1 autophagic function. E478G mutation in OPTN’s UBAN domain disrupts the intermolecular hydrogen bond between OPTN’s E478 and ubiquitin’s R74 sidechains, preventing an efficient polyubiquitin binding by OPTN. The sections of UBA/UBAN domains (gray) and ubiquitin (magenta) are shown as ribbon diagrams. Positions of other NDD-related mutations (indicated in each case) are marked red.

List of tables Table 1. Examples of proteins producing pathological aggregates associated with NDDs. Abbreviations: Aβ, β-amyloid peptide; AD, Alzheimer’s disease; ALS, amyotrophic lateral sclerosis; APP, amyloid precursor protein; ATXN3, Ataxin-3; DUB, deubiquitinating enzyme; FTD, frontotemporal dementia; FUS, fused in sarcoma; GEF, guanine nucleotide exchange 36

factor; HD, Huntington’s disease; HTT, huntingtin; MAPT, microtubule-associated protein tau; NDD, neurodegenerative disease; NFT, neurofibrillary tangle; PD, Parkinson’s disease; polyQ, poly-glutamine; SNCA, α-synuclein; SOD1, superoxide dismutase; UPS, ubiquitinproteasome system.

37

References [1] Fricker M, Tolkovsky AM, Borutaite V, Coleman M, Brown GC. Neuronal Cell Death. Physiol Rev. 2018;98:813-80. [2] Kourtis N, Tavernarakis N. Cellular stress response pathways and ageing: intricate molecular relationships. EMBO J. 2011;30:2520-31. [3] Querfurth HW, LaFerla FM. Alzheimer's disease. N Engl J Med. 2010;362:329-44. [4] Kalia LV, Lang AE. Parkinson's disease. Lancet. 2015;386:896-912. [5] Wang J, Gu BJ, Masters CL, Wang YJ. A systemic view of Alzheimer disease - insights from amyloid-beta metabolism beyond the brain. Nat Rev Neurol. 2017;13:612-23. [6] Lashuel HA, Overk CR, Oueslati A, Masliah E. The many faces of alpha-synuclein: from structure and toxicity to therapeutic target. Nat Rev Neurosci. 2013;14:38-48. [7] Lee EB, Lee VM, Trojanowski JQ. Gains or losses: molecular mechanisms of TDP43mediated neurodegeneration. Nat Rev Neurosci. 2011;13:38-50. [8] Spillantini MG, Goedert M. Tau pathology and neurodegeneration. Lancet Neurol. 2013;12:609-22. [9] Deng H, Gao K, Jankovic J. The role of FUS gene variants in neurodegenerative diseases. Nat Rev Neurol. 2014;10:337-48. [10] Saudou F, Humbert S. The Biology of Huntingtin. Neuron. 2016;89:910-26. [11] Balendra R, Isaacs AM. C9orf72-mediated ALS and FTD: multiple pathways to disease. Nat Rev Neurol. 2018;14:544-58. [12] Banci L, Bertini I, Boca M, Girotto S, Martinelli M, Valentine JS, et al. SOD1 and amyotrophic lateral sclerosis: mutations and oligomerization. PLoS One. 2008;3:e1677. [13] Brown RH, Al-Chalabi A. Amyotrophic Lateral Sclerosis. N Engl J Med. 2017;377:16272. [14] Nitschke F, Ahonen SJ, Nitschke S, Mitra S, Minassian BA. Lafora disease - from pathogenesis to treatment strategies. Nat Rev Neurol. 2018;14:606-17. [15] Levine B, Kroemer G. Biological Functions of Autophagy Genes: A Disease Perspective. Cell. 2019;176:11-42. 38

[16] Mizushima N, Yoshimori T, Ohsumi Y. The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol. 2011;27:107-32. [17] Dikic I, Elazar Z. Mechanism and medical implications of mammalian autophagy. Nat Rev Mol Cell Biol. 2018;19:349-64. [18] Li WW, Li J, Bao JK. Microautophagy: lesser-known self-eating. Cell Mol Life Sci. 2012;69:1125-36. [19] Cuervo AM, Wong E. Chaperone-mediated autophagy: roles in disease and aging. Cell Res. 2014;24:92-104. [20] Gomez-Sanchez R, Rose J, Guimaraes R, Mari M, Papinski D, Rieter E, et al. Atg9 establishes Atg2-dependent contact sites between the endoplasmic reticulum and phagophores. J Cell Biol. 2018;217:2743-63. [21] Valverde DP, Yu S, Boggavarapu V, Kumar N, Lees JA, Walz T, et al. ATG2 transports lipids to promote autophagosome biogenesis. J Cell Biol. 2019;218:1787-98. [22] Rogov V, Dotsch V, Johansen T, Kirkin V. Interactions between autophagy receptors and ubiquitin-like proteins form the molecular basis for selective autophagy. Mol Cell. 2014;53:167-78. [23] Stolz A, Ernst A, Dikic I. Cargo recognition and trafficking in selective autophagy. Nat Cell Biol. 2014;16:495-501. [24] Farre JC, Subramani S. Mechanistic insights into selective autophagy pathways: lessons from yeast. Nat Rev Mol Cell Biol. 2016;17:537-52. [25] Kirkin V. History of The Selective Autophagy Research: How Did It Begin and Where Does It Stand Today? J Mol Biol. 2019. [26] Deng Z, Purtell K, Lachance V, Wold MS, Chen S, Yue Z. Autophagy Receptors and Neurodegenerative Diseases. Trends Cell Biol. 2017;27:491-504. [27] Nikoletopoulou V, Papandreou ME, Tavernarakis N. Autophagy in the physiology and pathology of the central nervous system. Cell Death Differ. 2015;22:398-407.

39

[28] Menzies FM, Fleming A, Caricasole A, Bento CF, Andrews SP, Ashkenazi A, et al. Autophagy

and

Neurodegeneration:

Pathogenic

Mechanisms

and

Therapeutic

Opportunities. Neuron. 2017;93:1015-34. [29] Xi Y, Dhaliwal JS, Ceizar M, Vaculik M, Kumar KL, Lagace DC. Knockout of Atg5 delays the maturation and reduces the survival of adult-generated neurons in the hippocampus. Cell Death Dis. 2016;7:e2127. [30] Hara T, Nakamura K, Matsui M, Yamamoto A, Nakahara Y, Suzuki-Migishima R, et al. Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature. 2006;441:885-9. [31] Nishiyama J, Miura E, Mizushima N, Watanabe M, Yuzaki M. Aberrant membranes and double-membrane structures accumulate in the axons of Atg5-null Purkinje cells before neuronal death. Autophagy. 2007;3:591-6. [32] Komatsu M, Wang QJ, Holstein GR, Friedrich VL, Jr., Iwata J, Kominami E, et al. Essential role for autophagy protein Atg7 in the maintenance of axonal homeostasis and the prevention of axonal degeneration. Proc Natl Acad Sci U S A. 2007;104:14489-94. [33] Inoue K, Rispoli J, Kaphzan H, Klann E, Chen EI, Kim J, et al. Macroautophagy deficiency mediates age-dependent neurodegeneration through a phospho-tau pathway. Mol Neurodegener. 2012;7:48. [34] Komatsu M, Waguri S, Chiba T, Murata S, Iwata J, Tanida I, et al. Loss of autophagy in the central nervous system causes neurodegeneration in mice. Nature. 2006;441:880-4. [35] Kim M, Ho A, Lee JH. Autophagy and Human Neurodegenerative Diseases-A Fly's Perspective. Int J Mol Sci. 2017;18. [36] Khaminets A, Behl C, Dikic I. Ubiquitin-Dependent And Independent Signals In Selective Autophagy. Trends Cell Biol. 2016;26:6-16. [37] Kirkin V, McEwan DG, Novak I, Dikic I. A role for ubiquitin in selective autophagy. Mol Cell. 2009;34:259-69. [38] Moscat J, Karin M, Diaz-Meco MT. p62 in Cancer: Signaling Adaptor Beyond Autophagy. Cell. 2016;167:606-9. 40

[39] Matsumoto G, Wada K, Okuno M, Kurosawa M, Nukina N. Serine 403 phosphorylation of p62/SQSTM1 regulates selective autophagic clearance of ubiquitinated proteins. Mol Cell. 2011;44:279-89. [40] Pilli M, Arko-Mensah J, Ponpuak M, Roberts E, Master S, Mandell MA, et al. TBK-1 promotes autophagy-mediated antimicrobial defense by controlling autophagosome maturation. Immunity. 2012;37:223-34. [41] Lamark T, Perander M, Outzen H, Kristiansen K, Overvatn A, Michaelsen E, et al. Interaction codes within the family of mammalian Phox and Bem1p domain-containing proteins. J Biol Chem. 2003;278:34568-81. [42] Kirkin V, Lamark T, Sou YS, Bjorkoy G, Nunn JL, Bruun JA, et al. A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. Mol Cell. 2009;33:505-16. [43] Pankiv S, Clausen TH, Lamark T, Brech A, Bruun JA, Outzen H, et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem. 2007;282:24131-45. [44] Zatloukal K, Stumptner C, Fuchsbichler A, Heid H, Schnoelzer M, Kenner L, et al. p62 Is a common component of cytoplasmic inclusions in protein aggregation diseases. Am J Pathol. 2002;160:255-63. [45] Kuusisto E, Salminen A, Alafuzoff I. Ubiquitin-binding protein p62 is present in neuronal and

glial

inclusions

in

human

tauopathies

and

synucleinopathies.

Neuroreport.

2001;12:2085-90. [46] Turco E, Witt M, Abert C, Bock-Bierbaum T, Su MY, Trapannone R, et al. FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates. Mol Cell. 2019. [47]

Cha-Molstad

H,

Yu

JE,

Feng

Z,

Lee

SH,

Kim

JG,

Yang

P,

et

al.

p62/SQSTM1/Sequestosome-1 is an N-recognin of the N-end rule pathway which modulates autophagosome biogenesis. Nat Commun. 2017;8:102.

41

[48] Horos R, Buscher M, Kleinendorst R, Alleaume AM, Tarafder AK, Schwarzl T, et al. The Small Non-coding Vault RNA1-1 Acts as a Riboregulator of Autophagy. Cell. 2019;176:105467 e12. [49] Deosaran E, Larsen KB, Hua R, Sargent G, Wang Y, Kim S, et al. NBR1 acts as an autophagy receptor for peroxisomes. J Cell Sci. 2013;126:939-52. [50] Sanchez-Martin P, Komatsu M. p62/SQSTM1 - steering the cell through health and disease. J Cell Sci. 2018;131. [51] Sanchez-Martin P, Saito T, Komatsu M. p62/SQSTM1: 'Jack of all trades' in health and cancer. FEBS J. 2019;286:8-23. [52] Jain A, Rusten TE, Katheder N, Elvenes J, Bruun JA, Sjottem E, et al. p62/Sequestosome-1, Autophagy-related Gene 8, and Autophagy in Drosophila Are Regulated by Nuclear Factor Erythroid 2-related Factor 2 (NRF2), Independent of Transcription Factor TFEB. J Biol Chem. 2015;290:14945-62. [53] Carroll B, Otten EG, Manni D, Stefanatos R, Menzies FM, Smith GR, et al. Oxidation of SQSTM1/p62 mediates the link between redox state and protein homeostasis. Nat Commun. 2018;9:256. [54] Slowicka K, Vereecke L, van Loo G. Cellular Functions of Optineurin in Health and Disease. Trends Immunol. 2016;37:621-33. [55] Osawa T, Mizuno Y, Fujita Y, Takatama M, Nakazato Y, Okamoto K. Optineurin in neurodegenerative diseases. Neuropathology. 2011;31:569-74. [56] Wild P, Farhan H, McEwan DG, Wagner S, Rogov VV, Brady NR, et al. Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. Science. 2011;333:228-33. [57] Richter B, Sliter DA, Herhaus L, Stolz A, Wang C, Beli P, et al. Phosphorylation of OPTN by TBK1 enhances its binding to Ub chains and promotes selective autophagy of damaged mitochondria. Proc Natl Acad Sci U S A. 2016;113:4039-44. [58] Lazarou M, Sliter DA, Kane LA, Sarraf SA, Wang C, Burman JL, et al. The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy. Nature. 2015;524:309-14.

42

[59] Moore AS, Holzbaur EL. Dynamic recruitment and activation of ALS-associated TBK1 with its target optineurin are required for efficient mitophagy. Proc Natl Acad Sci U S A. 2016;113:E3349-58. [60] Padman BS, Nguyen TN, Uoselis L, Skulsuppaisarn M, Nguyen LK, Lazarou M. LC3/GABARAPs drive ubiquitin-independent recruitment of Optineurin and NDP52 to amplify mitophagy. Nat Commun. 2019;10:408. [61] Bansal M, Moharir SC, Sailasree SP, Sirohi K, Sudhakar C, Sarathi DP, et al. Optineurin promotes autophagosome formation by recruiting the autophagy-related Atg12-5-16L1 complex to phagophores containing the Wipi2 protein. J Biol Chem. 2018;293:132-47. [62] Tumbarello DA, Manna PT, Allen M, Bycroft M, Arden SD, Kendrick-Jones J, et al. The Autophagy Receptor TAX1BP1 and the Molecular Motor Myosin VI Are Required for Clearance of Salmonella Typhimurium by Autophagy. PLoS Pathog. 2015;11:e1005174. [63] Thurston TL, Ryzhakov G, Bloor S, von Muhlinen N, Randow F. The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria. Nat Immunol. 2009;10:1215-21. [64] Vargas JNS, Wang C, Bunker E, Hao L, Maric D, Schiavo G, et al. Spatiotemporal Control of ULK1 Activation by NDP52 and TBK1 during Selective Autophagy. Mol Cell. 2019. [65] Ravenhill BJ, Boyle KB, von Muhlinen N, Ellison CJ, Masson GR, Otten EG, et al. The Cargo Receptor NDP52 Initiates Selective Autophagy by Recruiting the ULK Complex to Cytosol-Invading Bacteria. Mol Cell. 2019;74:320-9 e6. [66] von Muhlinen N, Akutsu M, Ravenhill BJ, Foeglein A, Bloor S, Rutherford TJ, et al. LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy. Mol Cell. 2012;48:329-42. [67] Newman AC, Scholefield CL, Kemp AJ, Newman M, McIver EG, Kamal A, et al. TBK1 kinase addiction in lung cancer cells is mediated via autophagy of Tax1bp1/Ndp52 and noncanonical NF-kappaB signalling. PLoS One. 2012;7:e50672. [68] Lu K, Psakhye I, Jentsch S. Autophagic clearance of polyQ proteins mediated by ubiquitin-Atg8 adaptors of the conserved CUET protein family. Cell. 2014;158:549-63. 43

[69] Capelluto DG. Tollip: a multitasking protein in innate immunity and protein trafficking. Microbes Infect. 2012;14:140-7. [70] Oguro A, Kubota H, Shimizu M, Ishiura S, Atomi Y. Protective role of the ubiquitin binding protein Tollip against the toxicity of polyglutamine-expansion proteins. Neurosci Lett. 2011;503:234-9. [71] Fujita N, Morita E, Itoh T, Tanaka A, Nakaoka M, Osada Y, et al. Recruitment of the autophagic machinery to endosomes during infection is mediated by ubiquitin. J Cell Biol. 2013;203:115-28. [72] Nishimura T, Kaizuka T, Cadwell K, Sahani MH, Saitoh T, Akira S, et al. FIP200 regulates targeting of Atg16L1 to the isolation membrane. EMBO Rep. 2013;14:284-91. [73] Gammoh N, Florey O, Overholtzer M, Jiang X. Interaction between FIP200 and ATG16L1 distinguishes ULK1 complex-dependent and -independent autophagy. Nat Struct Mol Biol. 2013;20:144-9. [74] Dooley HC, Razi M, Polson HE, Girardin SE, Wilson MI, Tooze SA. WIPI2 links LC3 conjugation with PI3P, autophagosome formation, and pathogen clearance by recruiting Atg12-5-16L1. Mol Cell. 2014;55:238-52. [75] Filimonenko M, Isakson P, Finley KD, Anderson M, Jeong H, Melia TJ, et al. The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Mol Cell. 2010;38:265-79. [76] Lystad AH, Ichimura Y, Takagi K, Yang Y, Pankiv S, Kanegae Y, et al. Structural determinants in GABARAP required for the selective binding and recruitment of ALFY to LC3B-positive structures. EMBO Rep. 2014;15:557-65. [77] Kawaguchi Y, Kovacs JJ, McLaurin A, Vance JM, Ito A, Yao TP. The deacetylase HDAC6 regulates aggresome formation and cell viability in response to misfolded protein stress. Cell. 2003;115:727-38. [78] N'Diaye EN, Kajihara KK, Hsieh I, Morisaki H, Debnath J, Brown EJ. PLIC proteins or ubiquilins regulate autophagy-dependent cell survival during nutrient starvation. EMBO Rep. 2009;10:173-9. 44

[79] Zhang J, Ney PA. Role of BNIP3 and NIX in cell death, autophagy, and mitophagy. Cell Death Differ. 2009;16:939-46. [80] Wilhelm M, Xu Z, Kukekov NV, Gire S, Greene LA. Proapoptotic Nix activates the JNK pathway by interacting with POSH and mediates death in a Parkinson disease model. J Biol Chem. 2007;282:1288-95. [81] Shi RY, Zhu SH, Li V, Gibson SB, Xu XS, Kong JM. BNIP3 interacting with LC3 triggers excessive mitophagy in delayed neuronal death in stroke. CNS Neurosci Ther. 2014;20:1045-55. [82] Novak I, Kirkin V, McEwan DG, Zhang J, Wild P, Rozenknop A, et al. Nix is a selective autophagy receptor for mitochondrial clearance. EMBO Rep. 2010;11:45-51. [83] Hanna RA, Quinsay MN, Orogo AM, Giang K, Rikka S, Gustafsson AB. Microtubuleassociated protein 1 light chain 3 (LC3) interacts with Bnip3 protein to selectively remove endoplasmic reticulum and mitochondria via autophagy. J Biol Chem. 2012;287:19094-104. [84] Sandoval H, Thiagarajan P, Dasgupta SK, Schumacher A, Prchal JT, Chen M, et al. Essential role for Nix in autophagic maturation of erythroid cells. Nature. 2008;454:232-5. [85] Guo K, Searfoss G, Krolikowski D, Pagnoni M, Franks C, Clark K, et al. Hypoxia induces the expression of the pro-apoptotic gene BNIP3. Cell Death Differ. 2001;8:367-76. [86] Kataoka T, Holler N, Micheau O, Martinon F, Tinel A, Hofmann K, et al. Bcl-rambo, a novel Bcl-2 homologue that induces apoptosis via its unique C-terminal extension. J Biol Chem. 2001;276:19548-54. [87] Murakawa T, Yamaguchi O, Hashimoto A, Hikoso S, Takeda T, Oka T, et al. Bcl-2-like protein 13 is a mammalian Atg32 homologue that mediates mitophagy and mitochondrial fragmentation. Nat Commun. 2015;6:7527. [88] Liu L, Feng D, Chen G, Chen M, Zheng Q, Song P, et al. Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells. Nat Cell Biol. 2012;14:177-85. [89] Edlich F, Lucke C. From cell death to viral replication: the diverse functions of the membrane-associated FKBP38. Curr Opin Pharmacol. 2011;11:348-53. 45

[90] Bhujabal Z, Birgisdottir AB, Sjottem E, Brenne HB, Overvatn A, Habisov S, et al. FKBP8 recruits LC3A to mediate Parkin-independent mitophagy. EMBO Rep. 2017;18:947-61. [91] Fimia GM, Stoykova A, Romagnoli A, Giunta L, Di Bartolomeo S, Nardacci R, et al. Ambra1 regulates autophagy and development of the nervous system. Nature. 2007;447:1121-5. [92] Strappazzon F, Nazio F, Corrado M, Cianfanelli V, Romagnoli A, Fimia GM, et al. AMBRA1 is able to induce mitophagy via LC3 binding, regardless of PARKIN and p62/SQSTM1. Cell Death Differ. 2015;22:419-32. [93] Wei Y, Chiang WC, Sumpter R, Jr., Mishra P, Levine B. Prohibitin 2 Is an Inner Mitochondrial Membrane Mitophagy Receptor. Cell. 2017;168:224-38 e10. [94] Princely Abudu Y, Pankiv S, Mathai BJ, Hakon Lystad A, Bindesboll C, Brenne HB, et al. NIPSNAP1 and NIPSNAP2 Act as "Eat Me" Signals for Mitophagy. Dev Cell. 2019. [95] Wilkinson S. Emerging Principles of Selective ER Autophagy. J Mol Biol. 2019. [96] Khaminets A, Heinrich T, Mari M, Grumati P, Huebner AK, Akutsu M, et al. Regulation of endoplasmic reticulum turnover by selective autophagy. Nature. 2015;522:354-8. [97] Forrester A, De Leonibus C, Grumati P, Fasana E, Piemontese M, Staiano L, et al. A selective ER-phagy exerts procollagen quality control via a Calnexin-FAM134B complex. EMBO J. 2019;38. [98] Fregno I, Fasana E, Bergmann TJ, Raimondi A, Loi M, Solda T, et al. ER-to-lysosomeassociated degradation of proteasome-resistant ATZ polymers occurs via receptor-mediated vesicular transport. EMBO J. 2018;37. [99] Grumati P, Morozzi G, Holper S, Mari M, Harwardt MI, Yan R, et al. Full length RTN3 regulates turnover of tubular endoplasmic reticulum via selective autophagy. Elife. 2017;6. [100] Fumagalli F, Noack J, Bergmann TJ, Cebollero E, Pisoni GB, Fasana E, et al. Translocon component Sec62 acts in endoplasmic reticulum turnover during stress recovery. Nat Cell Biol. 2016;18:1173-84.

46

[101] Smith MD, Harley ME, Kemp AJ, Wills J, Lee M, Arends M, et al. CCPG1 Is a Noncanonical Autophagy Cargo Receptor Essential for ER-Phagy and Pancreatic ER Proteostasis. Dev Cell. 2018;44:217-32 e11. [102] Chino H, Hatta T, Natsume T, Mizushima N. Intrinsically Disordered Protein TEX264 Mediates ER-phagy. Mol Cell. 2019. [103] An H, Ordureau A, Paulo JA, Shoemaker CJ, Denic V, Harper JW. TEX264 Is an Endoplasmic Reticulum-Resident ATG8-Interacting Protein Critical for ER Remodeling during Nutrient Stress. Mol Cell. 2019. [104] Chen Q, Xiao Y, Chai P, Zheng P, Teng J, Chen J. ATL3 Is a Tubular ER-Phagy Receptor for GABARAP-Mediated Selective Autophagy. Curr Biol. 2019. [105] Zurek N, Sparks L, Voeltz G. Reticulon short hairpin transmembrane domains are used to shape ER tubules. Traffic. 2011;12:28-41. [106] Bhaskara RM, Grumati P, Garcia-Pardo J, Kalayil S, Covarrubias-Pinto A, Chen W, et al. Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nat Commun. 2019;10:2370. [107] Walther TC, Chung J, Farese RV, Jr. Lipid Droplet Biogenesis. Annu Rev Cell Dev Biol. 2017;33:491-510. [108] Schulze RJ, Sathyanarayan A, Mashek DG. Breaking fat: The regulation and mechanisms of lipophagy. Biochim Biophys Acta Mol Cell Biol Lipids. 2017;1862:1178-87. [109] Martinez-Lopez N, Garcia-Macia M, Sahu S, Athonvarangkul D, Liebling E, Merlo P, et al. Autophagy in the CNS and Periphery Coordinate Lipophagy and Lipolysis in the Brown Adipose Tissue and Liver. Cell Metab. 2016;23:113-27. [110] Mancias JD, Wang X, Gygi SP, Harper JW, Kimmelman AC. Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy. Nature. 2014;509:105-9. [111] Dowdle WE, Nyfeler B, Nagel J, Elling RA, Liu S, Triantafellow E, et al. Selective VPS34 inhibitor blocks autophagy and uncovers a role for NCOA4 in ferritin degradation and iron homeostasis in vivo. Nat Cell Biol. 2014;16:1069-79.

47

[112] Jiang S, Wells CD, Roach PJ. Starch-binding domain-containing protein 1 (Stbd1) and glycogen metabolism: Identification of the Atg8 family interacting motif (AIM) in Stbd1 required for interaction with GABARAPL1. Biochem Biophys Res Commun. 2011;413:420-5. [113] Wyant GA, Abu-Remaileh M, Frenkel EM, Laqtom NN, Dharamdasani V, Lewis CA, et al. NUFIP1 is a ribosome receptor for starvation-induced ribophagy. Science. 2018;360:7518. [114] Zaffagnini G, Savova A, Danieli A, Romanov J, Tremel S, Ebner M, et al. p62 filaments capture and present ubiquitinated cargos for autophagy. EMBO J. 2018;37. [115] Sun D, Wu R, Zheng J, Li P, Yu L. Polyubiquitin chain-induced p62 phase separation drives autophagic cargo segregation. Cell Res. 2018;28:405-15. [116] Thurston TL, Boyle KB, Allen M, Ravenhill BJ, Karpiyevich M, Bloor S, et al. Recruitment of TBK1 to cytosol-invading Salmonella induces WIPI2-dependent antibacterial autophagy. EMBO J. 2016;35:1779-92. [117] Ichimura Y, Kumanomidou T, Sou YS, Mizushima T, Ezaki J, Ueno T, et al. Structural basis for sorting mechanism of p62 in selective autophagy. J Biol Chem. 2008;283:2284757. [118] Noda NN, Kumeta H, Nakatogawa H, Satoo K, Adachi W, Ishii J, et al. Structural basis of target recognition by Atg8/LC3 during selective autophagy. Genes Cells. 2008;13:1211-8. [119] Marshall RS, Hua Z, Mali S, McLoughlin F, Vierstra RD. ATG8-Binding UIM Proteins Define a New Class of Autophagy Adaptors and Receptors. Cell. 2019;177:766-81 e24. [120] Alemu EA, Lamark T, Torgersen KM, Birgisdottir AB, Larsen KB, Jain A, et al. ATG8 family proteins act as scaffolds for assembly of the ULK complex: sequence requirements for LC3-interacting region (LIR) motifs. J Biol Chem. 2012;287:39275-90. [121] Kraft C, Kijanska M, Kalie E, Siergiejuk E, Lee SS, Semplicio G, et al. Binding of the Atg1/ULK1 kinase to the ubiquitin-like protein Atg8 regulates autophagy. EMBO J. 2012;31:3691-703. [122] Nakatogawa H, Ohbayashi S, Sakoh-Nakatogawa M, Kakuta S, Suzuki SW, Kirisako H, et al. The autophagy-related protein kinase Atg1 interacts with the ubiquitin-like protein 48

Atg8 via the Atg8 family interacting motif to facilitate autophagosome formation. J Biol Chem. 2012;287:28503-7. [123] Joachim J, Jefferies HB, Razi M, Frith D, Snijders AP, Chakravarty P, et al. Activation of ULK Kinase and Autophagy by GABARAP Trafficking from the Centrosome Is Regulated by WAC and GM130. Mol Cell. 2015;60:899-913. [124] Birgisdottir AB, Mouilleron S, Bhujabal Z, Wirth M, Sjottem E, Evjen G, et al. Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs. Autophagy. 2019:1-23. [125] Torggler R, Papinski D, Brach T, Bas L, Schuschnig M, Pfaffenwimmer T, et al. Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole. Mol Cell. 2016;64:221-35. [126] Shintani T, Huang WP, Stromhaug PE, Klionsky DJ. Mechanism of cargo selection in the cytoplasm to vacuole targeting pathway. Dev Cell. 2002;3:825-37. [127] Ochaba J, Lukacsovich T, Csikos G, Zheng S, Margulis J, Salazar L, et al. Potential function for the Huntingtin protein as a scaffold for selective autophagy. Proc Natl Acad Sci U S A. 2014;111:16889-94. [128] Rui YN, Xu Z, Patel B, Chen Z, Chen D, Tito A, et al. Huntingtin functions as a scaffold for selective macroautophagy. Nat Cell Biol. 2015;17:262-75. [129] Martinez-Vicente M, Talloczy Z, Wong E, Tang G, Koga H, Kaushik S, et al. Cargo recognition failure is responsible for inefficient autophagy in Huntington's disease. Nat Neurosci. 2010;13:567-76. [130] Orsi A, Razi M, Dooley HC, Robinson D, Weston AE, Collinson LM, et al. Dynamic and transient interactions of Atg9 with autophagosomes, but not membrane integration, are required for autophagy. Mol Biol Cell. 2012;23:1860-73. [131] He C, Song H, Yorimitsu T, Monastyrska I, Yen WL, Legakis JE, et al. Recruitment of Atg9 to the preautophagosomal structure by Atg11 is essential for selective autophagy in budding yeast. J Cell Biol. 2006;175:925-35.

49

[132] Cheignon C, Tomas M, Bonnefont-Rousselot D, Faller P, Hureau C, Collin F. Oxidative stress and the amyloid beta peptide in Alzheimer's disease. Redox Biol. 2018;14:450-64. [133] Medinas DB, Rozas P, Martinez Traub F, Woehlbier U, Brown RH, Bosco DA, et al. Endoplasmic reticulum stress leads to accumulation of wild-type SOD1 aggregates associated with sporadic amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A. 2018;115:8209-14. [134] Saibil H. Chaperone machines for protein folding, unfolding and disaggregation. Nat Rev Mol Cell Biol. 2013;14:630-42. [135] Murata S, Minami Y, Minami M, Chiba T, Tanaka K. CHIP is a chaperone-dependent E3 ligase that ubiquitylates unfolded protein. EMBO Rep. 2001;2:1133-8. [136] Saeki Y. Ubiquitin recognition by the proteasome. J Biochem. 2017;161:113-24. [137] Riley BE, Kaiser SE, Shaler TA, Ng AC, Hara T, Hipp MS, et al. Ubiquitin accumulation in autophagy-deficient mice is dependent on the Nrf2-mediated stress response pathway: a potential role for protein aggregation in autophagic substrate selection. J Cell Biol. 2010;191:537-52. [138] Lu K, den Brave F, Jentsch S. Receptor oligomerization guides pathway choice between proteasomal and autophagic degradation. Nat Cell Biol. 2017;19:732-9. [139] Lee DY, Arnott D, Brown EJ. Ubiquilin4 is an adaptor protein that recruits Ubiquilin1 to the autophagy machinery. EMBO Rep. 2013;14:373-81. [140] Rothenberg C, Srinivasan D, Mah L, Kaushik S, Peterhoff CM, Ugolino J, et al. Ubiquilin functions in autophagy and is degraded by chaperone-mediated autophagy. Hum Mol Genet. 2010;19:3219-32. [141] Deng HX, Chen W, Hong ST, Boycott KM, Gorrie GH, Siddique N, et al. Mutations in UBQLN2 cause dominant X-linked juvenile and adult-onset ALS and ALS/dementia. Nature. 2011;477:211-5. [142] Dillen L, Van Langenhove T, Engelborghs S, Vandenbulcke M, Sarafov S, Tournev I, et al. Explorative genetic study of UBQLN2 and PFN1 in an extended Flanders-Belgian cohort of frontotemporal lobar degeneration patients. Neurobiol Aging. 2013;34:1711 e1-5. 50

[143] Mizuno Y, Amari M, Takatama M, Aizawa H, Mihara B, Okamoto K. Immunoreactivities of p62, an ubiqutin-binding protein, in the spinal anterior horn cells of patients with amyotrophic lateral sclerosis. J Neurol Sci. 2006;249:13-8. [144] Arai T, Nonaka T, Hasegawa M, Akiyama H, Yoshida M, Hashizume Y, et al. Neuronal and glial inclusions in frontotemporal dementia with or without motor neuron disease are immunopositive for p62. Neurosci Lett. 2003;342:41-4. [145] Hiji M, Takahashi T, Fukuba H, Yamashita H, Kohriyama T, Matsumoto M. White matter lesions in the brain with frontotemporal lobar degeneration with motor neuron disease: TDP-43-immunopositive inclusions co-localize with p62, but not ubiquitin. Acta Neuropathol. 2008;116:183-91. [146] Kim S, Lee D, Song JC, Cho SJ, Yun SM, Koh YH, et al. NDP52 associates with phosphorylated tau in brains of an Alzheimer disease mouse model. Biochem Biophys Res Commun. 2014;454:196-201. [147] Odagiri S, Tanji K, Mori F, Kakita A, Takahashi H, Wakabayashi K. Autophagic adapter protein NBR1 is localized in Lewy bodies and glial cytoplasmic inclusions and is involved in aggregate formation in alpha-synucleinopathy. Acta Neuropathol. 2012;124:173-86. [148] Ramesh Babu J, Lamar Seibenhener M, Peng J, Strom AL, Kemppainen R, Cox N, et al. Genetic inactivation of p62 leads to accumulation of hyperphosphorylated tau and neurodegeneration. J Neurochem. 2008;106:107-20. [149] Lattante S, de Calbiac H, Le Ber I, Brice A, Ciura S, Kabashi E. Sqstm1 knock-down causes a locomotor phenotype ameliorated by rapamycin in a zebrafish model of ALS/FTLD. Hum Mol Genet. 2015;24:1682-90. [150] de Castro IP, Costa AC, Celardo I, Tufi R, Dinsdale D, Loh SH, et al. Drosophila ref(2)P is required for the parkin-mediated suppression of mitochondrial dysfunction in pink1 mutants. Cell Death Dis. 2013;4:e873. [151] Caccamo A, Ferreira E, Branca C, Oddo S. p62 improves AD-like pathology by increasing autophagy. Mol Psychiatry. 2017;22:865-73.

51

[152] Komatsu M, Waguri S, Koike M, Sou YS, Ueno T, Hara T, et al. Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell. 2007;131:1149-63. [153] Tanji K, Odagiri S, Miki Y, Maruyama A, Nikaido Y, Mimura J, et al. p62 Deficiency Enhances alpha-Synuclein Pathology in Mice. Brain Pathol. 2015;25:552-64. [154] Korac J, Schaeffer V, Kovacevic I, Clement AM, Jungblut B, Behl C, et al. Ubiquitinindependent function of optineurin in autophagic clearance of protein aggregates. J Cell Sci. 2013;126:580-92. [155] Chen K, Yuan R, Geng S, Zhang Y, Ran T, Kowalski E, et al. Toll-interacting protein deficiency promotes neurodegeneration via impeding autophagy completion in high-fat dietfed ApoE(-/-) mouse model. Brain Behav Immun. 2017;59:200-10. [156] Ichimura Y, Waguri S, Sou YS, Kageyama S, Hasegawa J, Ishimura R, et al. Phosphorylation of p62 activates the Keap1-Nrf2 pathway during selective autophagy. Mol Cell. 2013;51:618-31. [157] Tanji K, Miki Y, Ozaki T, Maruyama A, Yoshida H, Mimura J, et al. Phosphorylation of serine 349 of p62 in Alzheimer's disease brain. Acta Neuropathol Commun. 2014;2:50. [158] Jo C, Gundemir S, Pritchard S, Jin YN, Rahman I, Johnson GV. Nrf2 reduces levels of phosphorylated tau protein by inducing autophagy adaptor protein NDP52. Nat Commun. 2014;5:3496. [159] Falcon B, Noad J, McMahon H, Randow F, Goedert M. Galectin-8-mediated selective autophagy protects against seeded tau aggregation. J Biol Chem. 2018;293:2438-51. [160] Shen WC, Li HY, Chen GC, Chern Y, Tu PH. Mutations in the ubiquitin-binding domain of OPTN/optineurin interfere with autophagy-mediated degradation of misfolded proteins by a dominant-negative mechanism. Autophagy. 2015;11:685-700. [161] van der Zee J, Van Langenhove T, Kovacs GG, Dillen L, Deschamps W, Engelborghs S, et al. Rare mutations in SQSTM1 modify susceptibility to frontotemporal lobar degeneration. Acta Neuropathol. 2014;128:397-410.

52

[162] Alonso N, Calero-Paniagua I, Del Pino-Montes J. Clinical and Genetic Advances in Paget's Disease of Bone: a Review. Clin Rev Bone Miner Metab. 2017;15:37-48. [163] Goode A, Butler K, Long J, Cavey J, Scott D, Shaw B, et al. Defective recognition of LC3B by mutant SQSTM1/p62 implicates impairment of autophagy as a pathogenic mechanism in ALS-FTLD. Autophagy. 2016;12:1094-104. [164] Goode A, Rea S, Sultana M, Shaw B, Searle MS, Layfield R. ALS-FTLD associated mutations of SQSTM1 impact on Keap1-Nrf2 signalling. Mol Cell Neurosci. 2016;76:52-8. [165] Deng Z, Lim J, Wang Q, Purtell K, Wu S, Palomo GM, et al. ALS-FTLD-linked mutations of SQSTM1/p62 disrupt selective autophagy and NFE2L2/NRF2 anti-oxidative stress pathway. Autophagy. 2019:1-15. [166] Ayaki T, Ito H, Fukushima H, Inoue T, Kondo T, Ikemoto A, et al. Immunoreactivity of valosin-containing protein in sporadic amyotrophic lateral sclerosis and in a case of its novel mutant. Acta Neuropathol Commun. 2014;2:172. [167] Cirulli ET, Lasseigne BN, Petrovski S, Sapp PC, Dion PA, Leblond CS, et al. Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways. Science. 2015;347:1436-41. [168] Freischmidt A, Wieland T, Richter B, Ruf W, Schaeffer V, Muller K, et al. Haploinsufficiency of TBK1 causes familial ALS and fronto-temporal dementia. Nat Neurosci. 2015;18:631-6. [169] Bjorkoy G, Lamark T, Brech A, Outzen H, Perander M, Overvatn A, et al. p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtininduced cell death. J Cell Biol. 2005;171:603-14. [170] Ito Y, Ofengeim D, Najafov A, Das S, Saberi S, Li Y, et al. RIPK1 mediates axonal degeneration by promoting inflammation and necroptosis in ALS. Science. 2016;353:603-8. [171] McWilliams TG, Prescott AR, Allen GF, Tamjar J, Munson MJ, Thomson C, et al. mitoQC illuminates mitophagy and mitochondrial architecture in vivo. J Cell Biol. 2016;214:33345.

53

[172] McWilliams TG, Prescott AR, Montava-Garriga L, Ball G, Singh F, Barini E, et al. Basal Mitophagy Occurs Independently of PINK1 in Mouse Tissues of High Metabolic Demand. Cell Metab. 2018;27:439-49 e5. [173] Burte F, Carelli V, Chinnery PF, Yu-Wai-Man P. Disturbed mitochondrial dynamics and neurodegenerative disorders. Nat Rev Neurol. 2015;11:11-24. [174] Kitada T, Asakawa S, Hattori N, Matsumine H, Yamamura Y, Minoshima S, et al. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature. 1998;392:605-8. [175] Narendra D, Tanaka A, Suen DF, Youle RJ. Parkin is recruited selectively to impaired mitochondria and promotes their autophagy. J Cell Biol. 2008;183:795-803. [176] Valente EM, Abou-Sleiman PM, Caputo V, Muqit MM, Harvey K, Gispert S, et al. Hereditary early-onset Parkinson's disease caused by mutations in PINK1. Science. 2004;304:1158-60. [177] Kane LA, Lazarou M, Fogel AI, Li Y, Yamano K, Sarraf SA, et al. PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity. J Cell Biol. 2014;205:143-53. [178] Narendra DP, Jin SM, Tanaka A, Suen DF, Gautier CA, Shen J, et al. PINK1 is selectively

stabilized

on

impaired

mitochondria

to

activate

Parkin.

PLoS

Biol.

2010;8:e1000298. [179] Matsuda N, Sato S, Shiba K, Okatsu K, Saisho K, Gautier CA, et al. PINK1 stabilized by mitochondrial depolarization recruits Parkin to damaged mitochondria and activates latent Parkin for mitophagy. J Cell Biol. 2010;189:211-21. [180] Koyano F, Okatsu K, Kosako H, Tamura Y, Go E, Kimura M, et al. Ubiquitin is phosphorylated by PINK1 to activate parkin. Nature. 2014;510:162-6. [181] Kazlauskaite A, Kondapalli C, Gourlay R, Campbell DG, Ritorto MS, Hofmann K, et al. Parkin is activated by PINK1-dependent phosphorylation of ubiquitin at Ser65. Biochem J. 2014;460:127-39.

54

[182] Shiba-Fukushima K, Imai Y, Yoshida S, Ishihama Y, Kanao T, Sato S, et al. PINK1mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy. Sci Rep. 2012;2:1002. [183] Shiba-Fukushima K, Arano T, Matsumoto G, Inoshita T, Yoshida S, Ishihama Y, et al. Phosphorylation of mitochondrial polyubiquitin by PINK1 promotes Parkin mitochondrial tethering. PLoS Genet. 2014;10:e1004861. [184] Matsuda N. Phospho-ubiquitin: upending the PINK-Parkin-ubiquitin cascade. J Biochem. 2016;159:379-85. [185] Ordureau A, Paulo JA, Zhang W, Ahfeldt T, Zhang J, Cohn EF, et al. Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Mol Cell. 2018;70:211-27 e8. [186] Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, et al. Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization. Nature. 2013;496:372-6. [187] Tanaka A, Cleland MM, Xu S, Narendra DP, Suen DF, Karbowski M, et al. Proteasome and p97 mediate mitophagy and degradation of mitofusins induced by Parkin. J Cell Biol. 2010;191:1367-80. [188] Yoshii SR, Kishi C, Ishihara N, Mizushima N. Parkin mediates proteasome-dependent protein degradation and rupture of the outer mitochondrial membrane. J Biol Chem. 2011;286:19630-40. [189] Pickrell AM, Youle RJ. The roles of PINK1, parkin, and mitochondrial fidelity in Parkinson's disease. Neuron. 2015;85:257-73. [190] Cornelissen T, Vilain S, Vints K, Gounko N, Verstreken P, Vandenberghe W. Deficiency of parkin and PINK1 impairs age-dependent mitophagy in Drosophila. Elife. 2018;7. [191] Wong YC, Holzbaur EL. Optineurin is an autophagy receptor for damaged mitochondria in parkin-mediated mitophagy that is disrupted by an ALS-linked mutation. Proc Natl Acad Sci U S A. 2014;111:E4439-48. 55

[192] Nguyen TD, Shaid S, Vakhrusheva O, Koschade SE, Klann K, Tholken M, et al. Loss of the selective autophagy receptor p62 impairs murine myeloid leukemia progression and mitophagy. Blood. 2019;133:168-79. [193] Ding WX, Ni HM, Li M, Liao Y, Chen X, Stolz DB, et al. Nix is critical to two distinct phases of mitophagy, reactive oxygen species-mediated autophagy induction and Parkinubiquitin-p62-mediated mitochondrial priming. J Biol Chem. 2010;285:27879-90. [194] Geisler S, Holmstrom KM, Skujat D, Fiesel FC, Rothfuss OC, Kahle PJ, et al. PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1. Nat Cell Biol. 2010;12:119-31. [195] Narendra D, Kane LA, Hauser DN, Fearnley IM, Youle RJ. p62/SQSTM1 is required for Parkin-induced mitochondrial clustering but not mitophagy; VDAC1 is dispensable for both. Autophagy. 2010;6:1090-106. [196] Shi J, Fung G, Deng H, Zhang J, Fiesel FC, Springer W, et al. NBR1 is dispensable for PARK2-mediated mitophagy regardless of the presence or absence of SQSTM1. Cell Death Dis. 2015;6:e1943. [197] Fang EF, Hou Y, Palikaras K, Adriaanse BA, Kerr JS, Yang B, et al. Mitophagy inhibits amyloid-beta and tau pathology and reverses cognitive deficits in models of Alzheimer's disease. Nat Neurosci. 2019;22:401-12. [198] Du F, Yu Q, Yan S, Hu G, Lue LF, Walker DG, et al. PINK1 signalling rescues amyloid pathology and mitochondrial dysfunction in Alzheimer's disease. Brain. 2017;140:3233-51. [199] Liu J, Wang X, Lu Y, Duan C, Gao G, Lu L, et al. Pink1 interacts with alpha-synuclein and abrogates alpha-synuclein-induced neurotoxicity by activating autophagy. Cell Death Dis. 2017;8:e3056. [200] Yamada T, Murata D, Adachi Y, Itoh K, Kameoka S, Igarashi A, et al. Mitochondrial Stasis Reveals p62-Mediated Ubiquitination in Parkin-Independent Mitophagy and Mitigates Nonalcoholic Fatty Liver Disease. Cell Metab. 2018;28:588-604 e5.

56

[201] Di Rita A, Peschiaroli A, P DA, Strobbe D, Hu Z, Gruber J, et al. HUWE1 E3 ligase promotes PINK1/PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKalpha. Nat Commun. 2018;9:3755. [202] Koentjoro B, Park JS, Sue CM. Nix restores mitophagy and mitochondrial function to protect against PINK1/Parkin-related Parkinson's disease. Sci Rep. 2017;7:44373. [203] Berger J, Dorninger F, Forss-Petter S, Kunze M. Peroxisomes in brain development and function. Biochim Biophys Acta. 2016;1863:934-55. [204] Mitchell J, Paul P, Chen HJ, Morris A, Payling M, Falchi M, et al. Familial amyotrophic lateral sclerosis is associated with a mutation in D-amino acid oxidase. Proc Natl Acad Sci U S A. 2010;107:7556-61. [205] Sargent G, van Zutphen T, Shatseva T, Zhang L, Di Giovanni V, Bandsma R, et al. PEX2 is the E3 ubiquitin ligase required for pexophagy during starvation. J Cell Biol. 2016;214:677-90. [206] Yamashita S, Abe K, Tatemichi Y, Fujiki Y. The membrane peroxin PEX3 induces peroxisome-ubiquitination-linked pexophagy. Autophagy. 2014;10:1549-64. [207] Hetz C, Saxena S. ER stress and the unfolded protein response in neurodegeneration. Nat Rev Neurol. 2017;13:477-91. [208] Kurth I, Pamminger T, Hennings JC, Soehendra D, Huebner AK, Rotthier A, et al. Mutations in FAM134B, encoding a newly identified Golgi protein, cause severe sensory and autonomic neuropathy. Nat Genet. 2009;41:1179-81. [209] Murphy SM, Davidson GL, Brandner S, Houlden H, Reilly MM. Mutation in FAM134B causing

severe

hereditary

sensory

neuropathy.

J

Neurol

Neurosurg

Psychiatry.

2012;83:119-20. [210] Deng M, He W, Tan Y, Han H, Hu X, Xia K, et al. Increased expression of reticulon 3 in neurons leads to reduced axonal transport of beta site amyloid precursor protein-cleaving enzyme 1. J Biol Chem. 2013;288:30236-45. [211] Shi Q, Ge Y, He W, Hu X, Yan R. RTN1 and RTN3 protein are differentially associated with senile plaques in Alzheimer's brains. Sci Rep. 2017;7:6145. 57

[212] Shi Q, Ge Y, Sharoar MG, He W, Xiang R, Zhang Z, et al. Impact of RTN3 deficiency on expression of BACE1 and amyloid deposition. J Neurosci. 2014;34:13954-62. [213] Liang JR, Lingeman E, Ahmed S, Corn JE. Atlastins remodel the endoplasmic reticulum for selective autophagy. J Cell Biol. 2018;217:3354-67. [214] Protter DSW, Parker R. Principles and Properties of Stress Granules. Trends Cell Biol. 2016;26:668-79. [215] Bosco DA, Lemay N, Ko HK, Zhou H, Burke C, Kwiatkowski TJ, Jr., et al. Mutant FUS proteins that cause amyotrophic lateral sclerosis incorporate into stress granules. Hum Mol Genet. 2010;19:4160-75. [216] Liu-Yesucevitz L, Bilgutay A, Zhang YJ, Vanderweyde T, Citro A, Mehta T, et al. Tar DNA binding protein-43 (TDP-43) associates with stress granules: analysis of cultured cells and pathological brain tissue. PLoS One. 2010;5:e13250. [217] Khalfallah Y, Kuta R, Grasmuck C, Prat A, Durham HD, Vande Velde C. TDP-43 regulation of stress granule dynamics in neurodegenerative disease-relevant cell types. Sci Rep. 2018;8:7551. [218] Maharjan N, Kunzli C, Buthey K, Saxena S. C9ORF72 Regulates Stress Granule Formation and Its Deficiency Impairs Stress Granule Assembly, Hypersensitizing Cells to Stress. Mol Neurobiol. 2017;54:3062-77. [219] Boeynaems S, Bogaert E, Kovacs D, Konijnenberg A, Timmerman E, Volkov A, et al. Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics. Mol Cell. 2017;65:1044-55 e5. [220] Buchan JR, Kolaitis RM, Taylor JP, Parker R. Eukaryotic stress granules are cleared by autophagy and Cdc48/VCP function. Cell. 2013;153:1461-74. [221] Alexander EJ, Ghanbari Niaki A, Zhang T, Sarkar J, Liu Y, Nirujogi RS, et al. Ubiquilin 2 modulates ALS/FTD-linked FUS-RNA complex dynamics and stress granule formation. Proc Natl Acad Sci U S A. 2018;115:E11485-E94.

58

[222] Chitiprolu M, Jagow C, Tremblay V, Bondy-Chorney E, Paris G, Savard A, et al. A complex of C9ORF72 and p62 uses arginine methylation to eliminate stress granules by autophagy. Nat Commun. 2018;9:2794. [223] Carpio MA, Lopez Sambrooks C, Durand ES, Hallak ME. The arginylation-dependent association of calreticulin with stress granules is regulated by calcium. Biochem J. 2010;429:63-72. [224] Zhang YJ, Gendron TF, Ebbert MTW, O'Raw AD, Yue M, Jansen-West K, et al. Poly(GR) impairs protein translation and stress granule dynamics in C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis. Nat Med. 2018;24:1136-42. [225] Kim SH, Dong WK, Weiler IJ, Greenough WT. Fragile X mental retardation protein shifts between polyribosomes and stress granules after neuronal injury by arsenite stress or in vivo hippocampal electrode insertion. J Neurosci. 2006;26:2413-8. [226] Pennetta G, Welte MA. Emerging Links between Lipid Droplets and Motor Neuron Diseases. Dev Cell. 2018;45:427-32. [227] Stallings NR, Puttaparthi K, Dowling KJ, Luther CM, Burns DK, Davis K, et al. TDP-43, an ALS linked protein, regulates fat deposition and glucose homeostasis. PLoS One. 2013;8:e71793. [228] Inloes JM, Hsu KL, Dix MM, Viader A, Masuda K, Takei T, et al. The hereditary spastic paraplegia-related enzyme DDHD2 is a principal brain triglyceride lipase. Proc Natl Acad Sci U S A. 2014;111:14924-9. [229] Jung WH, Liu CC, Yu YL, Chang YC, Lien WY, Chao HC, et al. Lipophagy prevents activity-dependent neurodegeneration due to dihydroceramide accumulation in vivo. EMBO Rep. 2017;18:1150-65. [230] Kaushik S, Cuervo AM. Degradation of lipid droplet-associated proteins by chaperonemediated autophagy facilitates lipolysis. Nat Cell Biol. 2015;17:759-70. [231] Ward RJ, Zucca FA, Duyn JH, Crichton RR, Zecca L. The role of iron in brain ageing and neurodegenerative disorders. Lancet Neurol. 2014;13:1045-60.

59

[232] Kishi-Itakura C, Koyama-Honda I, Itakura E, Mizushima N. Ultrastructural analysis of autophagosome organization using mammalian autophagy-deficient cells. J Cell Sci. 2014;127:4089-102. [233] Asano T, Komatsu M, Yamaguchi-Iwai Y, Ishikawa F, Mizushima N, Iwai K. Distinct mechanisms of ferritin delivery to lysosomes in iron-depleted and iron-replete cells. Mol Cell Biol. 2011;31:2040-52. [234] Quiles Del Rey M, Mancias JD. NCOA4-Mediated Ferritinophagy: A Potential Link to Neurodegeneration. Front Neurosci. 2019;13:238. [235] Brown AM. Brain glycogen re-awakened. J Neurochem. 2004;89:537-52. [236] Duran J, Gruart A, Garcia-Rocha M, Delgado-Garcia JM, Guinovart JJ. Glycogen accumulation underlies neurodegeneration and autophagy impairment in Lafora disease. Hum Mol Genet. 2014;23:3147-56. [237] Rai A, Singh PK, Singh V, Kumar V, Mishra R, Thakur AK, et al. Glycogen synthase protects neurons from cytotoxicity of mutant huntingtin by enhancing the autophagy flux. Cell Death Dis. 2018;9:201. [238] Martini R, Klein D, Groh J. Similarities between inherited demyelinating neuropathies and Wallerian degeneration: an old repair program may cause myelin and axon perturbation under nonlesion conditions. Am J Pathol. 2013;183:655-60. [239] Gomez-Sanchez JA, Carty L, Iruarrizaga-Lejarreta M, Palomo-Irigoyen M, Varela-Rey M, Griffith M, et al. Schwann cell autophagy, myelinophagy, initiates myelin clearance from injured nerves. J Cell Biol. 2015;210:153-68. [240] Liu S, Li Y, Choi HMC, Sarkar C, Koh EY, Wu J, et al. Lysosomal damage after spinal cord injury causes accumulation of RIPK1 and RIPK3 proteins and potentiation of necroptosis. Cell Death Dis. 2018;9:476. [241] Papadopoulos C, Meyer H. Detection and Clearance of Damaged Lysosomes by the Endo-Lysosomal Damage Response and Lysophagy. Curr Biol. 2017;27:R1330-R41.

60

[242] Thurston TL, Wandel MP, von Muhlinen N, Foeglein A, Randow F. Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion. Nature. 2012;482:414-8. [243] Yoshida Y, Yasuda S, Fujita T, Hamasaki M, Murakami A, Kawawaki J, et al. Ubiquitination of exposed glycoproteins by SCF(FBXO27) directs damaged lysosomes for autophagy. Proc Natl Acad Sci U S A. 2017;114:8574-9. [244] Papadopoulos C, Kirchner P, Bug M, Grum D, Koerver L, Schulze N, et al. VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy. EMBO J. 2017;36:135-50. [245] Marshall RS, McLoughlin F, Vierstra RD. Autophagic Turnover of Inactive 26S Proteasomes in Yeast Is Directed by the Ubiquitin Receptor Cue5 and the Hsp42 Chaperone. Cell Rep. 2016;16:1717-32. [246] Thibaudeau TA, Anderson RT, Smith DM. A common mechanism of proteasome impairment

by

neurodegenerative

disease-associated

oligomers.

Nat

Commun.

2018;9:1097. [247] Korolchuk VI, Mansilla A, Menzies FM, Rubinsztein DC. Autophagy inhibition compromises

degradation

of

ubiquitin-proteasome

pathway

substrates.

Mol

Cell.

2009;33:517-27. [248] Collins I, Wang H, Caldwell JJ, Chopra R. Chemical approaches to targeted protein degradation through modulation of the ubiquitin-proteasome pathway. Biochem J. 2017;474:1127-47. [249] Pluckthun A. Designed ankyrin repeat proteins (DARPins): binding proteins for research, diagnostics, and therapy. Annu Rev Pharmacol Toxicol. 2015;55:489-511. [250] Lalatsa A, Schatzlein AG, Uchegbu IF. Strategies to deliver peptide drugs to the brain. Mol Pharm. 2014;11:1081-93. [251] Heo JM, Ordureau A, Paulo JA, Rinehart J, Harper JW. The PINK1-PARKIN Mitochondrial Ubiquitylation Pathway Drives a Program of OPTN/NDP52 Recruitment and TBK1 Activation to Promote Mitophagy. Mol Cell. 2015;60:7-20. 61

[252] Simpson GL, Hughes JA, Washio Y, Bertrand SM. Direct small-molecule kinase activation: Novel approaches for a new era of drug discovery. Curr Opin Drug Discov Devel. 2009;12:585-96. [253] Ponpuak M, Mandell MA, Kimura T, Chauhan S, Cleyrat C, Deretic V. Secretory autophagy. Curr Opin Cell Biol. 2015;35:106-16.

62

Table 1. Examples of proteins producing pathological aggregates associated with NDDs. Protein (gene) α-synuclein (SNCA)

Description Reference(s) Neuronal protein that regulates synaptic vesicle trafficking and neurotransmitter release; (reviewed in [6]) mutated and aggregated α-synuclein is found in Lewy bodies found in neurons of patients with PD and other NDDs.

Ataxin-3 (ATXN3)

DUB with roles in the UPS and autophagy; polyQ expansion of ATXN3 leads to protein (reviewed in [254]) aggregation and sequestration of other UPS players, thus interfering with protein degradation, linked to a rare autosomal dominantly inherited NDD, Machado-Joseph disease, also known as spinocerebellar ataxia type 3 (SCA3).

β-amyloid peptide, Aβ (APP)

Peptide of 36-43 amino acids produced by the activity of β-secretase and γ-secretase from (reviewed in [5]) the integral membrane protein APP with a poorly defined function; main component of amyloid plaques found in the brains of patients with AD.

C9ORF72 (C9ORF72) GEF for Rab8A and Rab39B; hexanucleotide (GGGGCC) expansion in intron 1 of C9ORF72 (reviewed in [11]) leads to glycine-alanine (GA), glycine-arginine (GR), proline-alanine (PA), proline-arginine (PR) and glycine-proline (GP) dipeptide aggregates and intracellular RNA deposits, which is the most frequent cause of ALS/FTD. FUS (FUS)

RNA/DNA-binding protein that acts as a transcriptional modulator and has a role in DNA (reviewed in [9]) repair and RNA splicing; FUS-positive aggregates are found in ALS/FTD.

Huntingtin (HTT)

Large protein with a putative role in autophagy; polyQ expansion of HTT leads to HD.

Superoxide dismutase (SOD1)

Enzyme that destroys free radicals; misfolds and aggregates in the absence of intramolecular (reviewed in [12]) disulfide bonds or bound zinc ions; mutations in SOD1 are linked to familial forms of ALS.

Tau (MAPT)

Microtubule-associated protein that promotes tubulin polymerization and aggregates via a (reviewed in [8]) hexapeptide motif when detached from microtubules; NFTs containing mutated and hyperphosphorylated Tau are a hallmark of AD/FTD and other NDDs.

1

(reviewed in [10])

A. Neuronal selective autophagy

Axon terminal

Schwann cell CDC48-phagy

Myelinophagy

● UBXN7?

● Unknown

Proteaphagy ● Unknown

Pexophagy ● NBR1

Proteasome

Dendrite

Axonal AP transport

ER-phagy ● FAM134 ● Sec62 ● RTN3

● CCPG1 ● ATL3 ● TEX264

Aggrephagy

Protein aggregate

● p62/SQSTM1 ● NBR1 ● TAX1BP1 ● NDP52 ● OPTN

● TOLLIP ● ALFY ● TRIM5 ● ATG16L1

Nucleus

ER

Mitochondrion Ferritinophagy

P

● NCOA4

AP

Mitophagy

AL

● OPTN ● NDP52 ● NIPSNAP1/2 ● AMBRA1 ● NIX

Glycophagy ● STBD1 Ribosome Ribophagy ● NUFIP1 Granulophagy ● p62/SQSTM1

Stress granule

Lipid droplet Lipophagy ● ATGL ● HSL

● BNIP3 ● FUNDC1 ● BCL2L13 ● FKBP8 ● PHB2

B. Overview of aggrephagy SARs

Phagophore membrane

PB1

PB1 ZZ CC SKICH

LIR CC

CC

UBA

J

LIR

CC

UBA

CC

NBR1 (966aa)

ZF ZF SKICH FIR

CC

TAX1BP1 (789aa)

CC

cLIR

ZF

Ub

OPTN (577aa)

UBAN ZF

LIR

TOLLIP (274aa)

CUE

C2

p62/ SQSTM1 (440aa)

NDP52 (446aa)

LIR-like

CC

FIR

LIR

LIR FIR cLIR

Misfolded protein

ZZ

ATG16L1 (607aa)

LIR LIR WD40 (No LIR) CC

ALFY (3526aa)

FIR WD40

Protein aggregate TRIM5 (493aa)

FYVE LIR

BEACH PH

SPRY CC LIR

RING

General features

LC3/ GABARAPs

Protein domains

Associated SARs

Cargo-binding domain

Membrane-associated domain

LIR to LC3/GABARAPs

FIR

Oligomerisation domain

Ubiquitin-binding SARs

LIR/UIM

Other functional domains

C. Overview of mitophagy SARs

Phagophore membrane

TM

TM

BH3

BH3

LIR

LIR

3x TM

TM LIR BH2 BH1

LIR

BH3 NIX (219aa)

BNIP3 (259aa)

FUNDC1 (155aa)

TM

BH4

CaM PPlase

BCL2L13 (485aa)

LIR

LIR FKBP8 (412aa) TM

PHB2 (299aa)

DABB1

MTS

DABB2

(No LIR)

NIPSNAP1/2 (284/286aa)

Ub

SKICH NDP52 (446aa)

Dysfunctional mitochondrian

• ↓∆ψm • Hypoxia • Iron depletion • Calcium dysregulation

OPTN (577aa)

FIR cLIR

CC

General features

ZF

LIR-like

LIR CC

AMBRA1 (1298aa)

LC3/ GABARAPs

CC

UBAN ZF

LIR

Protein domains

Associated SARs

Cargo-binding domain

Membrane-associated domain

LIR to LC3/GABARAPs

FIR

Oligomerisation domain

Mitochondrion-associated SARs

LIR/UIM

Other functional domains

Ubiquitin-binding SARs

D. Overview of ER–phagy SARs

Phagophore membrane

2x TM

2x TM LIR 2x TM

FAM134B (497aa) LIR

LIR LIR LIR LIR LIR LIR

4x TM

Sec62 (399aa)

RTN3 (1032aa)

CCPG1 (757aa)

TM

2x FIR

ER remodelling and stress

Misfolded protein ATL3 (541aa)

LIR

2x TM TEX264 (313aa) LIR LIR

LIR

TM

General features ER-associated SARs LIR to LC3/GABARAPs

Protein domains Cargo-binding domain

LIR/UIM

Membraneassociated domain

A

PB1

ZZ

p62/SQSTM1

B

UBA

OPTN

NEMO

UBAN

C

ZF

LC3/GABARAP

HP1 577 aa

440 aa LCK-binding PRKCZ-binding, dimerization PAWR-binding GABRR3-binding LIM-binding TRAF6-binding NTRK11-binding

Monomer

W338

LIR

FIR LIR KIR

Rab8-binding

Interaction partners

Monomer

Oligomers

p62/SQSTM1 PB1 PKC zeta PB 1

HD-binding MYO6-binding

Interaction partners

p62/SQSTM1 fiaments

TBK1 CTD

Oligomers

OPTN NEMO

L341

NEMO PB1

NEMO_N domain 5EOF PB 1 domain 4UF8 Zn

Homo- and heterodimers 4MJS

Homo- and heterooligomers 4UF8, 4UF9

p62/SQSTM1 ZZ

Arg

Homo- and heterodimers 5EOF

LIR

p62/SQSTM1 LIR

Short linear peptide (symulated)

Ubiquitin chain

ATG8-family proteins 2LUE Linear diubiquitin

p62/SQSTM1 UBA

UBAN

LC3B

LIR

p62/SQSTM1 LIR

LC3B Short linear peptide (symulated)

N-terminal residues 6MJ7

Homo- and heterooligomers 5EOF

OPTN LIR

ZZ Zn-finger ZZ-type 5YP7

HP2

UBAN (CC2-LZ) domain 5B83

Polyubiquitin 5B83

Homo- and heterodimers 5B83

L71

E396

ZF

Ubiquitin chain

Keap1

KIR

Zn-finger (ZF_CCHC_NOA) 2LO4

p62/SQSTM1 KIR

Short linear peptide (symulated)

R74

Keap1 (Kelch domain) 3ADE Ubiquitin

T430

G425

Zn

ATG8-family proteins 2ZJD

P391

V70

Folded domains UBA p62/SQSTM1

E478

Coiled coil regions

UBA

Motifs

OPTN UBAN

Disordered regions UBA domain 2K0B

Ubiquitin, UBL (modelled)

Homo- and heterodimers 2KNV

A481

The Journal of Molecular Biology, Special Issue “Autophagy in Neurodegenerative Disease” Manuscript by Conway et al: “Selective autophagy receptors in neuronal health and disease”

Highlights •

Principles of selective autophagy

•

Main selective autophagy receptors (SARs)

•

Roles of different SARs and selective autophagy pathways in neurodegenerative diseases (NDDs)

•

Potential therapeutic approaches to NDDs exploiting SARs and selective autophagy

1