Atg8: an autophagy-related ubiquitin-like protein family.

“Although mammalian Atg8 proteins were originally implicated in intracellular trafficking processes, they are all found within autophagosomes [73-75].”

“The motif in p62 responsible for binding Atg8, the LC3interacting region (LIR, also known as Atg8-interacting motif, AIM) [104,105], is common to other proteins that interact with Atg8 proteins, including Nbr1 [106], Atg3 [107], Nix [96] and the yeast cytoplasm-to-vacuole targeting receptor Atg19 [108].”

“[113] show the conservation (overall height) and residue prevalence of multiple alignment positions.”

“These adaptors bind simultaneously to Atg8 proteins and to ubiquitinated proteins, organelles, and in some cases pathogens [18,94,103].”

“Sequences for the alignments were taken from the CDD [114] and PFAM [115] database entries cd01611 and PF02991, respectively, and sequences”

“Sequences for the alignments were taken from the CDD [114] and PFAM [115] database entries cd01611 and PF02991, respectively, and sequences”

“Thus, transgenic mice and tissue-culture cells expressing GFP-LC3 have been used to investigate autophagy [84,85].”

“Atg4 regulates a critical step in the autophagic process and is therefore subjected to regulation by reactive oxygen species, for example, which prevent it from reversing the conjugation of Atg8 proteins to PE during autophagy [83].”

“Unlike ubiquitin, which is conjugated to a protein, Atg8 is covalently conjugated to PE lipid through its carboxy-terminal exposed glycine [64].”

“Although the transcriptional regulation of Atg8 genes is largely unknown, several reports have shown that the transcription factors FoxO1, FoxO3 and E2F1 regulate Atg8s in this process in mammalian cells [31-34].”

“Although the transcriptional regulation of Atg8 genes is largely unknown, several reports have shown that the transcription factors FoxO1, FoxO3 and E2F1 regulate Atg8s in this process in mammalian cells [31-34].”

“Several approaches aimed at disrupting the functioning of Atg8 proteins by preventing their conjugation to PE have therefore been used, including the generation of Atg3-null mice and expression of a dominant-negative mutant of the promiscuous protease Atg4B.”

“Although mammalian Atg8 proteins were originally implicated in intracellular trafficking processes, they are all found within autophagosomes [73-75].”

“autophagy-linked FYVE protein (Alfy) [98-100], nuclear dot protein 52 kDa (NDP52) [101], and Optineurin [102] as autophagic receptors.”

“This role was further established using an in vitro liposome-based system, where it can promote membrane fusion [20,22].”

“Considerable progress in establishing this idea was achieved by the characterization of the ubiquitin-binding proteins p62/SQSTM1 [94], neighbor of Brca1 (Nbr1) [95], the Bcl2-related protein Nix [96,97], Shpilka et al.”

“Choanoflagellates, unicellular species that are the closest known relatives of animals [6], have ATG8 genes that do not belong to the three metazoan subfamilies (Figure 1a).”

“The Atg5-Atg12 conjugate acts as an E3-like ligase, mediating the formation of Atg8-PE conjugate in vitro, suggesting a role for this complex in determining the Atg8 conjugation site in cells [67].”

“It was suggested that Atg16L (the mammalian Atg16) determines the lipida tion site of LC3 and serves as its E3 ligase [77].”

“These have led to the conclusion that PE-conjugated Atg8 proteins are active during autophagosome formation and are essential for the elongation and closure of the initial autophagic membrane, the phagophore [86-88].”

“Similar to many other cytoplasm-tovacuole targeting and autophagic factors, Atg8 is localized to the pre-autophagosomal structure under basal and nitrogen depletion conditions [65], a process dependent on the phagophore resident complex Atg5-Atg12Atg16 [66].”

“mediated by the cysteine protease Atg4, which is specific to Atg8 proteins [60,61].”

“Upregulation of Atg8s is observed under various stress conditions [27-30].”

“autophagy-linked FYVE protein (Alfy) [98-100], nuclear dot protein 52 kDa (NDP52) [101], and Optineurin [102] as autophagic receptors.”

“The motif in p62 responsible for binding Atg8, the LC3interacting region (LIR, also known as Atg8-interacting motif, AIM) [104,105], is common to other proteins that interact with Atg8 proteins, including Nbr1 [106], Atg3 [107], Nix [96] and the yeast cytoplasm-to-vacuole targeting receptor Atg19 [108].”

“Apparently, both the LC3 and the GABARAP/GATE-16 subfamilies are essential for autophagy, as they act at different stages of autophagosome formation: members of the LC3 subfamily are responsible for the elongation of the autophagic membrane, whereas GABARAP/GATE-16 subfamily members act downstream in a step coupled to…”

“Atg8 also participates in formation of the autophagosome and is essential for elongation of the autophagic membrane [68,69].”

“GABARAP, however, was identified as a cytosolic protein that is localized to trans port vesicles, the Golgi network and the endoplasmic reticulum (ER) and that interacts with the γ2 subunit of GABA(A) receptors [40].”

“The motif in p62 responsible for binding Atg8, the LC3interacting region (LIR, also known as Atg8-interacting motif, AIM) [104,105], is common to other proteins that interact with Atg8 proteins, including Nbr1 [106], Atg3 [107], Nix [96] and the yeast cytoplasm-to-vacuole targeting receptor Atg19 [108].”

“autophagy-linked FYVE protein (Alfy) [98-100], nuclear dot protein 52 kDa (NDP52) [101], and Optineurin [102] as autophagic receptors.”

“Furthermore, the overexpression approach is not optimal as LC3 proteins tend to form aggregates when transiently expressed [110].”

“These have led to the conclusion that PE-conjugated Atg8 proteins are active during autophagosome formation and are essential for the elongation and closure of the initial autophagic membrane, the phagophore [86-88].”

“autophagic factors The first link between Atg8 proteins and autophagy was established in Saccharomyces cerevisiae, where the single Atg8 protein was identified as an autophagy and cytoplasm-to-vacuole targeting essential factor [54-56].”

“These have led to the conclusion that PE-conjugated Atg8 proteins are active during autophagosome formation and are essential for the elongation and closure of the initial autophagic membrane, the phagophore [86-88].”

“Arrival of Atg8 proteins at the autophagic membrane depends on the hierarchical recruitment of numerous auto phagic factors, including phosphatidylinositol-3phosphate-binding proteins [18].”

“autophagy-linked FYVE protein (Alfy) [98-100], nuclear dot protein 52 kDa (NDP52) [101], and Optineurin [102] as autophagic receptors.”

“The motif in p62 responsible for binding Atg8, the LC3interacting region (LIR, also known as Atg8-interacting motif, AIM) [104,105], is common to other proteins that interact with Atg8 proteins, including Nbr1 [106], Atg3 [107], Nix [96] and the yeast cytoplasm-to-vacuole targeting receptor Atg19 [108].”

“Although the transcriptional regulation of Atg8 genes is largely unknown, several reports have shown that the transcription factors FoxO1, FoxO3 and E2F1 regulate Atg8s in this process in mammalian cells [31-34].”

“The cleaved Atg8 is than processed by a ubiquitin-like conjugation machinery composed of Atg7, an E1-like enzyme [62], and Atg3, a specific E2-like ligase [63].”

“Upregulation of Atg8s is observed under various stress conditions [27-30].”

“Cytoplasm-to-vacuole targeting is responsible for transporting vacuolar protein residents, such as aminopeptidase I (Ape1) and α-mannosidase (Ams1), to the vacuole [57,58].”

“This study [22] revealed that the first amino-terminal α helix of the Atg8 proteins was both essential and sufficient for this activity.”

“autophagy-linked FYVE protein (Alfy) [98-100], nuclear dot protein 52 kDa (NDP52) [101], and Optineurin [102] as autophagic receptors.”

“LC3 was first characterized as a protein that co-purified with microtubule-associated proteins 1A and 1B [38,39], but no direct involvement of this protein in membrane trafficking processes has been reported.”

“Atg8 also participates in formation of the autophagosome and is essential for elongation of the autophagic membrane [68,69].”

“Acetyla tion of the autophagic factors Atg5, Atg7, Atg8 and Atg12 is mediated by the acetyltransferase p300 and negatively regulates their activity [92].”

“Of the LC3 subfamily, LC3C, which is transcribed at lower levels than other members of this subfamily, is expressed predominantly in the lung [23,24].”

“brevicollis (Mbe) [6], the ichthyosporean Sphaeroforma arctica (Sar) and the amoeba Capsaspora owczarzaki (Cow) [111].”

“autophagic factors The first link between Atg8 proteins and autophagy was established in Saccharomyces cerevisiae, where the single Atg8 protein was identified as an autophagy and cytoplasm-to-vacuole targeting essential factor [54-56].”

“Atg4 might function in pathways other than autophagy, as cleavage of Atg4D by caspase increases its activity and consequently promotes GABARAP-L1 processing [82].”

“Although the transcriptional regulation of Atg8 genes is largely unknown, several reports have shown that the transcription factors FoxO1, FoxO3 and E2F1 regulate Atg8s in this process in mammalian cells [31-34].”

“autophagic factors The first link between Atg8 proteins and autophagy was established in Saccharomyces cerevisiae, where the single Atg8 protein was identified as an autophagy and cytoplasm-to-vacuole targeting essential factor [54-56].”

“The motif in p62 responsible for binding Atg8, the LC3interacting region (LIR, also known as Atg8-interacting motif, AIM) [104,105], is common to other proteins that interact with Atg8 proteins, including Nbr1 [106], Atg3 [107], Nix [96] and the yeast cytoplasm-to-vacuole targeting receptor Atg19 [108].”

“These homologs show different specificities toward Atg8 proteins: Atg4B shows a broad spectrum for all family members [78,79], whereas Atg4A is specific to the GABARAP and GATE-16 subfamilies [80,81].”

“These homologs show different specificities toward Atg8 proteins: Atg4B shows a broad spectrum for all family members [78,79], whereas Atg4A is specific to the GABARAP and GATE-16 subfamilies [80,81].”

“These homologs show different specificities toward Atg8 proteins: Atg4B shows a broad spectrum for all family members [78,79], whereas Atg4A is specific to the GABARAP and GATE-16 subfamilies [80,81].”

“In yeast, Atg8 expression is upregu lated during nitrogen starvation and is degraded in the vacuole following recruitment into autophagosomes [59].”

“Expression analysis of the different GABARAP proteins reveals a distinct pattern: GABARAP-L1 is expressed predominantly in the central nervous system, similar to GATE-16, which is strongly expressed in the brain, whereas the expression of GABARAP is more marked in the endocrine glands [25,26].”

“In addition to its interaction with the conjugation proteins, Atg8 also binds to other autophagic factors, such as Atg1, which might regulate its recruitment and activity on the autophagic membrane [60].”

“The role of GABARAP in intracellular transport is also supported by its interaction with NSF, a component essential for SNARE-mediated fusion [41,45].”

“A conformational change was also reported in an in vitro reconstitution assay of yeast Atg8, in which accessibility of the amino terminus to antibody increased on conjugation of Atg8 to phosphatidylethanolamine (PE)-containing liposomes [19].”

“Similar to LC3, GABARAP binds to tubulin through its amino-terminal region, an interaction that regulates clustering of GABA(A) receptors [8,46,47].”

“Similar to many other cytoplasm-tovacuole targeting and autophagic factors, Atg8 is localized to the pre-autophagosomal structure under basal and nitrogen depletion conditions [65], a process dependent on the phagophore resident complex Atg5-Atg12Atg16 [66].”

“This interaction is thought to be essential for trafficking of the GABA(A) receptor to the plasma membrane [41].”

“thaliana ATG8 genes showed distinct spatial and temporal expression patterns in different tissues [7].”

“Subsequent studies confirmed that these features are a unique characteristic of all Atg8 proteins [8-15] (Figure 2).”

“Thus, transgenic mice and tissue-culture cells expressing GFP-LC3 have been used to investigate autophagy [84,85].”

“These adaptors bind simultaneously to Atg8 proteins and to ubiquitinated proteins, organelles, and in some cases pathogens [18,94,103].”

“GATE-16, the first Atg8 to be crystallized, contains two amino-terminal α-helices in addition to its carboxy-terminal ubiquitin core [13].”

“This interaction results in the arrival of glycogen at the lysosome and is therefore suggested to regulate cellular glucose levels [109].”

“This interaction was suggested to control the forma tion of autophagosomes [72], indicating that Atg8 might provide a link between classical autophagic machinery and general trafficking factors that are crucial for autophagy.”

“In addition to their direct role in fusion events during autophagosome biogenesis, Atg8 proteins have an indirect role in which their binding to diabetes- and obesity-regulated protein (DOR) and to tumor protein 53-induced nuclear protein 1 (TP53INP2), two proteins that shuttle between the nucleus and the cytoplasm, r…”

“Of the LC3 subfamily, LC3C, which is transcribed at lower levels than other members of this subfamily, is expressed predominantly in the lung [23,24].”

“Although mammalian Atg8 proteins were originally implicated in intracellular trafficking processes, they are all found within autophagosomes [73-75].”

“Several approaches aimed at disrupting the functioning of Atg8 proteins by preventing their conjugation to PE have therefore been used, including the generation of Atg3-null mice and expression of a dominant-negative mutant of the promiscuous protease Atg4B.”

“Cytoplasm-to-vacuole targeting is responsible for transporting vacuolar protein residents, such as aminopeptidase I (Ape1) and α-mannosidase (Ams1), to the vacuole [57, 58 ].”

“Subsequent studies confirmed that these features are a unique characteristic of all Atg8 proteins [8-15] (Figure 2).”

“The cleaved Atg8 is than processed by a ubiquitin-like conjugation machinery composed of Atg7, an E1-like enzyme [62], and Atg3, a specific E2-like ligase [63].”

“GABARAP-L1 also binds directly to the G-protein-coupled κ-opioid receptor and mediates its transport in a manner dependent on modification of the carboxyl terminus [ 48 ,50,51].”

“In addition to their direct role in fusion events during autophagosome biogenesis, Atg8 proteins have an indirect role in which their binding to diabetes- and obesity-regulated protein (DOR) and to tumor protein 53-induced nuclear protein 1 (TP53INP2), two proteins that shuttle between the nucleus and the cytoplasm, r…”

“GATE-16 has been implicated in intra-Golgi transport through its interaction with Golgi SNARE protein 28 (GOS-28).”

“These homologs show different specificities toward Atg8 proteins: Atg4B shows a broad spectrum for all family members [78,79], whereas Atg4A is specific to the GABARAP and GATE-16 subfamilies [80,81].”

“Between these strands lie two α helices: α3 between β2 and β3, and α4 between β3 and β4 [16].”

“The molecular surface lying on the opposite side of the three-dimensional structure is poorly conserved and might mediate interactions specific to different Atg8 proteins [17], whereas the conserved domain is probably responsible for characteristic interactions of Atg8 proteins, such as binding to the conjugation mach…”

“This activity might involve the previously reported interaction of Atg8 with SNAREs in the yeast system [53].”

“Consistent with the involvement of mammalian Atg8s in membrane fusion events, the yeast Pichia pastoris Atg8 was recently found to mediate vacuolar fusion during adaptation from glucose- to methanol-containing medium [52].”

“GATE-16 has been implicated in intra-Golgi transport through its interaction with Golgi SNARE protein 28 (GOS-28).”

“Taken together, these findings suggest that the Atg8 amino-terminal region has a crucial role in the functions of these proteins [20-22].”

“GATE-16 GOS28 GABA(A) receptor Transferrin receptor κ Opioid receptor PXRICS ER Golgi G B GB G B 1 G B / G B 1 G B 1 Golgi PM G B NSF NSF G B / G B 1 GB/ GB1 β-catβ-cat N-cad herin (a) (b) mediated by the cysteine protease Atg4, which is specific to Atg8 proteins [60,61].”

“GABARAP’s involvement in vesicle transport is not limited to the GABA(A) receptor; other plasma membrane proteins, such as the transferrin receptor, interact with GABARAP, although the role of GABARAP in their transport is not well established [43].”

“Subsequent studies confirmed that these features are a unique characteristic of all Atg8 proteins [8-15] (Figure 2).”

“on processing of the GABARAP carboxyl terminus [42].”

“Expression analysis of the different GABARAP proteins reveals a distinct pattern: GABARAP-L1 is expressed predominantly in the central nervous system, similar to GATE-16, which is strongly expressed in the brain, whereas the expression of GABARAP is more marked in the endocrine glands [25,26].”

“binding to Atg19 receptor also disrupt autophagosome biogenesis [70,71].”

“It has been suggested that these factors mediate the transport of the transmembrane protein N-cadherin and its receptor β-catenin from the ER, thus controlling cell-cell adhesion [44].”

“Upregulation of Atg8s is observed under various stress conditions [27-30].”

“Subsequent studies confirmed that these features are a unique characteristic of all Atg8 proteins [8-15] (Figure 2).”

“GABARAP-L1 also binds directly to the G-protein-coupled κ-opioid receptor and mediates its transport in a manner dependent on modification of the carboxyl terminus [48,50,51].”

“Subsequent studies confirmed that these features are a unique characteristic of all Atg8 proteins [8-15] (Figure 2).”

“The role of Atg8 in intracellular trafficking processes Atg8s were originally implicated in membrane trafficking processes [35].”

“Subsequent studies confirmed that these features are a unique characteristic of all Atg8 proteins [8-15] (Figure 2).”

“binding to Atg19 receptor also disrupt autophagosome biogenesis [70,71].”

“and invariant proportions as previously described [112].”

“Upregulation of Atg8s is observed under various stress conditions [27-30].”

“For instance, the human genome codes for at least six distinct Atg8-like proteins, namely microtubule-associated protein 1 light chain 3 alpha (MAP1LC3A; best known as LC3A), LC3B, microtubule-associated protein 1 light chain 3 gamma (MAP1LC3C; best known as LC3C), GABA type A receptor-associated protein (GABARAP), GA…”

“Yeast has only one Atg8 homolog, Caenorhabditis elegans and Drosophila melanogaster have two, whereas Arabidopsis thaliana has nine ATG8 homologs (reviewed by Shpilka et al., 2011).”

“Similarly, LC3-II protein, another marker of failed autophagy (Shpilka et al., 2011), also accumulated in MMe macrophages (Figure 6F).”

“The human ATG8 family proteins are encoded by seven genes expressing LC3A (two alternatively Please cite this article as: T. Johansen and T. Lamark, Selectiv Receptors..., Journal of Molecular Biology, https://doi.org/10.1016/j. spliced isoforms with different N termini), LC3B, LC3B2 (only one amino acid differs from…”

“…are found: the three members of the microtubule-associated protein 1 light chain 3 (MAP1LC3) subfamily (LC3A, LC3B and LC3C, respectively) and the three members of the gamma-a-minobutyric receptor-associated protein (GABARAP) subfamily (GABARAP, GABARAP-L1 and GABAR-AP-L2/GATE-16) [77 – 80].”

“Mammalian ATG8 homologues are grouped into three subfamilies, that is, the LC3 subfamily (LC3A, B, and C), the GABARAP subfamily (GABARAP and GABARAPL1/GEC1), and GABARAPL2/GATE-16 [22].”

“The second of the ubiquitin-like reactions involves the conjugation of ubiquitin-like molecules of the Atg8 family, which comprises the three subfamilies LC3, GABARAP and GATE-16 [10], to the lipid phosphatidylethanolamine.”

“On the other hand, AMPK activation led to the phosphorylation of FOXO3a and ULK1, inducing MAP1LC3, GABARAP, and BECN1 expression and subsequent autophagy activation (Sanchez et al., 2012).”

“The mammalian ATG8 family has three LC3 (microtubule associated protein 1 light chain 3) subfamily members, LC3A-C, and three GABARAP (gamma amino butyrate-associated protein) subfamily members [5].”

“cerevisiae encodes only a single ATG8 gene, the genomes of plants, metazoans and certain protists harbor multiple, in some cases up to 25 ATG8 orthologs (Williams et al., 2009; Shpilka et al., 2011).”

“C, with two isoforms of LC3A, GABARAP and GABARAPL1–2 (11).”

“Humans have a single GATE-16 gene, two GABARAP genes [GABARAP and GABARAPL1 (γ-aminobutyric acid receptor-associated protein-like 1)] and four LC3 genes (LC3A, LC3B, LC3B2 and LC3C) [6].”

“These can be subdivided into two families: (1) the LC3 subfamily consisting of microtubuleassociated proteins 1A/1B light chain 3A (MAP1LC3A or briefly LC3A; two splice variants), LC3B, LC3B2, and LC3C, and (2) the GABARAP/GATE16 subfamily consisting of the c-aminobutyric acid receptor-associated protein (GABARAP), GA…”

“Structural data from homologs across the eukaryotes indicate that Atg8 family members adopt a β-grasp fold(19,20) resembling a ubiquitin-like structure, despite no direct sequence similarities to ubiquitins.(21) The yeast genome encodes a single member of the family, whereas family expansion is observed in higher euka…”

“…associated on the organellar surface interact directly, or indirectly via adaptor proteins, with Atg8 (LC3, GABARAP, and GATE-16 in mammalian cells), a highly conserved ubiquitin-like protein essential for all autophagyrelated pathways (Shpilka et al., 2011; Rogov et al., 2014; Wild et al., 2014).”

“…associated protein 1 light chain 3 beta), MAP1LC3B2, MAP1LC3C (microtubule associated protein 1 light chain 3 gamma), GABARAP (GABA type A receptor-associated protein), GABARAPL1 (GABA type A receptor associated protein like 1), and GABARAPL2 (GABA type A receptor associated protein like 2) [312].”

“brevicollis represents the single ATG8 gene within this taxa reflecting the ancestral configuration[31].”

“somal membrane protein and a marker of autophagosome formation [150].”

“2000), including a single member in yeast and several homologs, subdivided into three subfamilies—LC3, GABARAP, and GATE16, in mammals (Shpilka et al. 2011).”

“ATG9 is the only ATG member characterized so far, capable of shuttling between cytosolic compartments and transferring membrane cargo to the developing autophagosome.20 The mammalian Atg8 family consists of 3 subfamilies: LC3, GABARAP and GATE-16.”

“similar way to its function in canonical autophagy (Shpilka et al., 2011).”

“Autophagy is a cellular catabolic process allowing for the degradation of numerous cytoplasmic components in a controlled and specific manner through the action of protein receptors that interact with Atg8/LC3/GABARAP-family proteins (hereafter refers as ‘Atg8-family proteins’).(1)”

“Unlike Saccharomyces cerevisiae, however, there are six Atg8 homologues in mammals (mammalian Atg8s; mATG8s) that, presumably, have distinct or overlapping functions: MAP1LC3A (microtubule-associated protein light chain 3 alpha; LC3A), LC3B, LC3C, GABARAP (γ-aminobutyric acid receptor-associated protein), GABARAP-L1 a…”

“The mammalian Atg8 is a UBL protein family consisting of eight family members grouped into the LC3 and GABARAP subfamilies [120].”

“Genetic characterization of ATG8 genes suggested that they are functionally redundant [52].”

“ATG8s promote phagophore expansion and closure of the autophagosome, and are crucial for its fusion with the lysosome (Weidberg et al., 2010; Mizushima et al., 2011; Shpilka et al., 2011; Nguyen et al., 2016; Tsuboyama et al., 2016).”

“family members may be responsible for specific roles in protein trafficking and selective target engulfment, and they may be upregulated in response to different cues.(72) It has been suggested that GABARAPL1 interacts with starch-binding domain 1 and therefore may play a role in autophagic degradation of glycogen gra…”

“The receptors bind both to ATG8 and to ubiquitinated proteins, organelles or even pathogens which are targeted for degradation, leading to their incorporation into autophagosomes [9].”

“Characteristic positions specific of the GABARAP or LC3 families (Shpilka et al., 2011) are conserved in LGG-1 and LGG-2 (Figure S1 available online) that suggests that LGG-1 and LGG-2 arise from an ancestral duplication and are the C.”

“It has to be noted that mammals possess at least 7 genes coding for LC3/Atg8 proteins that can be grouped into three subfamilies: (1) the LC3 subfamily containing LC3A, LC3B, LC3B2 and LC3C; (2) the gammaaminobutyrate receptor-associated protein (GABARAP) subfamily comprising GABARAP and GABARAPL1 (also called GEC1);…”

“For the purpose of this minireview, it is important to know that autophagy requires two ubiquitin-like conjugation reactions: conjugation of Atg5 to Atg12, and conjugation of Atg8 (referred to as LC3 in mammals, though it is noteworthy that other Atg8 homologues are present in mammals [2]) to the lipid phosphatidyleth…”

“The most widely used such protein is Atg8 (homologous to MAPLC3, GABARAP and GATE16 proteins in mammals), an ubiquitin-like protein that becomes conjugated to lipids of the inner and outer membranes of the autophagosome as it forms [15].”

“Today, the mammalian LC3/ GABARAP family counts six members: LC3A (encoded by the MAP1LC3A gene), LC3B (in human cells encoded by two genes MAP1LC3B and MAP1LC3B2), LC3C (encoded by MAP1LC3C), GABARAP, GABARAPL1, and GABARAPL2/GATE16 [43].”

“We examined GABARAP, which localizes to the Golgi complex (Shpilka et al., 2011), and saw that GM130 in fed cells was distributed around an enlarged GABARAP structure, as well as occasionally colocalized with starvation-induced GABARAP puncta (Figure 4G).”

“2020 conjugate phosphatidylethanolamine (PE) to the GABARAP/light chain 3 (LC3) family of proteins, the most well characterized being LC3B (Shpilka et al., 2011; Dikic and Elazar, 2018).”

“Six human ATG8 proteins form three phylogenetic groups: one containing LC3A, -B, and -C, a second harboring -aminobutyric acid receptor-associated protein (GABARAP) and GABARAP-like 1 (GABARAPL1), with GABARAPL2/GATE16 alone in the third group (2).”

“The latter one serves to lipidate ATG8 family members, including microtubule-associated protein 1 light chain 3 (MAP1LC3 or LC3, hereafter referred to as LC3) [12, 13].”

“γ-aminobutyric-acid type A receptor-associated proteins (GABARAPs) and Golgi-associated ATPase enhancer of 16 kDa (GATE-16) subfamilies based on their amino acid sequence homology [15].”

“In mammals, the Atg8 homologs constitute 2 subfamilies based on amino-acidsequence homology: MAP1LC3/LC3 (microtubule associated protein 1 light chain 3) family with LC3A (2 N-terminal splice variants), LC3B, LC3B2 and LC3C and the GABARAP (γaminobutyric acid receptor-associated protein) family with GABARAP, GABARAPL1…”

“Mammalian homologues of ATG8 are divided into two clades: microtubule- 5 associated protein 1 light chain 3 (LC3) A/B/C and γ-aminobutyric acid receptor-associated protein (GABARAP), GABARAPL1/L2 (Shpilka et al., 2011), LC3B being the most extensively studied member.”

“Mammals express 2 subfamilies of ATG8 proteins defined by amino acid sequence similarity: the LC3 subfamily consisting of LC3A, LC3B, LC3B2, and LC3C (referred to as LC3 proteins or simply LC3s); the GABARAP subfamily consisting of GABARAP, GABARAPL1, and GABARAPL2 (referred to as GABARAP proteins or GABARAPs) [13].”

“After autophagosomal fusion with the lysosome, LC3-II inside the autolysosome is degraded, whereas LC3-II at the cytoplasmic face is recycled in an Atg4-dependent delipidation process (reviewed by Geng and Klionsky, 2008; Shpilka et al., 2011).”

“Whereas there was little or no interaction between ALFY and LC3A or LC3B, ALFY was found to co-IP with GABARAP, GABARAPL1 and GABARAPL2, but also weakly with LC3C (Fig 1A).”

“By directing carbon flux into TAG synthesis, the E1a subunit of pPDHC plays a role in stress responses in microalgae (Li et al., 2014; Shtaida et al., 2014; Avidan et al., 2015).”

“Despite the fact that LC3C and GABARAPL2 are branched into separate clades on the phylogenetic tree [64,65], human Atg8-family proteins can be broadly categorized into two groups: LC3s and GABARAPs.”

“During autophagy, Atg8 binds to phosphatidylethanolamine on the phagophore membrane and remains there through the maturation process of the autophagosome.(13) This membrane binding is facilitated by the carboxyl-terminal glycine residue in Atg8.”

“82 Both subfamilies are involved in macroautophagy, but the members of the GABARAP subfamily play additional roles in diverse membrane traf fi cking processes, such as transport from the Golgi to the plasma membrane, endoplasmic reticulum to Golgi transport and intra-Golgi transport.”

“play an important role in autophagosome formation and macroautopahgy regulation [24–26].”

“Key to this machinery is the Atg8 family of ubiquitin-like proteins, which associate with the growing phagophore through conjugation to the lipid phosphatidylethanolamine (PE) [7].”

“The GABARAP subgroup is evolutionary conserved, while the LC3 subgroup is metazoan specific [6,8].”

“During the process of autophagy, the expression of LC3-II is proportional to the number of autophagic vacuoles, and LC3II is regarded as a marker of autophagosome formation (Shpilka et al. 2011).”

“ATG8 proteins are members of the family of small ubiquitin-like modifier (UBL) proteins and contain in addition to the common ubiquitin-like fold two extra N-terminal α-helices [13,14].”

“Future studies may examine which of the numerous ATG8 orthologs or LC3-family proteins in mammalian cells may participate in this mechanism (Shpilka et al., 2011).”

“corroborates the notion that the increase in genome complexity of higher metazoans includes extended subfamilies of ATG8 as compared to protists and invertebrates.(88) The A.”

“, LC3A, LC3B, GABARAP, GABARAPL1, and GABARAPL2 in the murine system) are conjugated primarily to phosphatidylethanolamine in lipid bilayer membranes, through the sequential action of the E1-like activating enzyme ATG7, E2-like conjugating enzyme ATG3, and E3-like ligase ATG12– ATG5-ATG16L1 complex in vivo.(2) It is t…”

“tion of further specialized functions in more complex animals.(70) Similarly, the Atg4 paralogs and the Atg16 paralog in the 2 Ubl conjugation systems may enable the fine-tuning of the activation of the different Atg8/LC3 family members.”

“The second ubiquitin-like reaction involves the conjugation of mammalian LC3-II, GABARAP and GATE-16, homologs of yeast Atg8 [54], to phosphatidylethanolamine (PE) by Atg7 and Atg3 (another E2-like), resulting in autophagosome-associated LC3-II.”

“…complex (Fracchiolla et al., 2020; Lystad et al., 2019), which acts similarly to ubiquitin ligase complexes but instead conjugates ATG8 family (e.g., LC3 and GABARAP) proteins to phosphatidyleth-anolamine at the phagophore membrane (Hanada et al., 2007; Kirisako et al., 1999; Shpilka et al., 2011).”

“Autophagy-related protein 8 (Atg8/LC3), an ubiquitin-like protein, has different homologues encoded by different chromosomes in animals, including MAP1LC3A, B and C, as well as the GABARAP proteins, which are the most important constituents of the autophagosomal membranes (Shpilka et al, 2011).”

“To further examine the possible involvement of autophagy, we inhibited ATG5, a key regulator of all known human ATG8 homologous [reviewed in 31].”