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Atg8: an autophagy-related ubiquitin-like protein family.
Open accessAbstract
Autophagy-related (Atg) proteins are eukaryotic factors participating in various stages of the autophagic process. Thus far 34 Atgs have been identified in yeast, including the key autophagic protein Atg8. The Atg8 gene family encodes ubiquitin-like proteins that share a similar structure consisting of two amino-terminal α helices and a ubiquitin-like core. Atg8 family members are expressed in various tissues, where they participate in multiple cellular processes, such as intracellular membrane trafficking and autophagy. Their role in autophagy has been intensively studied. Atg8 proteins undergo a unique ubiquitin-like conjugation to phosphatidylethanolamine on the autophagic membrane, a process essential for autophagosome formation. Whereas yeast has a single Atg8 gene, many other eukaryotes contain multiple Atg8 orthologs. Atg8 genes of multicellular animals can be divided, by sequence similarities, into three subfamilies: microtubule-associated protein 1 light chain 3 (MAP1LC3 or LC3), γ-aminobutyric acid receptor-associated protein (GABARAP) and Golgi-associated ATPase enhancer of 16 kDa (GATE-16), which are present in sponges, cnidarians (such as sea anemones, corals and hydras) and bilateral animals. Although genes from all three subfamilies are found in vertebrates, some invertebrate lineages have lost the genes from one or two subfamilies. The amino terminus of Atg8 proteins varies between the subfamilies and has a regulatory role in their various functions. Here we discuss the evolution of Atg8 proteins and summarize the current view of their function in intracellular trafficking and autophagy from a structural perspective.
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“Yet in other settings, autophagy induction triggers a significant decrease in LC3-I levels, along with an increase in LC3-II levels, presumably due to its increased conversion into LC3-II [280].”
From Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) 1 (2021) · cites this paper as [280]
Experimental — accuracy not yet measuredIn the citing paper
“some studies suggest isoform specificity in selective autophagy (Shpilka et al., 2011; Maruyama et al., 2014; Koukourakis et al., 2015).”
From Microtubule-associated protein 1 light chain 3B, (LC3B) is necessary to maintain lipid-mediated homeostasis in the retinal pigment epithelium (2018) · cites this paper as Shpilka et al., 2011
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Citations
Cites
The Pfam Protein Families Database
Bateman, A. G. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,075
LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing.
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“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].”
BackgroundSequence logos: a new way to display consensus sequences
Schneider, T. D., & Stephens, R. M. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.20.6097 · Cited by 3,354 · cited 1×
“[113] show the conservation (overall height) and residue prevalence of multiple alignment positions.”
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“These adaptors bind simultaneously to Atg8 proteins and to ubiquitinated proteins, organelles, and in some cases pathogens [18,94,103].”
BackgroundCDD: a Conserved Domain Database for the functional annotation of proteins
Marchler‐Bauer, A., Lu, S., Anderson, J. B., Chitsaz, F., Derbyshire, M. K., DeWeese-Scott, C., Fong, J. H., Geer, L. Y., Geer, R. C., Gonzales, N. R., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1189 · Cited by 3,126 · cited 2×
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“Sequences for the alignments were taken from the CDD [114] and PFAM [115] database entries cd01611 and PF02991, respectively, and sequences”
MethodA ubiquitin-like system mediates protein lipidation
Ichimura, Y., Kirisako, T., Takao, T., Satomi, Y., Shimonishi, Y., Ishihara, N., Mizushima, N., Tanida, I., Kominami, E., Ohsumi, M., et al. (2000) · Nature · doi:10.1038/35044114 · Cited by 2,139 · cited 2×
“Unlike ubiquitin, which is conjugated to a protein, Atg8 is covalently conjugated to PE lipid through its carboxy-terminal exposed glycine [64].”
BackgroundMizushima, N., Yamamoto, A., Matsui, M., Yoshimori, T., & Ohsumi, Y. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e03-09-0704 · Cited by 2,105 · cited 1×
“Thus, transgenic mice and tissue-culture cells expressing GFP-LC3 have been used to investigate autophagy [84,85].”
BackgroundReactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4
Scherz‐Shouval, R., Shvets, E., Fass, E., Shorer, H., Gil, L., & Elazar, Z. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601623 · Cited by 2,101 · cited 1×
“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].”
BackgroundSelf-citation
Cited by
Sorted by citations
Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).
Klionsky, D. J., Abdelmohsen, K., Abe, A., Abedin, M. J., Abeliovich, H., Acevedo Arozena, A., Adachi, H., Adams, C. M., Adams, P. D., Adeli, K., et al. (2016) · Autophagy · doi:10.1080/15548627.2015.1100356 · Cited by 5,894
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Klionsky, D. J., Abdalla, F. C., Abeliovich, H., Abraham, R. T., Acevedo-Arozena, A., Adeli, K., Agholme, L., Agnello, M., Agostinis, P., Aguirre-Ghiso, J. A., et al. (2012) · Autophagy · doi:10.4161/auto.19496 · Cited by 3,996
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“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…”
The LIR motif – crucial for selective autophagy
Birgisdottir, Å. B., Lamark, T., & Johansen, T. (2013) · Journal of Cell Science · doi:10.1242/jcs.126128 · Cited by 914
“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).”
BackgroundKratz, M., Coats, B. R., Hisert, K. B., Hagman, D. K., Mutskov, V. J., Peris, E., Schoenfelt, K. Q., Kuzma, J. N., Larson, I. A., Billing, P. S., et al. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.08.010 · Cited by 866
“Similarly, LC3-II protein, another marker of failed autophagy (Shpilka et al., 2011), also accumulated in MMe macrophages (Figure 6F).”
BackgroundRegulation of selective autophagy: the p62/SQSTM1 paradigm
Lamark, T., Svenning, S., & Johansen, T. (2017) · Essays in Biochemistry · doi:10.1042/ebc20170035 · Cited by 753
Selective Autophagy: ATG8 Family Proteins, LIR Motifs and Cargo Receptors
Johansen, T., & Lamark, T. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.07.016 · Cited by 736
“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…”
BackgroundInfluentialMechanisms of Selective Autophagy
Zaffagnini, G., & Martens, S. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.02.004 · Cited by 636
“…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].”
Aggrephagy: Selective Disposal of Protein Aggregates by Macroautophagy
Lamark, T., & Johansen, T. (2012) · International Journal of Cell Biology · doi:10.1155/2012/736905 · Cited by 514
“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].”
BackgroundMechanisms of Autophagosome Biogenesis
Rubinsztein, D. C., Shpilka, T., & Elazar, Z. (2012) · Current Biology · doi:10.1016/j.cub.2011.11.034 · Cited by 517
“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.”
The ATG conjugation systems in autophagy
Mizushima, N. (2019) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2019.12.001 · Cited by 483
Mechanisms of Selective Autophagy
Lamark, T., & Johansen, T. (2021) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120219-035530 · Cited by 429
Crosstalk Between Mammalian Autophagy and the Ubiquitin-Proteasome System
Kocatürk, N. M., & Gözüaçık, D. (2018) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2018.00128 · Cited by 442
“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).”
BackgroundInfluentialFKBP8 recruits LC3A to mediate Parkin‐independent mitophagy
Bhujabal, Z., Birgisdottir, Å. B., Sjøttem, E., Brenne, H. B., Øvervatn, A., Habisov, S., Kirkin, V., Lamark, T., & Johansen, T. (2017) · EMBO Reports · doi:10.15252/embr.201643147 · Cited by 430
“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].”
Autophagy as a molecular target for cancer treatment
Kocatürk, N. M., Akkoç, Y., Kığ, C., Bayraktar, O., Gözüaçık, D., & Kutlu, Ö. (2019) · European Journal of Pharmaceutical Sciences · doi:10.1016/j.ejps.2019.04.011 · Cited by 394
von Muhlinen, N., Akutsu, M., Ravenhill, B. J., Foeglein, Á., Bloor, S., Rutherford, T. J., Freund, S. M. V., Komander, D., & Randow, F. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.08.024 · Cited by 332
“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).”
Targeted protein degradation: advances in drug discovery and clinical practice
Zhong, G., Chang, X., Xie, W., & Zhou, X. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-02004-x · Cited by 326
ATG8 Family Proteins Act as Scaffolds for Assembly of the ULK Complex
Alemu, E. A., Lamark, T., Torgersen, K. M., Birgisdottir, Å. B., Larsen, K. B., Jain, A., Olsvik, H. L., Øvervatn, A., Kirkin, V., & Johansen, T. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.378109 · Cited by 303
“C, with two isoforms of LC3A, GABARAP and GABARAPL1–2 (11).”
BackgroundStarvation induces rapid degradation of selective autophagy receptors by endosomal microautophagy
Mejlvang, J., Olsvik, H. L., Svenning, S., Bruun, J., Abudu, Y. P., Larsen, K. B., Brech, A., Hansen, T. E., Brenne, H. B., Hansen, T., et al. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201711002 · Cited by 292
Nath, S., Dancourt, J., Shteyn, V., Puente, G., Fong, W. M., Nag, S., Bewersdorf, J., Yamamoto, A., Antonny, B., & Melia, T. J. (2014) · Nature Cell Biology · doi:10.1038/ncb2940 · Cited by 279
The Atg8 family: multifunctional ubiquitin-like key regulators of autophagy
Rawet-Slobodkin, M., & Elazar, Z. (2013) · Essays in Biochemistry · doi:10.1042/bse0550051 · Cited by 259
“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].”
BackgroundInfluentialDetection and Clearance of Damaged Lysosomes by the Endo-Lysosomal Damage Response and Lysophagy
Papadopoulos, C., & Meyer, H. (2017) · Current Biology · doi:10.1016/j.cub.2017.11.012 · Cited by 230
Wang, C., Zhang, X., Teng, Z., Zhang, T., & Li, Y. (2014) · European Journal of Pharmacology · doi:10.1016/j.ejphar.2014.06.051 · Cited by 233
Autophagy signal transduction by ATG proteins: from hierarchies to networks
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“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…”
BackgroundBhatia, V., & Sharma, S. (2020) · Journal of the Neurological Sciences · doi:10.1016/j.jns.2020.117253 · Cited by 228
Kalvari, I., Tsompanis, S., Mulakkal, N. C., Osgood, R., Johansen, T., Nezis, I. P., & Promponas, V. J. (2014) · Autophagy · doi:10.4161/auto.28260 · Cited by 218
“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…”
Organellophagy: Eliminating cellular building blocks via selective autophagy
Okamoto, K. (2014) · The Journal of Cell Biology · doi:10.1083/jcb.201402054 · Cited by 225
“…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).”
Chen, X., Tsvetkov, A. S., Shen, H., Isidoro, C., Ktistakis, N. T., Linkermann, A., Koopman, W. J. H., Simon, H., Galluzzi, L., Luo, S., et al. (2024) · Autophagy · doi:10.1080/15548627.2024.2319901 · Cited by 240
“…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].”
BackgroundTumbarello, D. A., Manna, P. T., Allen, M. D., Bycroft, M., Arden, S. D., Kendrick‐Jones, J., & Buß, F. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1005174 · Cited by 212
“brevicollis represents the single ATG8 gene within this taxa reflecting the ancestral configuration[31].”
BackgroundLiu, Z., Li, T., Li, P., Wei, N., Zhao, Z., Liang, H., Ji, X., Chen, W., Xue, M., & Wei, J. (2015) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2015/352723 · Cited by 221
“somal membrane protein and a marker of autophagosome formation [150].”
BackgroundActivation and targeting of ATG8 protein lipidation
Martens, S., & Fracchiolla, D. (2020) · Cell Discovery · doi:10.1038/s41421-020-0155-1 · Cited by 218
Endocytosis and Autophagy: Exploitation or Cooperation?
Tooze, S. A., Abada, A., & Elazar, Z. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a018358 · Cited by 202
“2000), including a single member in yeast and several homologs, subdivided into three subfamilies—LC3, GABARAP, and GATE16, in mammals (Shpilka et al. 2011).”
BackgroundSelf-citationCaspase involvement in autophagy
Tsapras, P., & Nezis, I. P. (2017) · Cell Death and Differentiation · doi:10.1038/cdd.2017.43 · Cited by 197
“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.”
BackgroundInfluentialChoi, J., Park, S., Biering, S. B., Selleck, E. M., Liu, C. Y., Zhang, X., Fujita, N., Saitoh, T., Akira, S., Yoshimori, T., et al. (2014) · Immunity · doi:10.1016/j.immuni.2014.05.006 · Cited by 186
“similar way to its function in canonical autophagy (Shpilka et al., 2011).”
InfluentialiLIR database: A web resource for LIR motif-containing proteins in eukaryotes
Jacomin, A., Samavedam, S., Promponas, V. J., & Nezis, I. P. (2016) · Autophagy · doi:10.1080/15548627.2016.1207016 · Cited by 186
“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)”
BackgroundStructural and functional analysis of the GABARAP interaction motif (GIM)
Rogov, V. V., Stolz, A., Ravichandran, A., Law, A., SUZUKI, H., Kniss, A., Rios-Szwed, D. O., Löhr, F., Wakatsuki, S., Dötsch, V., et al. (2017) · EMBO Reports · doi:10.15252/embr.201643587 · Cited by 177
“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…”
BackgroundGetting ready for building: signaling and autophagosome biogenesis
Abada, A., & Elazar, Z. (2014) · EMBO Reports · doi:10.15252/embr.201439076 · Cited by 178
“The mammalian Atg8 is a UBL protein family consisting of eight family members grouped into the LC3 and GABARAP subfamilies [120].”
ATG8 Expansion: A Driver of Selective Autophagy Diversification?
Kellner, R., la Concepción, J. C. D., Maqbool, A., Kamoun, S., & Dagdas, Y. (2016) · Trends in Plant Science · doi:10.1016/j.tplants.2016.11.015 · Cited by 163
“Genetic characterization of ATG8 genes suggested that they are functionally redundant [52].”
BackgroundAutophagy and endocytosis – interconnections and interdependencies
Birgisdottir, Å. B., & Johansen, T. (2020) · Journal of Cell Science · doi:10.1242/jcs.228114 · Cited by 175
“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).”
BackgroundUntangling Autophagy Measurements
Gottlieb, R. A., Andres, A. M., Sin, J., & TAYLOR, D. J. (2015) · Circulation Research · doi:10.1161/circresaha.116.303787 · Cited by 175
“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…”
Mutation in TECPR2 Reveals a Role for Autophagy in Hereditary Spastic Paraparesis
Oz-Levi, D., Ben‐Zeev, B., Ruzzo, E. K., Hitomi, Y., Gelman, A., Pelak, K., Anikster, Y., Reznik‐Wolf, H., Bar-Joseph, I., Olender, T., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.09.015 · Cited by 170
Tumbarello, D. A., Manna, P. T., Allen, M. D., Bycroft, M., Arden, S. D., Kendrick‐Jones, J., & Buß, F. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005433 · Cited by 161
Sadoul, B. C., & Vijayan, M. M. (2016) · Fish physiology · doi:10.1016/b978-0-12-802728-8.00005-9 · Cited by 175
Schläfli, A. M., Berezowska, S., Adams, O. J., Langer, R., & Tschan, M. P. (2015) · European Journal of Histochemistry · doi:10.4081/ejh.2015.2481 · Cited by 161
Identification of transcription factors that regulate ATG8 expression and autophagy in Arabidopsis
Wang, P., Nolan, T. M., Yin, Y., & Bassham, D. C. (2019) · Autophagy · doi:10.1080/15548627.2019.1598753 · Cited by 152
“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].”
BackgroundManil-Ségalen, M., Lefebvre, C., Jenzer, C., Trichet, M., Boulogne, C., Satiat-Jeunemaitre, B., & Legouis, R. (2014) · Developmental Cell · doi:10.1016/j.devcel.2013.11.022 · Cited by 144
“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.”
BackgroundInfluentialAutophagy: More Than a Nonselective Pathway
Reggiori, F., Komatsu, M., Finley, K. D., & Simonsen, A. (2012) · International Journal of Cell Biology · doi:10.1155/2012/219625 · Cited by 161
“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);…”
BackgroundInteractions of Pathogenic Bacteria with Autophagy Systems
Cemma, M., & Brumell, J. H. (2012) · Current Biology · doi:10.1016/j.cub.2012.06.001 · Cited by 152
“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…”
BackgroundAssays to monitor autophagy in Drosophila
Mauvezin, C., Ayala, C. I., Braden, C. R., Kim, J., & Neufeld, T. P. (2014) · Methods · doi:10.1016/j.ymeth.2014.03.014 · Cited by 147
“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].”
BackgroundATG16L1: A multifunctional susceptibility factor in Crohn disease
Salem, M. A., Ammitzboell, M., Nys, K., Seidelin, J. B., & Nielsen, O. H. (2015) · Autophagy · doi:10.1080/15548627.2015.1017187 · Cited by 166
History of the Selective Autophagy Research: How Did It Begin and Where Does It Stand Today?
Kirkin, V. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.05.010 · Cited by 143
“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].”
BackgroundJoachim, J., Jefferies, H. B. J., Razi, M., Frith, D., Snijders, A. P., Chakravarty, P., Judith, D., & Tooze, S. A. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.11.018 · Cited by 153
“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).”
Autophagy and cancer: Modulation of cell death pathways and cancer cell adaptations
Towers, C. G., Wodetzki, D., & Thorburn, A. M. (2019) · The Journal of Cell Biology · doi:10.1083/jcb.201909033 · Cited by 142
“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).”
BackgroundAutophagy and Cancer Metabolism
Goldsmith, J., Levine, B., & Debnath, J. (2014) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-416618-9.00002-9 · Cited by 139
Olsvik, H. L., Lamark, T., Takagi, K., Larsen, K. B., Evjen, G., Øvervatn, A., Mizushima, T., & Johansen, T. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.686915 · Cited by 134
“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).”
BackgroundThe role of ALFY in selective autophagy
Isakson, P., Holland, P., & Simonsen, A. (2012) · Cell Death and Differentiation · doi:10.1038/cdd.2012.66 · Cited by 129
Selective autophagy of the adaptor TRIF regulates innate inflammatory signaling
Samie, M., Lim, J., Verschueren, E., Baughman, J. M., Peng, I., Wong, A., Kwon, Y. C., Şenbabaoğlu, Y., Hackney, J. A., Keir, M. E., et al. (2018) · Nature Immunology · doi:10.1038/s41590-017-0042-6 · Cited by 133
Schläfli, A. M., Adams, O., Galván, J. A., Gugger, M., Savic, S., Bubendorf, L., Schmid, R. A., Becker, K.-F., Tschan, M. P., Langer, R., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.9647 · Cited by 123
“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].”
BackgroundTargeting PI3K-AKT/mTOR signaling in the prevention of autism
Sharma, A., & Mehan, S. (2021) · Neurochemistry International · doi:10.1016/j.neuint.2021.105067 · Cited by 134
Is targeting autophagy mechanism in cancer a good approach? The possible double-edge sword effect
Lim, S. M., Hanif, E. A. M., & Chin, S. (2021) · Cell & Bioscience · doi:10.1186/s13578-021-00570-z · Cited by 138
“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].”
BackgroundBirgisdottir, Å. B., Mouilleron, S., Bhujabal, Z., Wirth, M., Sjøttem, E., Evjen, G., Zhang, W., Lee, R., O’Reilly, N., Tooze, S. A., et al. (2019) · Autophagy · doi:10.1080/15548627.2019.1581009 · Cited by 123
“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…”
BackgroundAutophagy and Mammalian Viruses
Paul, P., & Münz, C. (2016) · Advances in virus research · doi:10.1016/bs.aivir.2016.02.002 · Cited by 119
“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.”
BackgroundGABARAPs and LC3s have opposite roles in regulating ULK1 for autophagy induction
Grunwald, D., Otto, N., Park, J.-M., Song, D., & Kim, D. (2019) · Autophagy · doi:10.1080/15548627.2019.1632620 · Cited by 116
“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].”
BackgroundMultiple Functions of ATG8 Family Proteins in Plant Autophagy
Bu, F., Yang, M., Guo, X., Huang, W., & Chen, L. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00466 · Cited by 115
Boyer‐Guittaut, M., Poillet-Perez, L., Liang, Q., Bôle‐Richard, E., Ouyang, X., Benavides, G. A., Chakrama, F. Z., Fraîchard, A., Darley-Usmar, V. M., Despouy, G., et al. (2014) · Autophagy · doi:10.4161/auto.28390 · Cited by 121
The role of membrane-trafficking small GTPases in the regulation of autophagy
Bento, C. F., Puri, C., Moreau, K., & Rubinsztein, D. C. (2013) · Journal of Cell Science · doi:10.1242/jcs.123075 · Cited by 118
“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).”
BackgroundMembrane Trafficking in Autophagy
Søreng, K., Neufeld, T. P., & Simonsen, A. (2017) · International review of cytology · doi:10.1016/bs.ircmb.2017.07.001 · Cited by 116
The IAP family member BRUCE regulates autophagosome–lysosome fusion
Ebner, P., Poetsch, I., Deszcz, L., Hoffmann, T., Zuber, J. A., & Ikeda, F. (2018) · Nature Communications · doi:10.1038/s41467-018-02823-x · Cited by 104
Lystad, A. H., Ichimura, Y., Takagi, K., Yang, Y., Pankiv, S., Kanegae, Y., Kageyama, S., Suzuki, M., Saito, I., Mizushima, T., et al. (2014) · EMBO Reports · doi:10.1002/embr.201338003 · Cited by 107
“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).”
InfluentialRasmussen, M. S., Mouilleron, S., Shrestha, B. K., Wirth, M., Lee, R., Larsen, K. B., Abudu, Y. P., O’Reilly, N., Sjøttem, E., Tooze, S. A., et al. (2017) · Autophagy · doi:10.1080/15548627.2017.1287651 · Cited by 102
Inhibition of Autophagy by a Small Molecule through Covalent Modification of the LC3 Protein
Fan, S., Yue, L., Wan, W., Zhang, Y., Zhang, B., Otomo, C., Li, Q., Lin, T., Hu, J., Xu, P., et al. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.202109464 · Cited by 101
Zienkiewicz, A., Zienkiewicz, K., Poliner, E., Pulman, J. A., Du, Z., Stefano, G., Tsai, C., Horn, P. J., Feußner, I., Farré, E. M., et al. (2019) · PLANT PHYSIOLOGY · doi:10.1104/pp.19.00854 · Cited by 104
“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).”
BackgroundAtg8-Family Proteins—Structural Features and Molecular Interactions in Autophagy and Beyond
Wesch, N., Kirkin, V., & Rogov, V. V. (2020) · Cells · doi:10.3390/cells9092008 · Cited by 95
“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.”
BackgroundLinkage of autophagy to fungal development, lipid storage and virulence inMetarhizium robertsii
Duan, Z., Chen, Y., Huang, W., Shang, Y., Chen, P., & Wang, C. (2013) · Autophagy · doi:10.4161/auto.23575 · Cited by 101
“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.”
BackgroundExploring autophagy with Gene Ontology
Denny, P., Feuermann, M., Hill, D. P., Lovering, R. C., Plun‐Favreau, H., & Roncaglia, P. (2018) · Autophagy · doi:10.1080/15548627.2017.1415189 · Cited by 95
“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.”
BackgroundWu, H., Chen, S., Al-Baadani, A., Xu, J., Wu, Q., Pan, K., Zhang, J., & Hong, Y. (2014) · Molecular Neurobiology · doi:10.1007/s12035-014-8933-0 · Cited by 103
“play an important role in autophagosome formation and macroautopahgy regulation [24–26].”
BackgroundeIF5A is required for autophagy by mediating ATG3 translation
Lubas, M., Harder, L. M., Kumsta, C., Tiessen, I., Hansen, M., Andersen, J., Lund, A. H., & Frankel, L. B. (2018) · EMBO Reports · doi:10.15252/embr.201846072 · Cited by 100
“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].”
Atg8 family proteins, LIR/AIM motifs and other interaction modes
Rogov, V. V., Nezis, I. P., Tsapras, P., Zhang, H., Dagdas, Y., Noda, N. N., Nakatogawa, H., Wirth, M., Mouilleron, S., McEwan, D. G., et al. (2023) · Autophagy Reports · doi:10.1080/27694127.2023.2188523 · Cited by 101
“The GABARAP subgroup is evolutionary conserved, while the LC3 subgroup is metazoan specific [6,8].”
Coordination of Autophagosome–Lysosome Fusion by Atg8 Family Members
Kriegenburg, F., Ungermann, C., & Reggiori, F. (2018) · Current Biology · doi:10.1016/j.cub.2018.02.034 · Cited by 95
Wei, Y., Cao, X., Tang, X., Shen, L., Lin, T., He, D., Wu, S., & Wei, G. (2017) · Toxicology Mechanisms and Methods · doi:10.1080/15376516.2017.1410743 · Cited by 93
“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).”
BackgroundMechanisms and Pathophysiological Roles of the ATG8 Conjugation Machinery
Lystad, A. H., & Simonsen, A. (2019) · Cells · doi:10.3390/cells8090973 · Cited by 89
“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].”
BackgroundSelective Lysosome Membrane Turnover Is Induced by Nutrient Starvation
Lee, C., Lamech, L. T., Johns, E., & Overholtzer, M. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.08.008 · Cited by 91
“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).”
BackgroundAbreu, S., Kriegenburg, F., Gómez‐Sánchez, R., Mari, M. C., Sánchez, J., Rasmussen, M. S., Guimarães, R. S., Zens, B., Schuschnig, M., Hardenberg, R., et al. (2017) · EMBO Reports · doi:10.15252/embr.201643146 · Cited by 88
Elucidating the composition and conservation of the autophagy pathway in photosynthetic eukaryotes
Shemi, A., Ben‐Dor, S., & Vardi, A. (2015) · Autophagy · doi:10.1080/15548627.2015.1034407 · Cited by 84
“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.”
BackgroundInfluentialSAMM50 acts with p62 in piecemeal basal- and OXPHOS-induced mitophagy of SAM and MICOS components
Abudu, Y. P., Shrestha, B. K., Zhang, W., Palara, A., Brenne, H. B., Larsen, K. B., Wolfson, D. L., Dumitriu, G., Øie, C. I., Ahluwalia, B. S., et al. (2021) · The Journal of Cell Biology · doi:10.1083/jcb.202009092 · Cited by 79
The E3 ubiquitin ligase NEDD4 is an LC3-interactive protein and regulates autophagy
Sun, A., Wei, J., Childress, C., Shaw, J. H., Peng, K., Shao, G., Yang, W., & Lin, Q. (2017) · Autophagy · doi:10.1080/15548627.2016.1268301 · Cited by 86
Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins
Li, J., Zhu, R., Chen, K., Zheng, H., Zhao, H., Yuan, C., Zhang, H., Wang, C., & Zhang, M. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0082-8 · Cited by 81
Park, S., Choi, J., Biering, S. B., Dominici, E., Williams, L. E., & Hwang, S. (2016) · Autophagy · doi:10.1080/15548627.2016.1178447 · Cited by 84
“, 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…”
BackgroundAutophagy in Dictyostelium: Mechanisms, regulation and disease in a simple biomedical model
Mesquita, A., Cardenal-Muñoz, E., Dominguez, E., Muñoz-Braceras, S., Nuñez-Corcuera, B., Phillips, B. A., Tábara, L. C., Xiong, Q., Coria, R., Eichinger, L., et al. (2017) · Autophagy · doi:10.1080/15548627.2016.1226737 · Cited by 84
“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.”
BackgroundChen, R., Shen, K.-L., Chen, Z., Fan, W., Xie, X., Meng, C., Chang, X.-J., Zheng, L., Jeswin, J., Li, C., et al. (2016) · Scientific Reports · doi:10.1038/srep28694 · Cited by 82
An updated review of autophagy in ischemic stroke: From mechanisms to therapies
Wang, X., Fang, Y., Huang, Q., Xu, P., Lenahan, C., Lü, J., Zheng, J., Dong, X., Shao, A., & Zhang, J. (2021) · Experimental Neurology · doi:10.1016/j.expneurol.2021.113684 · Cited by 80
Human apolipoprotein L1 (ApoL1) in cancer and chronic kidney disease
Hu, C. A., Klopfer, E. I., & Ray, P. E. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.03.002 · Cited by 80
“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.”
BackgroundGSK3B induces autophagy by phosphorylating ULK1
Ryu, H. Y., Kim, L. E., Jeong, H., Yeo, B. K., Lee, J., Nam, H., Ha, S., An, H., Park, H., Jung, S., et al. (2021) · Experimental & Molecular Medicine · doi:10.1038/s12276-021-00570-6 · Cited by 80
Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation
Broadbent, D. G., Barnaba, C., Perez, G. I., & Schmidt, J. C. (2023) · The Journal of Cell Biology · doi:10.1083/jcb.202210078 · Cited by 82
“…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).”
BackgroundHayashi, K., Taura, M., & Iwasaki, A. (2018) · Science Signaling · doi:10.1126/scisignal.aan4144 · Cited by 76
Immunohistochemical analysis of macroautophagy
Martinet, W., Schrijvers, D. M., Timmermans, J., Bult, H., & Meyer, G. R. Y. D. (2012) · Autophagy · doi:10.4161/auto.22968 · Cited by 76
Koukourakis, M. I., Mitrakas, A. G., & Giatromanolaki, A. N. (2016) · British Journal of Cancer · doi:10.1038/bjc.2016.19 · Cited by 79
“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).”
BackgroundAutophagic bulk sequestration of cytosolic cargo is independent of LC3, but requires GABARAPs
Szalai, P., Hagen, L. K., Sætre, F., Luhr, M., Sponheim, M., Øverbye, A., Mills, I. G., Seglen, P. O., & Engedal, N. (2015) · Experimental Cell Research · doi:10.1016/j.yexcr.2015.02.003 · Cited by 82
Liss, V., Liebl, D., Zhang, Y., Rajashekar, R., Chlanda, P., Giesker, K., Chikkaballi, D., & Hensel, M. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004374 · Cited by 76
“To further examine the possible involvement of autophagy, we inhibited ATG5, a key regulator of all known human ATG8 homologous [reviewed in 31].”
Background
Metadata
- Authors
- Shpilka, T., Weidberg, H., Pietrokovski, S., & Elazar, Z.
- Affiliations
- Weizmann Institute of Science (IL)
- Corresponding author
- Pietrokovski, Shmuel
- Elazar, Zvulun
- Venue
- Genome biology
- Published
- 2011
- Volume
- 12
- Issue
- 7
- Pages
- 226
- ISSN
- 1465-6906 (ISSN-L)
- PMC
- PMC3218822
- OpenAlex
- W2034198209
- Cited by
- 543
- References
- 115
- Citations by year
- 2026: 25 · 2025: 41 · 2024: 38 · 2023: 37 · 2022: 34 · 2021: 56 · 2020: 45 · 2019: 39 · 2018: 31 · 2017: 39 · 2016: 49 · 2015: 29 · 2014: 36 · 2013: 25 · 2012: 19
- FWCI
- 3.00
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Eli Lilly and Company
- Legacy Heritage Fund
- Hermann und Lilly Schilling-Stiftung für Medizinische Forschung
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Autophagy in Disease and Therapy
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Keywords
- ATG8, autophagy-related proteins, ubiquitin-like proteins, autophagy, autophagosome formation, phosphatidylethanolamine conjugation, LC3, GABARAP, protein evolution, intracellular membrane trafficking
- MeSH terms
- Animals, Autophagy, Humans, Ubiquitins, Evolution, Molecular, Protein Transport
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