ATG8/YBL078C Summary Help

Standard Name ATG8 1
Systematic Name YBL078C
Alias APG8 2 , 3 , CVT5 4 , AUT7 5
Feature Type ORF, Verified
Description Component of autophagosomes and Cvt vesicles; regulator of Atg1p, targets it to autophagosomes; binds the Atg1p-Atg13p complex, triggering its vacuolar degradation; unique ubiquitin-like protein whose conjugation target is lipid phosphatidylethanolamine (PE); Atg8p-PE is anchored to membranes, is involved in phagophore expansion, and may mediate membrane fusion during autophagosome formation; deconjugation of Atg8p-PE is required for efficient autophagosome biogenesis (3, 6, 7, 8, 9, 10, 11, 12 and see Summary Paragraph)
Name Description AuTophaGy related 1
Chromosomal Location
ChrII:80731 to 80378 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gbrowse
Gene Ontology Annotations All ATG8 GO evidence and references
  View Computational GO annotations for ATG8
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 6 genes
Resources
Classical genetics
null
reduction of function
repressible
Large-scale survey
null
Resources
201 total interaction(s) for 110 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 5
  • Affinity Capture-RNA: 1
  • Affinity Capture-Western: 25
  • Biochemical Activity: 12
  • Co-crystal Structure: 3
  • Co-fractionation: 1
  • Co-localization: 4
  • Co-purification: 1
  • PCA: 2
  • Protein-peptide: 1
  • Reconstituted Complex: 12
  • Two-hybrid: 20

Genetic Interactions
  • Dosage Lethality: 1
  • Dosage Rescue: 3
  • Negative Genetic: 82
  • Phenotypic Enhancement: 9
  • Phenotypic Suppression: 6
  • Positive Genetic: 7
  • Synthetic Growth Defect: 6

Resources
Expression Summary
histogram
Resources
Length (a.a.) 117
Molecular Weight (Da) 13,627
Isoelectric Point (pI) 9.92
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrII:80731 to 80378 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 1997-01-28
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
CDS 1..354 80731..80378 2011-02-03 1997-01-28
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
Resources
External Links All Associated Seq | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000000174
SUMMARY PARAGRAPH for ATG8

about autophagy...

Autophagy is a highly conserved eukaryotic pathway for sequestering and transporting bulk cytoplasm, including proteins and organelle material, to the lysosome for degradation (reviewed in 13). Upon starvation for nutrients such as carbon, nitrogen, sulfur, and various amino acids, or upon endoplasmic reticulum stress, cells initiate formation of a double-membrane vesicle, termed an autophagosome, that mediates this process (14, 15, reviewed in 16). Approximately 30 autophagy-related (Atg) proteins have been identified in S. cerevisiae, 17 of which are essential for formation of the autophagosome (reviewed in 17). Null mutations in most of these genes prevent induction of autophagy, and cells do not survive nutrient starvation; however, these mutants are viable in rich medium. Some of the Atg proteins are also involved in a constitutive biosynthetic process termed the cytoplasm-to-vacuole targeting (Cvt) pathway, which uses autophagosomal-like vesicles for selective transport of hydrolases aminopeptidase I (Lap4p) and alpha-mannosidase (Ams1p) to the vacuole (5, 18).

Autophagy proceeds via a multistep pathway (a summary diagram (download pdf) kindly provided by Dan Klionsky). First, nutrient availability is sensed by the TORC1 complex and also cooperatively by protein kinase A and Sch9p (19, 20). Second, signals generated by the sensors are transmitted to the autophagosome-generating machinery comprised of the 17 Atg gene products. These 17 proteins collectively form the pre-autophagosomal structure/phagophore assembly site (PAS). The PAS generates an isolation membrane (IM), which expands and eventually fuses along the edges to complete autophagosome formation. At the vacuole the outer membrane of the autophagosome fuses with the vacuolar membrane and autophagic bodies are released, disintegrated, and their contents degraded for reuse in biosynthesis (21 and reviewed in 17).

about autophagic ubiquitin-like conjugation

Formation of autophagosomes requires a number of autophagy proteins that are involved in one of two ubiquitin-like conjugation systems, the Atg12 and Atg8 systems (reviewed in 22 and 23). The final product of these two systems is a lipidated form of Atg8p that appears to be required for membrane tethering and hemifusion, which are essential for autophagosome formation (8). In the Atg12 system, the ubiquitin-like protein Atg12p is activated by the E1-like enzyme Atg7p and then transferred to Atg10p, an enzyme with E2-like activity (24, 25). Atg12p is then constitutively and irreversibly conjugated to Atg5p, which is the only Atg12p target (in contrast to ubiquitin which has many targets; (24 and reviewed in 22). After Atg12p-Atg5p conjugation, Atg16p associates with the conjugate, resulting in a ~350kDa complex (26). It is hypothesized that the role of Atg16p in this complex is to properly localize the Atp12p-Atg5p conjugate, which acts as an E3-like enzyme in the Atg8 conjugation system (27). In the Atg8 system, the other autophagic ubiquitin-like protein Atg8p is first cleaved at its C-terminal end by the cysteine protease Atg4p, which is structurally similar to deubiquitinating enzymes (7). The proteolytically processed form of Atg8p is then activated by Atg7p and transferred to Atg3p, another E2-like enzyme (24, 6). Finally, Atg8p is conjugated to the lipid phosphatidylethanolamine (PE), a reaction stimulated by the E3-like activity from the Atg5p-Atg12p complex (27). Atg8p-PE conjugation is reversible; deconjugation is mediated by Atg4p and interferes with membrane fusion (8).

about the Cytoplasm-to-vacuole targeting (Cvt) pathway

Cytoplasm-to-vacuole targeting (Cvt) is a constitutive and specific form of autophagy that uses autophagosomal-like vesicles for selective transport of hydrolases aminopeptidase I (Lap4p) and alpha-mannosidase (Ams1p) to the vacuole (5, 18). Unlike autophagy, which is primarily a catabolic process, Cvt is a biosynthetic process. Like autophagosomes, Cvt vesicles form at a structure known as the phagophore assembly site (PAS) (also called the pre-autophagosomal structure). The PAS structure generates an isolation membrane (IM), which expands and eventually fuses along the edges to complete vesicle formation. At the vacuole, the outer membrane of the Cvt vesicle fuses with the vacuolar membrane, the vesicle is degraded, and the cargos are released and processed into their mature forms by vacuolar peptidases (reviewed in 28). The Cvt pathway has not been observed outside of yeast, and enzymes specifically involved in this pathway are not well conserved in other organisms (29 and references therein).

about ATG8

Atg8p is required for both the Cvt and autophagy pathways; Atg8p plays a role in expansion of the phagophore during autophagosome formation, and levels of Atg8p determine the size of the autophagosome (9, 30). While most of the Atg8p-PE is released during formation of autophagosomes, a portion remains associated with the completed structure and thus serves as an experimental marker for these structures (9, reviewed in 31). ATG8 gene expression is induced at least 10-fold in response to starvation, with mRNA levels peaking after about 30 minutes (2, 32). Starvation causes localization of the protein to shift from small cytoplasmic structures to the isolation membranes of nascent autophagosomes, where Atg8p appears to promote the fusion of these membranes necessary for autophagosome formation (2, 30, 8). The change in Atg8p localization requires functional Atg4p, Atg7p, Atg3p, and the carboxy terminal glycine of Atg8p, all of which are required to mediate the conjugation of Atg8p to PE through an amide bond between the C-terminal glycine and the amino group of PE (reviewed in 22). Atg4p cleaves this amide bond, effectively releasing some of the Atg8p from the autophagosome, an important step in maturation of the structure (7). Null atg8 mutations severely impair formation of autophagosomes (2).

Atg8p in mammals is a multigene family, consisting of GATE16, GABARAP, and LC3 (reviewed in 33). Crystal structure studies indicate that Atg8p homologs consist of an N-terminal helical domain and a C-terminal ubiqutin-like domain (34, 35).

about autophagy nomenclature

The initial identification of factors involved in autophagy was carried out by several independent labs, which led to a proliferation of nomenclature for the genes and gene products involved. The differing gene name acronyms from these groups included APG, AUT, CVT, GSA, PAG, PAZ, and PDD (1 and references therein). A concerted effort was made in 2003 by the scientists working in the field to unify the nomenclature for these genes, and "AuTophaGy-related" genes are now denoted by the letters ATG (1). In addition to the ATG gene names that have been assigned to S. cerevisiae proteins and their orthologs, several ATG gene names, including ATG25, ATG28, and ATG30, have been used to designate proteins in other ascomycete yeast species for which there is no identifiable equivalent in S. cerevisiae (29, 36).

Last updated: 2008-02-08 Contact SGD

References cited on this page View Complete Literature Guide for ATG8
1) Klionsky DJ, et al.  (2003) A unified nomenclature for yeast autophagy-related genes. Dev Cell 5(4):539-45
2) Kirisako T, et al.  (1999) Formation process of autophagosome is traced with Apg8/Aut7p in yeast. J Cell Biol 147(2):435-46
3) Tsukada M and Ohsumi Y  (1993) Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett 333(1-2):169-74
4) Harding TM, et al.  (1995) Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway. J Cell Biol 131(3):591-602
5) Harding TM, et al.  (1996) Genetic and phenotypic overlap between autophagy and the cytoplasm to vacuole protein targeting pathway. J Biol Chem 271(30):17621-4
6) Ichimura Y, et al.  (2000) A ubiquitin-like system mediates protein lipidation. Nature 408(6811):488-92
7) Kirisako T, et al.  (2000) The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway. J Cell Biol 151(2):263-76
8) Nakatogawa H, et al.  (2007) Atg8, a Ubiquitin-like Protein Required for Autophagosome Formation, Mediates Membrane Tethering and Hemifusion. Cell 130(1):165-78
9) Xie Z, et al.  (2008) Atg8 Controls Phagophore Expansion during Autophagosome Formation. Mol Biol Cell 19(8):3290-8
10) Nair U, et al.  (2011) SNARE proteins are required for macroautophagy. Cell 146(2):290-302
11) Kraft C, et al.  (2012) Binding of the Atg1/ULK1 kinase to the ubiquitin-like protein Atg8 regulates autophagy. EMBO J 31(18):3691-703
12) Nair U, et al.  (2012) A role for Atg8-PE deconjugation in autophagosome biogenesis. Autophagy 8(5):780-93
13) Budovskaya YV, et al.  (2004) The Ras/cAMP-dependent protein kinase signaling pathway regulates an early step of the autophagy process in Saccharomyces cerevisiae. J Biol Chem 279(20):20663-71
14) Takeshige K, et al.  (1992) Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction. J Cell Biol 119(2):301-11
15) Matsuura A, et al.  (1997) Apg1p, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae. Gene 192(2):245-50
16) Yorimitsu T and Klionsky DJ  (2007) Endoplasmic reticulum stress: a new pathway to induce autophagy. Autophagy 3(2):160-2
17) Suzuki K and Ohsumi Y  (2007) Molecular machinery of autophagosome formation in yeast, Saccharomyces cerevisiae. FEBS Lett 581(11):2156-61
18) Yorimitsu T and Klionsky DJ  (2005) Atg11 links cargo to the vesicle-forming machinery in the cytoplasm to vacuole targeting pathway. Mol Biol Cell 16(4):1593-605
19) Yorimitsu T, et al.  (2007) Protein Kinase A and Sch9 Cooperatively Regulate Induction of Autophagy in Saccharomyces cerevisiae. Mol Biol Cell 18(10):4180-9
20) Noda T and Ohsumi Y  (1998) Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. J Biol Chem 273(7):3963-6
21) Suzuki K, et al.  (2001) The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. EMBO J 20(21):5971-81
22) Ohsumi Y  (2001) Molecular dissection of autophagy: two ubiquitin-like systems. Nat Rev Mol Cell Biol 2(3):211-6
23) Yorimitsu T and Klionsky DJ  (2005) Autophagy: molecular machinery for self-eating. Cell Death Differ 12 Suppl 2():1542-52
24) Mizushima N, et al.  (1998) A protein conjugation system essential for autophagy. Nature 395(6700):395-8
25) Shintani T, et al.  (1999) Apg10p, a novel protein-conjugating enzyme essential for autophagy in yeast. EMBO J 18(19):5234-41
26) Kuma A, et al.  (2002) Formation of the approximately 350-kDa Apg12-Apg5.Apg16 multimeric complex, mediated by Apg16 oligomerization, is essential for autophagy in yeast. J Biol Chem 277(21):18619-25
27) Hanada T, et al.  (2007) The Atg12-Atg5 Conjugate Has a Novel E3-like Activity for Protein Lipidation in Autophagy. J Biol Chem 282(52):37298-302
28) Kim J and Klionsky DJ  (2000) Autophagy, cytoplasm-to-vacuole targeting pathway, and pexophagy in yeast and mammalian cells. Annu Rev Biochem 69:303-42
29) Meijer WH, et al.  (2007) ATG genes involved in non-selective autophagy are conserved from yeast to man, but the selective Cvt and pexophagy pathways also require organism-specific genes. Autophagy 3(2):106-16
30) Huang WP, et al.  (2000) The itinerary of a vesicle component, Aut7p/Cvt5p, terminates in the yeast vacuole via the autophagy/Cvt pathways. J Biol Chem 275(8):5845-51
31) Klionsky DJ, et al.  (2007) Methods for monitoring autophagy from yeast to human. Autophagy 3(3):181-206
32) Gasch AP, et al.  (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11(12):4241-57
33) Amar N, et al.  (2006) Two newly identified sites in the ubiquitin-like protein Atg8 are essential for autophagy. EMBO Rep 7(6):635-42
34) Sugawara K, et al.  (2004) The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8. Genes Cells 9(7):611-8
35) Coyle JE, et al.  (2002) Structure of GABARAP in two conformations: implications for GABA(A) receptor localization and tubulin binding. Neuron 33(1):63-74
36) Farre JC, et al.  (2008) PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell 14(3):365-76