ATG4/YNL223W Summary Help

Standard Name ATG4 1
Systematic Name YNL223W
Alias APG4 2 , AUT2 3
Feature Type ORF, Verified
Description Conserved cysteine protease required for autophagy; cleaves Atg8p to a form required for autophagosome and Cvt vesicle generation (2, 4, 5 and see Summary Paragraph)
Name Description AuTophaGy related 1
Chromosomal Location
ChrXIV:227370 to 228854 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All ATG4 GO evidence and references
  View Computational GO annotations for ATG4
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 3 genes
Resources
Classical genetics
null
reduction of function
Large-scale survey
null
overexpression
Resources
44 total interaction(s) for 35 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 1
  • Affinity Capture-RNA: 1
  • Affinity Capture-Western: 1
  • Biochemical Activity: 1
  • Co-purification: 1
  • Reconstituted Complex: 1
  • Two-hybrid: 4

Genetic Interactions
  • Dosage Rescue: 1
  • Negative Genetic: 11
  • Phenotypic Enhancement: 6
  • Phenotypic Suppression: 1
  • Positive Genetic: 14
  • Synthetic Growth Defect: 1

Resources
Expression Summary
histogram
Resources
Length (a.a.) 494
Molecular Weight (Da) 55,142
Isoelectric Point (pI) 4.4
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrXIV:227370 to 228854 | ORF Map | GBrowse
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 2003-09-22
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
CDS 1..1485 227370..228854 2011-02-03 2003-09-22
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
Resources
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000005167
SUMMARY PARAGRAPH for ATG4

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 6). 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 (7, 8, reviewed in 9). Approximately 30 autophagy-related (Atg) proteins have been identified in S. cerevisiae, 17 of which are essential for formation of the autophagosome (reviewed in 10). 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 (11, 12).

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 (13, 14). 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 (15 and reviewed in 10).

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 16 and 17). 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 (18). 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 (19, 20). Atg12p is then constitutively and irreversibly conjugated to Atg5p, which is the only Atg12p target (in contrast to ubiquitin which has many targets; (19 and reviewed in 16). After Atg12p-Atg5p conjugation, Atg16p associates with the conjugate, resulting in a ~350kDa complex (21). 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 (22). 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 (4). The proteolytically processed form of Atg8p is then activated by Atg7p and transferred to Atg3p, another E2-like enzyme (19, 23). Finally, Atg8p is conjugated to the lipid phosphatidylethanolamine (PE), a reaction stimulated by the E3-like activity from the Atg5p-Atg12p complex (22). Atg8p-PE conjugation is reversible; deconjugation is mediated by Atg4p and interferes with membrane fusion (18).

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 (11, 12). 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 24). The Cvt pathway has not been observed outside of yeast, and enzymes specifically involved in this pathway are not well conserved in other organisms (5 and references therein).

about ATG4

Atg4p is a cysteine endoprotease that cleaves the carboxy terminal arginine residue of Atg8p in preparation for conjugation with phosphatidylethanolamine, and also cleaves the modified, membrane-bound form of Atg8p to reverse conjugation (4). Atg4p has been shown to interact with Tub1p and Tub2p; this interaction is thought to be important for the attachment of autophagosomes to microtubules (25).

Atg4p is conserved in higher eukaryotes (4, 5). Human cells have four Atg4p-like proteins: ATG4A, ATG4B, ATG4C, and ATG4D; ATG4B and ATG4C been shown to complement the autophagy deficiency exhibited by a yeast atg4 mutant (26, reviewed in 5). Two Atg4-like proteins have been identified in A. thaliana (5).

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 (5, 27).

Last updated: 2008-02-08 Contact SGD

References cited on this page View Complete Literature Guide for ATG4
1) Klionsky DJ, et al.  (2003) A unified nomenclature for yeast autophagy-related genes. Dev Cell 5(4):539-45
2) Tsukada M and Ohsumi Y  (1993) Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett 333(1-2):169-74
3) Thumm M, et al.  (1994) Isolation of autophagocytosis mutants of Saccharomyces cerevisiae. FEBS Lett 349(2):275-80
4) 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
5) 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
6) 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
7) 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
8) Matsuura A, et al.  (1997) Apg1p, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae. Gene 192(2):245-50
9) Yorimitsu T and Klionsky DJ  (2007) Endoplasmic reticulum stress: a new pathway to induce autophagy. Autophagy 3(2):160-2
10) Suzuki K and Ohsumi Y  (2007) Molecular machinery of autophagosome formation in yeast, Saccharomyces cerevisiae. FEBS Lett 581(11):2156-61
11) 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
12) 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
13) 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
14) Noda T and Ohsumi Y  (1998) Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. J Biol Chem 273(7):3963-6
15) 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
16) Ohsumi Y  (2001) Molecular dissection of autophagy: two ubiquitin-like systems. Nat Rev Mol Cell Biol 2(3):211-6
17) Yorimitsu T and Klionsky DJ  (2005) Autophagy: molecular machinery for self-eating. Cell Death Differ 12 Suppl 2():1542-52
18) Nakatogawa H, et al.  (2007) Atg8, a Ubiquitin-like Protein Required for Autophagosome Formation, Mediates Membrane Tethering and Hemifusion. Cell 130(1):165-78
19) Mizushima N, et al.  (1998) A protein conjugation system essential for autophagy. Nature 395(6700):395-8
20) Shintani T, et al.  (1999) Apg10p, a novel protein-conjugating enzyme essential for autophagy in yeast. EMBO J 18(19):5234-41
21) 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
22) 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
23) Ichimura Y, et al.  (2000) A ubiquitin-like system mediates protein lipidation. Nature 408(6811):488-92
24) 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
25) Lang T, et al.  (1998) Aut2p and Aut7p, two novel microtubule-associated proteins are essential for delivery of autophagic vesicles to the vacuole. EMBO J 17(13):3597-607
26) Marino G, et al.  (2003) Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy. J Biol Chem 278(6):3671-8
27) Farre JC, et al.  (2008) PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell 14(3):365-76