ATG13/YPR185W Summary Help

Standard Name ATG13 1
Systematic Name YPR185W
Alias APG13 2
Feature Type ORF, Verified
Description Regulatory subunit of the Atg1p signaling complex; stimulates Atg1p kinase activity; required for vesicle formation during autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; contains a HORMA domain required for autophagy and for recruitment of the phosphatidylinositol 3-kinase complex subunit Atg14p to the pre-autophagosomal structure (3, 4, 5, 6, 7 and see Summary Paragraph)
Name Description AuTophaGy related 1
Chromosomal Location
ChrXVI:907218 to 909434 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All ATG13 GO evidence and references
  View Computational GO annotations for ATG13
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
126 total interaction(s) for 76 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 2
  • Affinity Capture-RNA: 4
  • Affinity Capture-Western: 17
  • Biochemical Activity: 1
  • Co-purification: 1
  • Reconstituted Complex: 1
  • Two-hybrid: 11

Genetic Interactions
  • Dosage Rescue: 4
  • Negative Genetic: 61
  • Phenotypic Enhancement: 3
  • Phenotypic Suppression: 2
  • Positive Genetic: 19

Resources
Expression Summary
histogram
Resources
Length (a.a.) 738
Molecular Weight (Da) 83,281
Isoelectric Point (pI) 7.02
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrXVI:907218 to 909434 | ORF Map | GBrowse
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
CDS 1..2217 907218..909434 2011-02-03 1996-07-31
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 SGDIDS000006389
SUMMARY PARAGRAPH for ATG13

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 8). 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 (9, 10, reviewed in 11). Approximately 30 autophagy-related (Atg) proteins have been identified in S. cerevisiae, 17 of which are essential for formation of the autophagosome (reviewed in 12). 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 (13, 14).

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 (15, 16). 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 (17 and reviewed in 12).

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 (13, 14). 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 18). The Cvt pathway has not been observed outside of yeast, and enzymes specifically involved in this pathway are not well conserved in other organisms (19 and references therein).

about ATG13

ATG13 and ATG17 encode the regulatory subunits of the Atg1p protein kinase complex, and are required for vesicle expansion during autophagy (20, 6, and reviewed in 12). Atg13p and Atg17p stimulate Atg1p kinase activity, and formation of this complex is specific to autophagy and enhanced during starvation (6). An Atg1p-Atg13p complex is also required for proper localization and cycling of autophagy proteins such as Atg9p, Atg23p, and Atg27p (5, 21).

In nutrient-rich conditions, Atg13p is hyperphosphorylated in a Tor-dependent manner and phospho-Atg13p has a lower affinity for Atg1p and Atg17p. Upon starvation, Atg13p is dephosphorylated and Atg1p-Atg13p-Atg17p complex formation and subsequent induction of autophagy occurs (22, and reviewed in 23). atg13 mutants are defective in autophagy, sporulation, and survival under starvation conditions (2, 3). ATG13 is highly conserved and homologs have been identified from yeast to man (19).

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 (19, 24).

Last updated: 2008-02-08 Contact SGD

References cited on this page View Complete Literature Guide for ATG13
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) Funakoshi T, et al.  (1997) Analyses of APG13 gene involved in autophagy in yeast, Saccharomyces cerevisiae. Gene 192(2):207-13
4) Scott SV, et al.  (2000) Apg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm to vacuole targeting. J Biol Chem 275(33):25840-9
5) Reggiori F, et al.  (2004) The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure. Dev Cell 6(1):79-90
6) Kabeya Y, et al.  (2005) Atg17 functions in cooperation with Atg1 and Atg13 in yeast autophagy. Mol Biol Cell 16(5):2544-53
7) Jao CC, et al.  (2013) A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy. Proc Natl Acad Sci U S A 110(14):5486-91
8) 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
9) 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
10) Matsuura A, et al.  (1997) Apg1p, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae. Gene 192(2):245-50
11) Yorimitsu T and Klionsky DJ  (2007) Endoplasmic reticulum stress: a new pathway to induce autophagy. Autophagy 3(2):160-2
12) Suzuki K and Ohsumi Y  (2007) Molecular machinery of autophagosome formation in yeast, Saccharomyces cerevisiae. FEBS Lett 581(11):2156-61
13) 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
14) 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
15) 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
16) Noda T and Ohsumi Y  (1998) Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. J Biol Chem 273(7):3963-6
17) 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
18) 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
19) 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
20) Cheong H, et al.  (2005) Atg17 regulates the magnitude of the autophagic response. Mol Biol Cell 16(7):3438-53
21) He C, et al.  (2007) Atg27 is required for autophagy-dependent cycling of Atg9. Mol Biol Cell 18(2):581-93
22) Kamada Y, et al.  (2000) Tor-mediated induction of autophagy via an Apg1 protein kinase complex. J Cell Biol 150(6):1507-13
23) Yorimitsu T and Klionsky DJ  (2005) Autophagy: molecular machinery for self-eating. Cell Death Differ 12 Suppl 2():1542-52
24) Farre JC, et al.  (2008) PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell 14(3):365-76