ATG29/YPL166W Summary Help

Standard Name ATG29 1
Systematic Name YPL166W
Feature Type ORF, Verified
Description Autophagy-specific protein; required for recruiting other ATG proteins to the pre-autophagosomal structure (PAS); interacts with Atg17p and localizas to the PAS in a manner interdependent with Atg17p and Cis1p; not conserved; relocalizes from nucleus to cytoplasmic foci upon DNA replication stress (1, 2, 3, 4, 5 and see Summary Paragraph)
Name Description AuTophaGy related 1, 6
Chromosomal Location
ChrXVI:237338 to 237979 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All ATG29 GO evidence and references
  View Computational GO annotations for ATG29
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
High-throughput
Regulators 43 genes
Resources
Classical genetics
null
overexpression
Large-scale survey
null
Resources
47 total interaction(s) for 30 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 9
  • Affinity Capture-RNA: 1
  • Affinity Capture-Western: 7
  • Biochemical Activity: 2
  • Co-purification: 1
  • Reconstituted Complex: 1
  • Two-hybrid: 3

Genetic Interactions
  • Negative Genetic: 10
  • Phenotypic Enhancement: 1
  • Positive Genetic: 12

Resources
Expression Summary
histogram
Resources
Length (a.a.) 213
Molecular Weight (Da) 24,708
Isoelectric Point (pI) 4.91
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrXVI:237338 to 237979 | 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..642 237338..237979 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 SGDIDS000006087
SUMMARY PARAGRAPH for ATG29

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 7). 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 (8, 9, reviewed in 10). Approximately 30 autophagy-related (Atg) proteins have been identified in S. cerevisiae, 17 of which are essential for formation of the autophagosome (reviewed in 11). 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 (12, 13).

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 (14, 15). 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 (16 and reviewed in 11).

about ATG29

Atg29p is an autophagy-specific protein that localizes to the PAS and functions in PAS localization of other Atg proteins during nutrient stress (1, 4). atg29 null mutant cells show reduced viability in starvation conditions and severe defects in autophagy (the severity of the defect varies according to genetic background), but are normal for Cvt pathway function (1).

Atg29p interacts with Atg17p (apparently via coiled-coil domains in each protein), and localization of Atg29p, Atg17p, and Cis1p to the PAS is interdependent (4). These 3 autophagy-specific proteins and the Atg1p-Atg13p kinase complex are all required for PAS recruitment of other ATG proteins; thus it is proposed that Atg29p, Atg17p, and Cis1p form a complex that functions cooperatively with the Atg1p-Atg13p kinase complex to organize the PAS (4).

Proteins with similarity to Atg29p have been found in some other yeast species and filamentous fungi, but not in C. albicans, S. pombe, or higher eukaryotes, indicating Atg29p is not widely conserved (3).

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 (6 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 (6). 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 (3, 17).

Last updated: 2008-02-08 Contact SGD

References cited on this page View Complete Literature Guide for ATG29
1) Kawamata T, et al.  (2005) Characterization of a novel autophagy-specific gene, ATG29. Biochem Biophys Res Commun 338(4):1884-9
2) Huh WK, et al.  (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91
3) 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
4) Kawamata T, et al.  (2008) Organization of the Pre-autophagosomal Structure Responsible for Autophagosome Formation. Mol Biol Cell 19(5):2039-50
5) Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76
6) Klionsky DJ, et al.  (2003) A unified nomenclature for yeast autophagy-related genes. Dev Cell 5(4):539-45
7) 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
8) 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
9) Matsuura A, et al.  (1997) Apg1p, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae. Gene 192(2):245-50
10) Yorimitsu T and Klionsky DJ  (2007) Endoplasmic reticulum stress: a new pathway to induce autophagy. Autophagy 3(2):160-2
11) Suzuki K and Ohsumi Y  (2007) Molecular machinery of autophagosome formation in yeast, Saccharomyces cerevisiae. FEBS Lett 581(11):2156-61
12) 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
13) 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
14) 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
15) Noda T and Ohsumi Y  (1998) Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. J Biol Chem 273(7):3963-6
16) 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
17) Farre JC, et al.  (2008) PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell 14(3):365-76