SNX4/YJL036W Summary Help

Standard Name SNX4 1
Systematic Name YJL036W
Alias CVT13 2 , ATG24 3
Feature Type ORF, Verified
Description Sorting nexin; involved in retrieval of late-Golgi SNAREs from post-Golgi endosomes to the trans-Golgi network and in cytoplasm to vacuole transport; contains a PX phosphoinositide-binding domain; forms complexes with Snx41p and with Atg20p (4, 5, 6 and see Summary Paragraph)
Name Description Sorting NeXin 1
Chromosomal Location
ChrX:378825 to 380096 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All SNX4 GO evidence and references
  View Computational GO annotations for SNX4
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 5 genes
Resources
Classical genetics
null
overexpression
reduction of function
Large-scale survey
null
Resources
177 total interaction(s) for 133 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 8
  • Affinity Capture-RNA: 3
  • Affinity Capture-Western: 11
  • PCA: 2
  • Reconstituted Complex: 1
  • Two-hybrid: 48

Genetic Interactions
  • Negative Genetic: 70
  • Phenotypic Enhancement: 7
  • Positive Genetic: 16
  • Synthetic Growth Defect: 4
  • Synthetic Lethality: 3
  • Synthetic Rescue: 4

Resources
Expression Summary
histogram
Resources
Length (a.a.) 423
Molecular Weight (Da) 49,002
Isoelectric Point (pI) 6.46
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrX:378825 to 380096 | 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..1272 378825..380096 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 SGDIDS000003573
SUMMARY PARAGRAPH for SNX4

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 (2, 7). 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 8). The Cvt pathway has not been observed outside of yeast, and enzymes specifically involved in this pathway are not well conserved in other organisms (9 and references therein).

about SNX4

Snx4p encodes a member of the sorting nexin family, which includes proteins that contain a Phox homology (PX) phosphoinositide-binding domain and play a role in membrane protein sorting (10, 6). Of the SNX family members, Snx4p is part of a sub-group of proteins that contain large C-terminal regions with multiple coiled-coil domains (4). The Snx4p PX domain binds phosphatidylinositol 3-phosphate and is required for Snx4p localization to the PAS, where the protein plays a role in the Cvt pathway (10, 5). Snx4p also localizes to endosomes, where it functions in endosomal sorting (6).

Null snx4 mutations prevent maturation of aminopeptidase I (Lap4p), indicating defects in Cvt pathway function, and cause improper localization of the v-SNARE Snc1p to the vacuole (2, 6). The role of Snx4p in the Cvt pathway involves interaction with Atg20p (which also carries a PX domain); this complex appears to interact with the Atg1p-Atg13p complex via interaction with Atg17p and Atg11p (5, reviewed in 7 and 9). The Atg20p-Snx4p complex also helps mediate endosomal sorting of Snc1p, which is retrieved from post-Golgi endosomes back to the Golgi; Snc1p is mislocalized to the vacuole in an snx4 (or atg20) null mutant (6). Snx4p also interacts with Btn2p, which is the yeast ortholog of the mammalian Hook1 protein and is likely to function in late endosome-Golgi recycling (11).

Snx4p homologs have been identified in humans (SNX4 and SNX30) and fungi, but not in A. thaliana (9).

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 (3 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 (3). 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 (9, 12).

Last updated: 2008-04-23 Contact SGD

References cited on this page View Complete Literature Guide for SNX4
1) Haft CR, et al.  (1998) Identification of a family of sorting nexin molecules and characterization of their association with receptors. Mol Cell Biol 18(12):7278-87
2) 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
3) Klionsky DJ, et al.  (2003) A unified nomenclature for yeast autophagy-related genes. Dev Cell 5(4):539-45
4) Teasdale RD, et al.  (2001) A large family of endosome-localized proteins related to sorting nexin 1. Biochem J 358(Pt 1):7-16
5) Nice DC, et al.  (2002) Cooperative binding of the cytoplasm to vacuole targeting pathway proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-autophagosomal structure is required for selective autophagy. J Biol Chem 277(33):30198-207
6) Hettema EH, et al.  (2003) Retromer and the sorting nexins Snx4/41/42 mediate distinct retrieval pathways from yeast endosomes. EMBO J 22(3):548-57
7) 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
8) 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
9) 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
10) Yu JW and Lemmon MA  (2001) All phox homology (PX) domains from Saccharomyces cerevisiae specifically recognize phosphatidylinositol 3-phosphate. J Biol Chem 276(47):44179-84
11) Kama R, et al.  (2007) Btn2, a hook1 ortholog and potential batten disease-related protein, mediates late endosome-Golgi protein sorting in yeast. Mol Cell Biol 27(2):605-21
12) Farre JC, et al.  (2008) PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell 14(3):365-76