BioPAX pathway converted from "The phagophore extends from the PIP3-enriched structure" in the Reactome database. The phagophore extends from the PIP3-enriched structure The phagophore extends from the PIP3-enriched structure The first crucial event in autophagy is the induction or nucleation of the membrane that will become an autophagosome. This is also the least well understood step (Tooze & Yoshimuri 2010). Following PI3P enrichment of the membrane, the associated membrane is distinct from its precursor and considered to be a new cellular structure, called a phagophore or an isolation membrane. Though the origins of this membrane are not unequivocally established, recent studies using mammalian cells indicate a strong relationship between autophagosome formation sites and the ER. The PI3P binding protein DFCP1 is localized to the ER. In starved cells it forms dot-like structures on the ER. LC3-positive membranes were observed to emerge from these structures, and named omegasomes as they resembled the Greek letter omega (Axe et al. 2008). 3D tomographic imaging of isolation membranes have shown cup-shaped isolation membranes sandwiched between two sheets of ER, connected by a narrow membrane tube (Hayashi-Nishino et al. 2009, Yla-Anttila et al. 2009) suggesting that isolation membrane formation and elongation may be guided by the adjacent ER sheets (Shibutani & Yoshimuri 2014). ATG9 is a multi transmembrane spanning protein that may directly or indirectly participate in the formation of phagophore curvature, for example, by wedging of the membrane. It is also possible that ATG9 could function as a lipid transfer protein (Carlsson & Simonsen 2015). In nutrient rich conditions ATG9 localizes to the trans Golgi network and endosomes. Under starvation conditions it localizes to autophagosomes, in a process dependent on ULK1 (Young et al. 2006, Orsi et al. 2012). In yeast, the induction of autophagy leads to Atg9 rich Golgi derived vesicles 30 60nm in diameter (Mari et al. 2010, Yamamoto et al. 2012). These vesicles accumulate at the PAS in an Atg1 dependent manner, where Atg1 mediated phosphorylation of Atg9 facilitates the recruitment of Atg8 and Atg18 and subsequent phagophore expansion (Papinski et al. 2014). Vesicular or tubular trafficking from recycling endosomes might is thought to feed ATG9 and ATG16L1 positive membrane onto the growing phagophore in a process that appears to be regulated by the PX BAR protein SNX18 and by the RAB11 effector protein TBC1D14 in an opposite manner (Knævelsrud et al. 2013, Longatti et al. 2012, Puri et al. 2013). Authored: Jupe, Steve, 2015-02-02 Reviewed: Tooze, Sharon A, 2015-05-13 Reviewed: Klionsky, Daniel J, 2015-09-03 Edited: Jupe, Steve, 2015-05-13 Reactome DB_ID: 5679242 1 endoplasmic reticulum membrane GO 0005789 ATG14:PIK3C3:PIK3R4:p-S15-BECN1 [endoplasmic reticulum membrane] ATG14:PIK3C3:PIK3R4:p-S15-BECN1 Autophagy-specific class III PI3K complex Beclin-1 complex Bakor:Vps34:Vps15:p-Beclin-1 Reactome DB_ID: 188011 1 cytosol GO 0005829 UniProt:Q8NEB9 PIK3C3 PIK3C3 PIK3C3 VPS34 FUNCTION Catalytic subunit of the PI3K complex that mediates formation of phosphatidylinositol 3-phosphate; different complex forms are believed to play a role in multiple membrane trafficking pathways: PI3KC3-C1 is involved in initiation of autophagosomes and PI3KC3-C2 in maturation of autophagosomes and endocytosis. As part of PI3KC3-C1, promotes endoplasmic reticulum membrane curvature formation prior to vesicle budding (PubMed:32690950). Involved in regulation of degradative endocytic trafficking and required for the abcission step in cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123, PubMed:20208530). Involved in the transport of lysosomal enzyme precursors to lysosomes. Required for transport from early to late endosomes (By similarity).SUBUNIT Component of the PI3K (PI3KC3/PI3K-III/class III phosphatidylinositol 3-kinase) complex the core of which is composed of the catalytic subunit PIK3C3, the regulatory subunit PIK3R4 and BECN1 associating with additional regulatory/auxilliary subunits to form alternative complex forms. Alternative complex forms containing a forth regulatory subunit in a mutually exclusive manner are: the PI3K complex I (PI3KC3-C1) containing ATG14, and the PI3K complex II (PI3KC3-C2) containing UVRAG. PI3KC3-C1 displays a V-shaped architecture with PIK3R4 serving as a bridge between PIK3C3 and the ATG14:BECN1 subcomplex. Both, PI3KC3-C1 and PI3KC3-C2, can associate with further regulatory subunits such as RUBCN, SH3GLB1/Bif-1 and AMBRA1 (PubMed:7628435, PubMed:19050071, PubMed:20643123, PubMed:19270696, PubMed:23878393, PubMed:25490155). PI3KC3-C1 probably associates with PIK3CB (By similarity). Interacts with RAB7A in the presence of PIK3R4 (PubMed:14617358). Interacts with AMBRA1 (By similarity). Interacts with BECN1P1/BECN2 (PubMed:23954414). Interacts with SLAMF1(PubMed:22493499). May be a component of a complex composed of RAB5A (in GDP-bound form), DYN2 and PIK3C3 (By similarity). Interacts with NCKAP1L (PubMed:16417406). Interacts with ATG14; this interaction is increased in the absence of TMEM39A (PubMed:31806350). Interacts with STEEP1; the interaction is STING1-dependent and required for trafficking of STING1 from the endoplasmic reticulum (PubMed:32690950).TISSUE SPECIFICITY Ubiquitously expressed, with a highest expression in skeletal muscle.SIMILARITY Belongs to the PI3/PI4-kinase family. Reactome http://www.reactome.org Homo sapiens NCBI Taxonomy 9606 UniProt Q8NEB9 Chain Coordinates 1 EQUAL 887 EQUAL Reactome DB_ID: 5682391 1 UniProt:Q14457 BECN1 BECN1 BECN1 GT197 FUNCTION Plays a central role in autophagy (PubMed:23184933, PubMed:28445460). Acts as core subunit of the PI3K complex that mediates formation of phosphatidylinositol 3-phosphate; different complex forms are believed to play a role in multiple membrane trafficking pathways: PI3KC3-C1 is involved in initiation of autophagosomes and PI3KC3-C2 in maturation of autophagosomes and endocytosis. Involved in regulation of degradative endocytic trafficking and required for the abcission step in cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123, PubMed:20208530, PubMed:26783301). Essential for the formation of PI3KC3-C2 but not PI3KC3-C1 PI3K complex forms. Involved in endocytosis (PubMed:25275521). Protects against infection by a neurovirulent strain of Sindbis virus (PubMed:9765397). May play a role in antiviral host defense.FUNCTION Beclin-1-C 35 kDa localized to mitochondria can promote apoptosis; it induces the mitochondrial translocation of BAX and the release of proapoptotic factors.SUBUNIT A homodimeric form is proposed to exist; this metastable form readily transits to ATG14- or UVRAG-containing complexes with BECN1:UVRAG being more stable than BECN1:ATG14 (By similarity). Component of the PI3K (PI3KC3/PI3K-III/class III phosphatidylinositol 3-kinase) complex the core of which is composed of the catalytic subunit PIK3C3, the regulatory subunit PIK3R4 and BECN1 associating with additional regulatory/auxilliary subunits to form alternative complex forms. Alternative complex forms containing a forth regulatory subunit in a mutually exclusive manner are PI3K complex I (PI3KC3-C1) containing ATG14, and PI3K complex II (PI3KC3-C2) containing UVRAG. PI3KC3-C1 displays a V-shaped architecture with PIK3R4 serving as a bridge between PIK3C3 and the ATG14:BECN1 subcomplex (PubMed:18843052, PubMed:19050071, PubMed:19270696, PubMed:23878393, PubMed:25490155). Both, PI3KC3-C1 and PI3KC3-C2, can associate with further regulatory subunits, such as RUBCN, SH3GLB1/Bif-1 and AMBRA1 (PubMed:20643123, PubMed:19270696). PI3KC3-C1 probably associates with PIK3CB (By similarity). Interacts with AMBRA1, GOPC, GRID2 (By similarity). Interacts with BCL2 and BCL2L1 isoform Bcl-X(L); the interaction inhibits BECN1 function in promoting autophagy by interfering with the formation of the PI3K complex (PubMed:9765397, PubMed:16179260, PubMed:17446862, PubMed:17337444, PubMed:17659302). Interacts with cytosolic HMGB1; inhibits the interaction of BECN1 and BCL2 leading to promotion of autophagy (PubMed:20819940). Interacts with USP10, USP13, VMP1, DAPK1, RAB39A (PubMed:19180116, PubMed:17724469, PubMed:17337444, PubMed:21962518, PubMed:24349490). Interacts with the poly-Gln domain of ATXN3; the interaction causes deubiquitination at Lys-402 and stabilizes BECN1 (PubMed:28445460). Interacts with SLAMF1 (PubMed:22493499). Interacts with TRIM5; the interaction causes activation of BECN1 by causing its dissociation from its inhibitors BCL2 and TAB2 (PubMed:25127057). Interacts with active ULK1 (phosphorylated on 'Ser-317') and MEFV simultaneously (PubMed:26347139). Interacts with WDR81 and WDR91; negatively regulates the PI3 kinase/PI3K activity associated with endosomal membranes (PubMed:26783301). Interacts with LAPTM4B; competes with EGFR for LAPTM4B binding; regulates EGFR activity (PubMed:28479384). Interacts with TRIM50 (PubMed:29604308). Interacts with TRIM16. Interacts with ATG14; this interaction is increased in the absence of TMEM39A (PubMed:31806350).SUBUNIT (Microbial infection) Interacts with human cytomegalovirus/HHV-5 protein TRS1.SUBUNIT (Microbial infection) Interacts with murine gammaherpesvirus 68 M11.SUBUNIT (Microbial infection) Interacts with herpes simplex virus 1 (HHV-1) protein ICP34.5; this interaction antagonizes the host autophagy response.TISSUE SPECIFICITY Ubiquitous.DOMAIN The coiled coil domain can form antiparallel homodimers and mediates dimerization with the coiled coil domains of ATG14 or UVRAG involved in the formation of PI3K complexes.DOMAIN The C-terminal evolutionary conserved domain (ECD) contains poly-Gln-binding domains such as the ATXN3 poly-Gln motif, consistent with structural docking models revealing two highly scored poly-Gln-binding pockets in the ECD (PubMed:28445460). As some binding is observed with BECN1 lacking the ECD, other domains of BECN1 may also interact with ATXN3 (PubMed:28445460).PTM Phosphorylation at Thr-119 by DAPK1 reduces its interaction with BCL2 and BCL2L1 and promotes induction of autophagy (PubMed:19180116). In response to autophagic stimuli, phosphorylated at serine residues by AMPK in an ATG14-dependent manner, and this phosphorylation is critical for maximally efficient autophagy (PubMed:23878393).PTM Polyubiquitinated by NEDD4, both with 'Lys-11'- and 'Lys-63'-linkages (PubMed:21936852). 'Lys-11'-linked polyubiquitination leads to degradation and is enhanced when the stabilizing interaction partner VPS34 is depleted (PubMed:21936852). Deubiquitinated by USP10 and USP13, leading to stabilize the PIK3C3/VPS34-containing complexes (PubMed:21962518). Polyubiquitinated at Lys-402 with 'Lys-48'-linkages (PubMed:28445460). 'Lys-48'-linked polyubiquitination of Lys-402 leads to degradation (PubMed:28445460). Deubiquitinated by ATXN3, leading to stabilization (PubMed:28445460).PTM Proteolytically processed by caspases including CASP8 and CASP3; the C-terminal fragments lack autophagy-inducing capacity and are proposed to induce apoptosis. Thus the cleavage is proposed to be an determinant to switch from autophagy to apoptosis pathways affecting cellular homeostasis including viral infections and survival of tumor cells.MISCELLANEOUS Expanded poly-Gln tracts inhibit ATXN3-BECN1 interaction, decrease BECN1 levels and impair starvation-induced autophagy (PubMed:28445460).SIMILARITY Belongs to the beclin family. UniProt Q14457 O-phospho-L-serine at 15 15 EQUAL O-phospho-L-serine [MOD:00046] 1 EQUAL 450 EQUAL Reactome DB_ID: 188010 1 UniProt:Q99570 PIK3R4 PIK3R4 PIK3R4 VPS15 FUNCTION Regulatory subunit of the PI3K complex that mediates formation of phosphatidylinositol 3-phosphate; different complex forms are believed to play a role in multiple membrane trafficking pathways: PI3KC3-C1 is involved in initiation of autophagosomes and PI3KC3-C2 in maturation of autophagosomes and endocytosis. Involved in regulation of degradative endocytic trafficking and cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123).SUBUNIT Component of the PI3K (PI3KC3/PI3K-III/class III phosphatidylinositol 3-kinase) complex the core of which is composed of the catalytic subunit PIK3C3, the regulatory subunit PIK3R4 and BECN1 associating with additional regulatory/auxilliary subunits to form alternative complex forms. Alternative complex forms containing a forth regulatory subunit in a mutually exclusive manner are PI3K complex I (PI3KC3-C1) containing ATG14, and PI3K complex II (PI3KC3-C2) containing UVRAG (PubMed:8999962, PubMed:19270696, PubMed:23878393, PubMed:25490155). PI3KC3-C1 displays a V-shaped architecture with PIK3R4 serving as a bridge between PIK3C3 and the ATG14:BECN1 subcomplex (PubMed:25490155). Both, PI3KC3-C1 and PI3KC3-C2, can associate with further regulatory subunits, such as RUBCN, SH3GLB1/Bif-1, AMBRA1 and NRBF2 (PubMed:19270696, PubMed:20643123, PubMed:24785657). PI3KC3-C1 probably associates with PIK3CB (By similarity). Interacts with RAB7A in the presence of PIK3C3/VPS34 (PubMed:14617358). Interacts with NRBF2 (PubMed:24785657).TISSUE SPECIFICITY Ubiquitously expressed.PTM Myristoylated.PTM Probably autophosphorylated.SIMILARITY Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. UniProt Q99570 2 EQUAL 1358 EQUAL Reactome DB_ID: 5679263 1 UniProt:Q6ZNE5 ATG14 ATG14 KIAA0831 ATG14 ATG14L FUNCTION Required for both basal and inducible autophagy. Determines the localization of the autophagy-specific PI3-kinase complex PI3KC3-C1 (PubMed:18843052, PubMed:19050071). Plays a role in autophagosome formation and MAP1LC3/LC3 conjugation to phosphatidylethanolamine (PubMed:19270696, PubMed:20713597). Promotes BECN1 translocation from the trans-Golgi network to autophagosomes (PubMed:20713597). Enhances PIK3C3 activity in a BECN1-dependent manner. Essential for the autophagy-dependent phosphorylation of BECN1 (PubMed:23878393). Stimulates the phosphorylation of BECN1, but suppresses the phosphorylation PIK3C3 by AMPK (PubMed:23878393). Binds to STX17-SNAP29 binary t-SNARE complex on autophagosomes and primes it for VAMP8 interaction to promote autophagosome-endolysosome fusion (PubMed:25686604). Modulates the hepatic lipid metabolism (By similarity).SUBUNIT Forms homooligomers; homo-oligomerization is essential for the roles in membrane tethering and enhancement of SNARE-mediated fusion (PubMed:25686604). Component of the PI3K (PI3KC3/PI3K-III/class III phosphatidylinositol 3-kinase) complex I (PI3KC3-C1) in which the core composed of the catalytic subunit PIK3C3, the regulatory subunit PIK3R4 and BECN1 is associated with ATG14 (PubMed:18843052, PubMed:19050071, PubMed:19270696, PubMed:22314358, PubMed:23878393). PI3KC3-C1 displays a V-shaped architecture with PIK3R4 serving as a bridge between PIK3C3 and the ATG14:BECN1 subcomplex (PubMed:25490155). PI3KC3-C1 can associate with further regulatory subunits. Interacts with PIK3CB (By similarity). Interacts (via coiled-coil domain) with BECN2 (via coiled-coil domain); this interaction is tighter than BECN2 self-association (PubMed:23954414, PubMed:28218432). Interacts with the STX17-SNAP29 binary t-SNARE complex (PubMed:25686604). Interacts with NRBF2 (By similarity). Interacts with PIK3C3 and BECN1; this interaction is increased in the absence of TMEM39A (PubMed:31806350). Interacts with STEEP1; the interaction is required for trafficking of STING1 from the endoplasmic reticulum (PubMed:32690950).DOMAIN The coiled-coil domain is required for BECN1- and PIK3C3-binding and for autophagy.DOMAIN The final 80 residues in the C-terminus define a minimum required region for autophagosome binding called BATS.DOMAIN The N-terminal cysteine repeats are required for proper localization to the endoplasmic reticulum.SIMILARITY Belongs to the ATG14 family. UniProt Q6ZNE5 1 EQUAL 492 EQUAL Reactome Database ID Release 79 5679242 Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5679242 Reactome R-HSA-5679242 1 Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=R-HSA-5679242.1 Reactome DB_ID: 5682393 1 phagophore assembly site membrane GO 0034045 ATG14:PIK3C3:PIK3R4:p-S15-BECN1 [phagophore assembly site membrane] ATG14:PIK3C3:PIK3R4:p-S15-BECN1 Autophagy-specific class III PI3K complex Beclin-1 complex Bakor:Vps34:Vps15:p-Beclin-1 Reactome DB_ID: 188011 1 1 EQUAL 887 EQUAL Reactome DB_ID: 5682391 1 O-phospho-L-serine at 15 15 EQUAL 1 EQUAL 450 EQUAL Reactome DB_ID: 5682389 1 1 EQUAL 492 EQUAL Reactome DB_ID: 188010 1 2 EQUAL 1358 EQUAL Reactome Database ID Release 79 5682393 Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5682393 Reactome R-HSA-5682393 2 Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=R-HSA-5682393.2 Reactome Database ID Release 79 5682385 Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5682385 Reactome R-HSA-5682385 6 Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=R-HSA-5682385.6 22456507 Pubmed 2012 Dynamic and transient interactions of Atg9 with autophagosomes, but not membrane integration, are required for autophagy Orsi, A Razi, M Dooley, H C Robinson, D Weston, A E Collinson, L M Tooze, S A Mol. Biol. Cell 23:1860-73 22826123 Pubmed 2012 Atg9 vesicles are an important membrane source during early steps of autophagosome formation Yamamoto, Hayashi Kakuta, Soichiro Watanabe, Tomonobu M Kitamura, Akira Sekito, Takayuki Kondo-Kakuta, Chika Ichikawa, Rie Kinjo, Masataka Ohsumi, Yoshinori J. Cell Biol. 198:219-33 20855505 Pubmed 2010 An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis Mari, Muriel Griffith, Janice Rieter, Ester Krishnappa, Lakshmi Klionsky, Daniel J Reggiori, Fulvio J. Cell Biol. 190:1005-22 24296784 Pubmed 2014 A current perspective of autophagosome biogenesis Shibutani, Shusaku T Yoshimori, Tamotsu Cell Res. 24:58-68 20811355 Pubmed 2010 The origin of the autophagosomal membrane Tooze, Sharon A Yoshimori, Tamotsu Nat. Cell Biol. 12:831-5 25568151 Pubmed 2015 Membrane dynamics in autophagosome biogenesis Carlsson, Sven R Simonsen, Anne J. Cell. Sci. 128:193-205 19898463 Pubmed 2009 A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation Hayashi-Nishino, Mitsuko Fujita, Naonobu Noda, Takeshi Yamaguchi, Akihito Yoshimori, Tamotsu Yamamoto, A Nat. Cell Biol. 11:1433-7 22613832 Pubmed 2012 TBC1D14 regulates autophagosome formation via Rab11- and ULK1-positive recycling endosomes Longatti, Andrea Lamb, Christopher A Razi, Minoo Yoshimura, Shin-ichiro Barr, Francis A Tooze, Sharon A J. Cell Biol. 197:659-75 24034251 Pubmed 2013 Diverse autophagosome membrane sources coalesce in recycling endosomes Puri, Claudia Renna, Maurizio Bento, Carla F Moreau, Kevin Rubinsztein, David C Cell 154:1285-99 23878278 Pubmed 2013 Membrane remodeling by the PX-BAR protein SNX18 promotes autophagosome formation Knævelsrud, Helene Søreng, Kristiane Raiborg, Camilla Håberg, Karin Rasmuson, Fredrik Brech, A Liestøl, Knut Rusten, Tor Erik Stenmark, H Neufeld, Thomas P Carlsson, Sven R Simonsen, Anne J. Cell Biol. 202:331-49 19855179 Pubmed 2009 3D tomography reveals connections between the phagophore and endoplasmic reticulum Ylä-Anttila, Päivi Vihinen, Helena Jokitalo, Eija Eskelinen, Eeva-Liisa Autophagy 5:1180-5 18725538 Pubmed 2008 Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum Axe, Elizabeth L Walker, Simon A Manifava, Maria Chandra, Priya Roderick, H Llewelyn Habermann, A Griffiths, Gareth Ktistakis, Nicholas T J. Cell Biol. 182:685-701 16940348 Pubmed 2006 Starvation and ULK1-dependent cycling of mammalian Atg9 between the TGN and endosomes Young, Andrew R J Chan, Edmond Y W Hu, Xiao Wen Köchl, Robert Crawshaw, Samuel G High, Stephen Hailey, Dale W Lippincott-Schwartz, Jennifer Tooze, Sharon A J. Cell. Sci. 119:3888-900 ACTIVATION Reactome Database ID Release 79 5692985 Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5692985 Reactome R-HSA-5692985 1 Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=R-HSA-5692985.1 Converted from EntitySet in Reactome Reactome DB_ID: 5671731 ATG9A,(ATG9B) [phagophore assembly site membrane] Converted from EntitySet in Reactome. Each synonym is a name of a PhysicalEntity, and each XREF points to one PhysicalEntity ATG9A [phagophore assembly site membrane] UniProt Q7Z3C6