PHALY

PHALY: Phagosome/Lysosome Fusion

 

 

 

• Name: Boris Steipe
• eMail: boris.steipe@utoronto.ca

 

Stage 1: The System seed

Name

Phagosome/Lysosome Fusion

Code

PHALY

Definition

Control and process of phagosome-lysosome docking and fusion.

Description

Phagosome-lysosome fusion is a key step in autophagy, the process in which a lysosome - a package of acidic, lytic enzymes - fuses to a phagosome that has enveloped some cargo, which is targeted for degradation and recycling. The fusion is a highly regulated process, involving the preparation of lipid microdomains, positioning of vesicles by dynein motors that move along the cytoskeleton, membrane anchored SNAREs that provide core docking functions, the facilitating CORVET, HOPS and BORC complexes, and precise regulation of fusion initiation at the protein level, the lipid level, and through the ionic context which involves calcium-selective voltage gated channels.

Seed term (Biological Process ontology)

• GO:0090385 (phagosome-lysosome fusion)

Relevant related terms(according to GO graph and co-occurring terms)

• GO:0001845 phagolysosome assembly (P) (Parent)
• GO:0090384 phagosome-lysosome docking (P) (Sibling)
• GO:0048278 vesicle docking (P) (Parent)
• GO:0031201 SNARE complex (C) (Co-occurring)
• GO:0000149 SNARE binding (F)(Co-occurring)
• GO:0005484 SNAP receptor activity (F) (co-occurring)
• GO:0090383 phagosome acidification (P) (co-occurring)

Initial associated human genes

• RAB7A
• RAB39A
• RAB34
• RAB20

 

Seven additional proteins are annotated to GO:0090385 in GOA, they were excluded from the seed-term table because their evidence codes indicated insufficient curation.

 

Seed literature

Corona & Jackson (2018) Finding the Middle Ground for Autophagic Fusion Requirements. Trends Cell Biol 28:869-881. (pmid: 30115558)

[ PubMed ] [ DOI ] Autophagosome/amphisome-lysosome fusion is a highly regulated process at the protein, lipid, and biochemical level. Each primary component of fusion, such as the core SNAREs, HOPS complex, or physical positioning by microtubule-associated dynein motors, are regulated at multiple points to ensure optimum conditions for autophagic flux to proceed. With the complexity of the membrane fusion system, it is not difficult to imagine how autophagic flux defect-related disorders, such as Huntington's disease, non-familial Alzheimer's disease, and Vici syndrome develop. Each membrane fusion step is regulated at the protein, lipid, and ion level. This review aims to discuss the recent developments toward understanding the regulation of autophagosome, amphisome, and lysosome fusion requirements for successful autophagic flux.

Zhi et al. (2018) Anatomy of autophagy: from the beginning to the end. Cell Mol Life Sci 75:815-831. (pmid: 28939950)

[ PubMed ] [ DOI ] Autophagy is a highly regulated process in eukaryotes to maintain homeostasis and manage stress responses. Understanding the regulatory mechanisms and key players involved in autophagy will provide critical insights into disease-related pathogenesis and potential clinical treatments. In this review, we describe the hallmark events involved in autophagy, from its initiation, to the final destruction of engulfed targets. Furthermore, based on structural and biochemical data, we evaluate the roles of key players in these processes and provide rationale as to how they control autophagic events in a highly ordered manner.

 

1b: First Sketch

A first sketch of a system architecture that represents components and behaviour in the PHALY system, based on information in two recent reviews.

 

1c: Observables

 

• Components
  • Literature curation
  • Annotation to relevant GO terms

• Collaborations
  • SMART interactions
  • Known complexes
    • SNAREs
    • HOPS Complex
    • BORC complex
  • Crystal structures

• Behaviour
  • autophagic flux
  • Mislocalization of components
  • genetic interactions
  • Vici syndrome (autosomal recessive EPG5 mutations)

 

Stage 2: Concepts

Concepts

Phagosome - lysosome fusion is the effector step of phagocytosis and (macro)autophagy.

The context of the PHALY system is defined as follows:

• Phagosome vesicles and lysosome vesicles have been produced and co-localized;
• The PHALY system docks the two vesicles and fuses their membranes;
• As a result, lysosome contents gets mixed into the phagosome and its contents is digested.

Fusion is effected by membrane anchored SNARE proteins (soluble NSF attachment protein receptors) in concert with tether complexes that are activated by Rab proteins. SNAREs are small, membrane-anchored, helical proteins that can assemble into four-helix bundles. Based on sequence motifs, SNARES are subdivided into Q-SNARES and R-SNARES. Since parts of the bundle are be located in a vesicle membrane, and other parts in a target membrane, formation of the bundle brings vesicle and target in close proximity. Thus SNAREs are functionally divided into v-SNARES (incoming vesicle, e.g. lysosome), and t-SNARES (target of the vesicle, e.g. phagosome). On the target side, we usually have three Q-SNARE motifs (Qabc); on the vesicle side we usually have a single R-SNARE.

SNAREs alone cannot support efficient fusion. Additional membrane tethers are provided by the HOPS, CORVET and BORC complexes. These complexes are highly regulated by Rab proteins.

Rab proteins are members of one of the five major families of the Ras superfamily (Ras, Rho, Ran, Rab and Arf). These small, homologous GTPases are molecular switches that are localized to specific membrane microdomains. There, they are turned on through a conformational change due to binding GTP, and turned off by hydrolyzing GTP to GDP. These functions are assisted by auxiliary proteins: GAPs (GTPase Activitating Proteins) activate the GTPase activity, thus leading to conversion of GTP to GDP which brings the protein to the off-state, GEF (Guanine nucleotide exchange factors) promote the realease of GDB, followed by binding of GTP which leads to the on-state. Each of the Ras family members has a distinct profile of roles in the cell. The Rab family proteins are predominantly associated with membrane-trafficking and vesicular transport. In the phagosome-lysosome fusion process, Rab proteins are specifically implicated in SNARE/tether protein assembly, and lipid-domain driven localization.

To ensure that the fusion happens at the right time in the right place, the system must include

• functions to synthesize and assemble the required components;
• localization elements that create a targetable environment and localize the required components in the right place;
• contact elements that bring all participants into close proximity;
• on-switches that trigger fusion;
• components that provide energy and/or metabolites to make fusion proceed against the unfavourable geometry of high-curvature membrane domains;
• off-switches that limit the fusion event - if this is not a self-limiting process;
• degradation and recycling functions.

 

Stage 3: Adding Genes

 

Components added from literature review

• '''CODE''' is the product of ENST12345. Notes. {{#pmid: <PMID>|LABEL}}.
• '''CODE''' is a component of ''CODE''. Notes. {{#pmid: <PMID>|LABEL}}.
• '''CODE.<Roman numeral>''' is a state defined by: (COMPONENT CODE.STATE) and [OWN STATE VARIABLE REALIZATION]. {{#pmid: <PMID>|LABEL}}.
• '''CODE.<Roman numeral>'''changes to (STATE) when [STATE VARIABLE CHANGE]. {{#pmid: <PMID>|LABEL}}.

It is useful to start by collecting facts that are broken down to relate to one single component each. Summarizing knowledge in structured free-text helps parse the facts to enter them into a common data model. The sentence prototype is:

'''COMPONENT''' [SYMBOL] (NAME) is a component of ''SYSTEM''. NOTES. {{#pmid: <PMID>|LABEL}}.

Make special note of genes that are NOT in your system, even though they are homologous to system components or interact with components.

 

Preparing the phagosome

 

• The autophagosome is a component of the PHALY system. Fusion is the process of joining the outer phagosomal membrane of the autophagosome with the membrane of a lysosome. The outer autophagosomal membrane (OAM) and the inner autophagosomal membrane (IAM) form by membrane fission after closure of the phagosomal sac.
• The OAM (outer autophagosomal membrane) is a component of the autophagosome system. The outer autophagosomal membrane (OAM) forms by membrane fission after closure of the phagosomal sac.
• The IAM (inner autophagosomal membrane) is a component of the autophagosome system. The inner autophagosomal membrane (IAM) forms by membrane fission after closure of the phagosomal sac. The IAM is degraded after lysosomal fusion and degradation of the IAM leads to immediate dissociation of STX17 from the cis-SNARE complex.
• LC3-II is a component of the autophagosome. LC3-II (PE lipidated LC3) has been conjugated to the PE-enriched phagosome membrane and thereby serves as phagosome marker. The LC3-II conjugate is produced by the Atg8 conjugation system (Atg7, Atg3, Atg5, Atg12, Atg16L1/2, Atg4A/B/C/D). Priming of the Atg8 conjugation system requires the Atg12 conjugating system (Atg12, Atg5, Atg7, Atg10)
• LC3 [MAP1LC3A] (microtubule associated protein 1 light chain 3 alpha) is a component of LC3-II. LC3 is a member of the Atg8 protein family. LC3 is a cytosolic protein that is conjugated to PE in the PE-enriched phagosome membrane in a stress response. Conjugation of LC3 and PE involves a ubiquitin-like conjugation system.
• PE (phosphatidylethanolamine) is a component of LC3-II. PE is the lipid anchor of LC3 in the phagosome membrane.
• The SNAP29-STX17 Qabc-SNARE is a component of the SNAP29-STX17-VAMP8 SNARE-pin. The SNAP29-STX17 Qabc-SNARE forms through the interaction of SNAP29 and STX17 in the phagosome membrane.
• SNAP29 [SNAP29] (synaptosome associated protein 29) is a component of the SNAP29-STX17 Qabc-SNARE. SNAP29 is a Qa-SNARE (a t-SNARE) that localizes to the membrane in a lipidation independent manner through its STX17 interaction. SNAP29 is held in a non-interacting state by O-GlcNAcylation with GlcNAC.
• GlcNAC (N-acetyl-glucosamine) is a component of the PHALY system. O-GlcNAcylation of SNAP29 in nutrient-sufficient conditions inhibits the association of the SNAP29-STX17 Qabc-SNARE. SNAP29 is O-GlcNAcylated by the promiscuous OGT (UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase) under nutrient-sufficient conditions and thus links the nutrient status sensing system with autophagic flux. SNAP29 has its O-GlcNAcetylation reversed by the N-acetyl-β-glucosaminidase OGA (O-GlcNAcase).
• STX17 [STX17] (Syntaxin 17) is a component of the SNAP29-STX17 Qabc-SNARE. STX17 is a Qa-SNARE which localizes to the phagosome by binding the phagosome membrane marker LC3-II via its LC3-interacting region (LIR). STX17 phosporylation on S2 is a key decision point for fusion to proceed; dephosphorylation relieves an inhibitory interaction with VPS33A and the phosphomimetic S2E mutant cannot form a SNARE bundle. STX17 has two glycine-zipper motif transmembrane domains that are required for membrane insertion.
• LAMP2 [LAMP2] (lysosomal associated membrane protein 2) is a component of the PHALY system. LAMP2 is an integral membrane protein. The LAMP-2A isoform has a lysosomal targeting signature sequence. The presence of LAMP2 is required for the binding of STX17.
• IRGM [IRGM] (immunity related GTPase M) is a component of the PHALY system. IRGM forms a complex (an autophagosome recognition particle, ARP) with STX17 and the Atg8 homologues LC3 and GABARAPL1 that is responsible for phagosomal targeting of STX17. IRGM does not directly bind LC3. IRGM's active conformation is GTP bound. IRGM also has a role in autophagy initiation complexes, binding BECLIN1, ULK1 and ATG16L1, which is indpendent of STX17 binding.
• RAB7 [RAB7A] (RAB7A, member RAS oncogene family) is a component of the PHALY system. RAB7 is a small GTPase that replaces RAB5 in maturing endosomes. RAB7 localization to the membrane requires prenylation. RAB7 is held in an inactive, soluble state by GDI (ARHGDIA), this interaction - and membrane recruitment - is released by the Mon1-CCZ1 complex. RAB7 is activated on the phagosome by the Mon1-CCZ1 GEF complex which localizes to the phagosome by Atg8 homologue protein binding. RAB7 can be localized to the lysosome by interaction with active lysosomal proton pumping vacuolar-type ATPase (V-ATPase). Inits active conformation, RAB7 can bind RILP to promote minus-end directed microtubular transport of the lysosome towards the MTOC.
• Mon1-CCZ1 (Mon1-CCZ1 GEF complex) is a component of the PHALY system. The Mon1-CCZ1 GEF complex is a GEF that activates Rab7 by exchanging bound GDP (inactive form) to GTP (active form). It is found on both phagosome and lysosome membranes.

• MON1A [MON1A] (MON1 homolog A, secretory trafficking associated) is a component of the Mon1-CCZ1 system. MON1A is one of two proteins in the heterooligomeric Mon1-CCZ1 GEF complex.
• CCZ1 [CCZ1] (CCZ1 homolog, vacuolar protein trafficking and biogenesis associated) is a component of the Mon1-CCZ1 system. CCZ1 is one of two proteins in the heterooligomeric Mon1-CCZ1 GEF complex.

• GABARAPL1 [GABARAPL1] (GABA type A receptor associated protein like 1) is a component of the PHALY system. GABARAPL1 is a ubiquitin-like modifier that binds to the Mon1-CCZ1 GEF complex and localizes it to the autophagosome. As a yeast Atg8 family homologue (like LC3), GABARAPL1 is a downstream effector of the mTOR pathway. Lipidation by phosphatidylethanolamine causes it to be enriched in the autophagosome membrane, where it serves as a scaffold to recruit other proteins to the membrane.
• EPG5 [EPG5] (ectopic P-granules autophagy protein 5 homolog) is a component of the PHALY. EPG5 is a RAB7 effector that localizes to both the phagosome and the lysosome by RAB7 binding, and binds to and enhances the SNAP29-STX17 Qabc-SNARE, thus facilitating VAMP8 binding. Binding of EPG5 shifts STX17 affinity from SNAP25 (without EPG5) to SNAP29 (with EPG5). EPG5 mutations cause Vici syndrome.

 

Preparing the lysosome

 

• The lysosome is a component of the PHALY system. Fusion is the process of joining the outer phagosomal membrane of the phagosome with the membrane of a lysosome.
• LAMP1 [LAMP1] (lysosomal associated membrane protein 1) is a component of the lysosome. LAMP1 is an integral membrane protein that is a lysosomal marker.
• VAMP8 [VAMP8] (vesicle associated membrane protein) is a component of the SNAP29-STX17-VAMP8 SNARE-pin. VAMP8 is a component of the lysosome membrane. VAMP8 is the single v-SNARE (an R-SNARE) that is recruited into the Qabc-SNARE complex for fusion. This SNARE "pairing" forms a membrane-bridging trans-SNARE complex, the SNAP29-STX17-VAMP8 SNAREpin. Localization of VAMP8 to the lysosome is dependent on active RAB21. RAB21 activation by SBF2 (a guanine nucleotide exchange factor for GTPases) under starvation conditions is an interface to nutrient sensing.
• VAMP7 [VAMP7] (vesicle associated membrane protein 7) is a component of the lysosome. The v-SNARE VAMP7 has been considered to be characteristic of secretory lysosomes, i.e. not PHALY. However, VAMP7 interacts with the VPS33A domain of HOPS complex and has been found to be able to initiate fusion with the SNAP29-STX17 Qabc-SNARE by FRET. VAMP7 is part of the SNARE-pin with STX4 and SNAP23 in secretory lysosomes. VAMP7 has an autoinhibitory longin domain that VAMP8 does not have.

 

Tether Proteins and Docking

 

• The SNAP29-STX17-VAMP8 SNARE-pin is a component of the PHALY system. Binding of the SNAP29-STX17 Qabc-SNARE with VAMP8 forms the initial SNAP29-STX17-VAMP8 SNARE-pin which bridges the phagosome and the lysosome. This trans-SNARE complex (membrane bridging) is the fusion initiator which ultimately leads to "zippering" - membrane apposition, lipid mixing, pore-formation, membrane bilayer fusion, which results in the formation of the cis-SNARE complex (inserted into a single membrane), and bringing the cis-SNARE pin into a alpha-SNAP binding competent conformation.
• ATG14 [ATG14] (Barkor, beclin 1-associated autophagy-related key regulator) is a component of the PIK3C3 complex. ATG14 stimulates BECN1 phosphorylation. ATG14 regulates the PIK3C3 complex.. ATG14 binds to and stabilizes the SNAP29-STX17 Qabc-SNARE on the membrane. ATG14 homooligomers have a membrane-tethering function via their BATS domains (Barkor autophagosome targeting sequence), which is enhanced in membranes with low curvature and high PI(3)P.
• The HOPS complex (homotypic fusion and protein sorting complex) is a component of the PHALY system. The HOPS complex is a hexa-heterooligomeric membrane tethering complex (MTC complex) that bridges two membranes containing RAB7 molecules in active conformation. It bridges vesicle and target membranes via its Rab7 binding domains and acts as a SNARE chaperone via a SNARE binding domain. It is the major "clamping" factor in SNARE mediated fusion. The chaperoning function is crucial for topologically correct assembly of the trans-SNARE-pin, and prevention of reassembly of a cis-SNARE complex after SNARE disassembly by NSF-SNAP. The BORC complex recruits the HOPS complex to the lysosomal membrane. The BORC complex functions by interacting with kinesins and determining the position of the lysosome by regulating the balance of (+)-end and (-)-end microtubular transport. One of its effectors is Arl8. The BORC complex comprises BLOC1S1, BLOC1S2, SNAPIN, KXD1, BORCS5, BORCS6, BORCS7, and BORCS8.

• VPS16 [VPS16] (VPS16 core subunit of CORVET and HOPS complexes) is a component of the HOPS complex. VPS16 (Vacuolar Protein Sorting) is one of the four subunits that are common to the HOPS complex and the CORVET complex. It provides part of the SNARE-pin interaction interface.
• VPS33A [VPS33A] (VPS33A core subunit of CORVET and HOPS complexes) is a component of the HOPS complex. VPS33 (Vacuolar Protein Sorting) is one of the four subunits that are common to the HOPS complex and the CORVET complex. It provides part of the SNARE-pin interaction interface. VPS33A is an SM protein (Sec1/Munc18 protein) which stabilizes the nascent SNARE bundle by interacting with both v-SNARES and t-SNARES. VPS33A interacts with a "closed form of STX17.
• VPS18 [VPS18] (VPS18 core subunit of CORVET and HOPS complexes) is a component of the HOPS complex. VPS18 (Vacuolar Protein Sorting) is one of the four subunits that are common to the HOPS complex and the CORVET complex. It does not interact with the SNARE-pin.
• VPS11 [VPS11] (VPS18 core subunit of CORVET and HOPS complexes) is a component of the HOPS complex. VPS11 (Vacuolar Protein Sorting) is one of the four subunits that are common to the HOPS complex and the CORVET complex. It does not interact with the SNARE-pin.
• VPS41 [VPS41] (VPS41 subunit of HOPS complex) is a component of the HOPS complex. VPS41 (Vacuolar Protein Sorting) is one of the two subunits that are specific to the HOPS complex. It provides one of two Rab7 interaction interfaces.
• VPS39 [VPS39] (VPS39 subunit of HOPS complex) is a component of the HOPS complex. VPS39 (Vacuolar Protein Sorting) is one of the two subunits that are specific to the HOPS complex. It provides one of two Rab7 interaction interfaces.

 

Lipids

 

• lipid rafts are a component of the PHALY system. Lipid rafts are required for autophagic flux and play a role in the fusion event.

• cholesterol is a component of lipid rafts. Cholesterol provides specific binding domains and increases membrane thickness and stiffness.

• OSBPL1A [OSBPL1A] (Oxysterol binding protein like 1A) is a component of the PHALY system. OSBPL1A is a RAB7-GTP effector. In active form it interacts with cholesterol in lipd rafts through its ORD domain. This interaction recruits PLEKHM1 and through it the HOPS complex. In the absence of cholesterol, OSBPL1A interacts with VAPA via its FFAT domain. This inhibits PLEKHM1 binding to RAB7, whereupon PLEKHM1 and RILP recruit HOPS complex. The ER-bound VAPA protein can be bound by OSBPL1A via its FFAT domain.This interaction creates contact sites between the ER and the phagosome, which inhibits membrane tethers, microtubular transport, and stalls the fusion process.
• The PIK3C3 complex (RUBCNL-UVRAG–BECN1,2–PIK3C3 complex) is a component of the PHALY system. The PIK3C3 complex creates phosphoinositide-3-phosphate at the phagosome-lysosome fusion site. It integrates a number of general (GPCR) signalling pathways.

• PIK3C3 [PIK3C3] (phosphatidylinositol 3-kinase catalytic subunit type 3) is a component of the PIK3C3 complex. PIK3C3 (also: Vps34) produces phosphatidylinositol-3-phosphate (PI(3)P) from PI.
• UVRAG [UVRAG] (UV radiation resistance associated) is a component of the PIK3C3 complex. UVRAG increases RAB7 concentration in maturing endosomes. It provides an interface to the MTORC1 complex: phosporylation of UVRAG by MTORC1 causes it to sequester with RUBCN, away from the HOPS complex.
• NRBF2 [NRBF2] (nuclear receptor binding factor 2) is a component of the PIK3C3 complex. NRBF2 inhibts PIK3C3 activity and thus reduces PI(3)P levels.
• PIK3R4 [PIK3R4] (phosphoinositide-3-kinase regulatory subunit 4) is a component of the PIK3C3 complex. PK3R4 (also called Vps15) is a protein kinase that regulates PIK3C3.
• RUBCN [RUBCN] (rubicon autophagy regulator) is a component of the PIK3C3 complex. RUBCN sequesters UVRAG away from the HOPS complex.
• RUBCNL [RUBCNL] (rubicon like autophagy enhancer) is a component of the PIK3C3 complex. RUBCNL (Pacer, protein associated with UVRAG as autophagy enhancer) releases UVRAG from RUBCN.. RUBCNL also anchors PI3KC3 as well as HOPS to STX17. Its phosphorylation by mTORC1 integrates the mTOR pathway (active mTOR shuts down RUBCNL enhancement of the system); its acetylation by TIP60 integrates the GSK3-TIP60 pathway.
• BECN1 [BECN1] (Beclin 1) is a component of the PIK3C3 complex. BECN1 (Beclin1) is a core component of the RUBCNL-UVRAG–BECN1,2–PIK3C3 complex. Phosphorylation of BECN1 is stimulated by ATG14.
• PLEKHM1 [PLEKHM1] (pleckstrin homology and RUN domain containing M1) is a component of the PIK3C3 complex. PLEKHM1 (Pleckstrin homology domain-containing family M member 1) is a multivalent adaptor that enhances HOPS complex / LC3 (Atg8) interactions in a RAB7 dependent way.
• PI(3)P (phosphatidylinositol-3-phosphate) is a component of the PIK3C3 complex. PI(3)P interfaces with many signalling pathways. It is produced at the phagosome by PIK3C3 in the PIK3C3 complex, and is further phosphorylated to PI(3,5)P by PIKfyve after dissociation of PIK3C3. Degradation of PI(3)P to PI on phagosomes reduces autophagy.

• INPP5E [INPP5E] (inositol polyphosphate-5-phosphatase E) is a component of the PHALY system. INPP5E decreases lysosomal phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) and increases PI(3)P and is required for the fusion event. Both an excess and a reduction of the PI(3)P to PI(3,5)P2 ratio inhibits fusion.
• The PIKFYVE complex (PIKFYVE complex) is a component of the PHALY system. The PIKFYVE complex controls PI(3,5)P2 levels and consists of PIKFYVE, FIG4, VAC14 (ArPIKfyve), and WIPI1.

• PIKFYVE [PIKFYVE] (phosphoinositide kinase, FYVE-type zinc finger containing) is a component of the PIKFYVE complex. PIKFYVE phosphorylates PI(3)P to PI(3,5)P2. Both an excess and a reduction of the PI(3)P to PI(3,5)P2 ratio inhibits fusion.
• PI(3,5)P2 (phosphatidylinositol-3,5-bisphosphate) is a component of the PIKFYVE complex. (PI(3,5)P2) is produced by the action of PIKFYVE on PI3P. PI(3,5)P2 counteracts cortactin mediated actin filament stabilization on lysosomes; actin on the lysosome surface is required for fusion.

 

Cytoskeleton

 

• The RAB7-RILP-dynein-dynactin complex (RAB7-RILP-dynein-dynactin complex) is a component of the PHALY system. The RAB7-RILP-dynein-dynactin complex is responsible for minus-end transport of lysosomes along microtubules towards the MTOC, where most lysosomes are located.
• RILP [RILP] (Rab interacting lysosomal protein) is a component of the RAB7-RILP-dynein-dynactin complex. RILP associates with RAB7-GTP; the complex promotes dynein-dynactin association with the membrane and subsequent transport.
• An F-actin network (actin filament network) is a component of the PHALY system. A cortactin dependent, remodelled, local filamentous actin network between the phagosome and the lysosome promotes fusion.

• CTTN [CTTN] (cortactin) is a component of the F-actin network. CTTN is a branch-stabilizing interactor that remodels the F-actin network, which is a fusion requirement by recruiting the ARP2/3 complex to the fusion site.
• HDAC6 [HDAC6] (histone deacetylase 6) is a component of the F-actin network. HDAC6, a ubiquitin binding deacylase, recruits CTTN to the autophagosome.
• ARP2/3 complex (ARP2/3 complex) is a component of the F-actin network. The actin-nucleator ARP2/3 complex is a seven-subunit complex that can nucleate actin-filament branchpoints to establish a network. It stimulates the local assembly of an F-actin network for efficient fusion. It consists of ARP2, ARP3, ARPC1, ARPC2, ARPC3, ARPC4, and ARPC5.
• F-actin (filamentous actin) is a component of the F-actin network. F-actin is a filament of ACTB (G-actin) monomers which is a scaffold for myosin-motors like the fusion-promoting MYO1C myosin to move on.
• ACTB [ACTB] (actin beta) is a component of F-actin. The cytoplasmic, soluble globular G-actin polymerizes in to a filamentous form: F-actin.
• MYO1C [MYO1C] (myosin 1C) is a component of the F-actin network. MYO1C is a monomeric class I myosin, which associates with cholesterol lipid rafts. It contains a PH domain that binds specifically to PI(4,5)P2. It is a "slow" motor, ideal for translocating heavy cargos, not tethering, and thus is able to move lipid rafts from storage compartments to their site of action.
• PI(4,5)P2 (phosphatidylinositol-4,5-bisphosphate) is a component of the F-actin network. PI(4,5)P2 clusters at lipid rafts in a cholesterol and Ca2+ dependent fashion. These clusters bind the ARP2/3 complex.

 

Ion regulation

 

• Ca2+ (calcium ion) is a component of the PHALY system. Ca2+ is required to stabilize the SNAREpin.
• CACNA1A [CACNA1A] (Voltage-dependent P/Q-type calcium channel subunit alpha-1A) is a component of the PHALY system. The lysosome resident population of voltage-gated calcium channel CACNA1A is required for calcium efflux from the lysosome for the fusion event.

 

Fusion mechanism

 

• A SNAREpin team is a component of the PHALY system. From three to six SNAP29-STX17-VAMP8 SNARE-pins form a mechanically coupled SNAREpin team in a rigid membrane (cholesterol lipid-raft) which accelerates fusion by four orders of magnitude.

 

Disassembly and recycling

 

• The 20s supercomplex is a component of the PHALY system. The 20s supercomplex forms around the cis-SNARE complex, by binding two to four molecules of alpha-SNAP and an NSF homohexamer to the cis-SNARE-pin.
• alpha-SNAP [NAPA] (NSF attachment protein alpha) is a component of the 20s supercomplex. Two to four molecules of cytoplasmic alpha-SNAP wrap around the cis-SNARE-pin to form a SNAP-SNARE subcomplex.
• NSF [NSF] (N-ethylmaleimide sensitive factor) is a component of the 20s supercomplex. NSF is a cytoplasmic AAA+ ATPase that binds to the SNAP-SNARE subcomplex in an ATP-bound state. Subsequent ATP hydrolysis induces major conformational rearrangements of NSF that disassociate the SNARE-pin into individual constituent molecules. Nucleotide exchange presumably disassociates the remaining NSF-SNAP subcomplex, and allows the cycle to restart.
• TBC1D2 [TBC1D2] (TBC1 domain family member 2A) is a component of the PHALY system. TBC1D2 (Armus) is a RAB7 specific GAP that activates hydrolysis of RAB7 bound GTP to GDP and thus catalyzes conversion of RAB7 to its inactive state.

 

Not in the system

 

• NOT IN PHALY are genes that are not in the PHALY system. "NOT IN PHALY" genes are related to PHALY system components, but are demonstrably not part of PHALY. Genes that are NOT IN PHALY would need to be present in the cell even if the cell did not have a PHALY system.

• VTI1B [VTI1B] (vesicle transport through interaction with t-SNAREs 1B) is NOT IN PHALY. The t-SNARE VTI1B may work in a pathway that is parallel to STX17, in pathogen containing autophagosomes or recycling endosomes.
• STX6 [STX6] (syntaxin 6) is NOT IN PHALY. The t-SNARE STX6 is the interaction partner of VTI1B.
• VAMP3 [VAMP3] (vesicle associated membrane protein 3) is NOT IN PHALY. The v-SNARE VAMP3 forms a SNAREpin with the VTI1B-STX6 complex.

 

Since each of the facts above relates to only one component of the system, they can be imported into an Excel spreadsheet that supports the systems data model. Code is in text2tsv.R on the GitHub repository.

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Parallel and/or specialized pathways ...

• YKT6 may work in a pathway that is parallell to STX17.

Open questions ...

• Which phospatase dephosphorylates the STX17 N-terminal S2 in the VPS33A complex to switch STX17 into a fusion-competent interaction with HOPS complex? This appears to be a key checkpoint.

 

System hierachy

The Excel spreadsheet has the system and subsystem hierarchy stored in a systemComponent join table. Code to represent this is a tree is in excel2tree.R on the GitHub repository.

 

 --PHALY
   |__20s supercomplex
      |__alpha-SNAP
      |__NSF
   |__autophagosome
      |__IAM
      |__LC3-II
         |__LC3
         |__PE
      |__OAM
   |__Ca2+
   |__CACNA1A
   |__EPG5
   |__F-actin network
      |__ARP2/3 complex
      |__CTTN
      |__F-actin
         |__ACTB
      |__HDAC6
      |__MYO1C
      |__PI(4,5)P2
   |__GABARAPL1
   |__GlcNAC
   |__HOPS complex
      |__VPS11
      |__VPS16
      |__VPS18
      |__VPS33A
      |__VPS39
      |__VPS41
   |__INPP5E
   |__IRGM
   |__LAMP2
   |__lipid rafts
      |__cholesterol
   |__lysosome
      |__LAMP1
      |__VAMP7
   |__Mon1-CCZ1
      |__CCZ1
      |__MON1A
   |__NOT IN PHALY
      |__STX6
      |__VAMP3
      |__VTI1B
   |__OSBPL1A
   |__PIK3C3 complex
      |__ATG14
      |__BECN1
      |__NRBF2
      |__PI(3)P
      |__PIK3C3
      |__PIK3R4
      |__PLEKHM1
      |__RUBCN
      |__RUBCNL
      |__UVRAG
   |__PIKFYVE complex
      |__PI(3,5)P2
      |__PIKFYVE
   |__RAB7
   |__RAB7-RILP-dynein-dynactin complex
      |__RILP
   |__SNAP29-STX17-VAMP8 SNARE-pin
      |__SNAP29-STX17 Qabc-SNARE
         |__SNAP29
         |__STX17
      |__VAMP8
   |__SNAREpin team
   |__TBC1D2

 

Genes added from direct annotation

It is useful to collect links to gene information via the HGNC resource. Code to generate Wikitext for a table with linked information is in text2annotationLinks.R on the GitHub repository.

 

This includes genes discovered because they have been annotated with a relationship to the system, in a database such as UniProt, NCBI-Protein or any of the three GO ontologies represented in GOA (GO annotations).

LC3-II

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
MAP1LC3A	microtubule associated protein 1 light chain 3 alpha	Q9H492	ENSG00000101460	uc002xaq.3	84557	MAP1LC3A

 

SNAP29-STX17 Qabc-SNARE

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
SNAP29	synaptosome associated protein 29	O95721	ENSG00000099940	uc011ahw.3	9342	SNAP29
STX17	Syntaxin 17	P56962	ENSG00000136874	uc004bal.5	55014	STX17

 

PHALY

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
LAMP2	lysosomal associated membrane protein 2	P13473	ENSG00000005893	uc004ess.5	3920	LAMP2
IRGM	immunity related GTPase M	A1A4Y4	ENSG00000237693	uc010jhk.3	345611	IRGM
RAB7A	RAB7A, member RAS oncogene family	P51149	ENSG00000075785	uc003eks.2	7879	RAB7A
GABARAPL1	GABA type A receptor associated protein like 1	Q9H0R8	ENSG00000139112	uc001qxs.4	23710	GABARAPL1
EPG5	ectopic P-granules autophagy protein 5 homolog	Q9HCE0	ENSG00000152223	uc002lbm.4	57724	EPG5
OSBPL1A	Oxysterol binding protein like 1A	Q9BXW6	ENSG00000141447	uc002kve.5	114876	OSBPL1A
INPP5E	inositol polyphosphate-5-phosphatase E	Q9NRR6	ENSG00000148384	uc004cho.4	56623	INPP5E
CACNA1A	Voltage-dependent P/Q-type calcium channel subunit alpha-1A	O00555	ENSG00000141837	uc002mwy.5	773	CACNA1A
TBC1D2	TBC1 domain family member 2A	Q9BYX2	ENSG00000095383	uc011lvb.3	55357	TBC1D2

 

Mon1-CCZ1

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
MON1A	MON1 homolog A, secretory trafficking associated	Q86VX9	ENSG00000164077	uc003cxz.4	84315	MON1A
CCZ1	CCZ1 homolog, vacuolar protein trafficking and biogenesis associated	P86791	ENSG00000122674	uc003spf.4	51622	CCZ1

 

lysosome

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
LAMP1	lysosomal associated membrane protein 1	P11279	ENSG00000185896	uc001vtm.2	3916	LAMP1
VAMP7	vesicle associated membrane protein 7	P51809	ENSG00000124333	uc004fxj.4	6845	VAMP7

 

SNAP29-STX17-VAMP8 SNARE-pin

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
VAMP8	vesicle associated membrane protein	Q9BV40	ENSG00000118640	uc002spt.5	8673	VAMP8

 

PIK3C3 complex

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
ATG14	Barkor, beclin 1-associated autophagy-related key regulator	Q6ZNE5	ENSG00000126775	uc001xbx.3	22863	ATG14
PIK3C3	phosphatidylinositol 3-kinase catalytic subunit type 3	Q8NEB9	ENSG00000078142	uc002lap.4	5289	PIK3C3
UVRAG	UV radiation resistance associated	Q9P2Y5	ENSG00000198382	uc001oxc.4	7405	UVRAG
NRBF2	nuclear receptor binding factor 2	Q96F24	ENSG00000148572	uc001jmj.6	29982	NRBF2
PIK3R4	phosphoinositide-3-kinase regulatory subunit 4	Q99570	ENSG00000196455	uc003enj.4	30849	PIK3R4
RUBCN	rubicon autophagy regulator	Q92622	ENSG00000145016	NA	9711	RUBCN
RUBCNL	rubicon like autophagy enhancer	Q9H714	ENSG00000102445	uc001vbi.6	80183	RUBCNL
BECN1	Beclin 1	Q14457	ENSG00000126581	uc002ibn.3	8678	BECN1
PLEKHM1	pleckstrin homology and RUN domain containing M1	Q9Y4G2	ENSG00000225190	uc002ija.4	9842	PLEKHM1

 

HOPS complex

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
VPS16	VPS16 core subunit of CORVET and HOPS complexes	Q9H269	ENSG00000215305	uc002whe.5	64601	VPS16
VPS33A	VPS33A core subunit of CORVET and HOPS complexes	Q96AX1	ENSG00000139719	uc001ucd.4	65082	VPS33A
VPS18	VPS18 core subunit of CORVET and HOPS complexes	Q9P253	ENSG00000104142	uc001zne.3	57617	VPS18
VPS11	VPS18 core subunit of CORVET and HOPS complexes	Q9H270	ENSG00000160695	uc058iep.1	55823	VPS11
VPS41	VPS41 subunit of HOPS complex	P49754	ENSG00000006715	uc003tgy.4	27072	VPS41
VPS39	VPS39 subunit of HOPS complex	Q96JC1	ENSG00000166887	uc001zpc.4	23339	VPS39

 

PIKFYVE complex

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
PIKFYVE	phosphoinositide kinase, FYVE-type zinc finger containing	Q9Y2I7	ENSG00000115020	uc002vcz.3	200576	PIKFYVE

 

RAB7-RILP-dynein-dynactin complex

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
RILP	Rab interacting lysosomal protein	Q96NA2	ENSG00000167705	uc002ftd.4	83547	RILP

 

F-actin network

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
CTTN	cortactin	Q14247	ENSG00000085733	uc001opw.5	2017	CTTN
HDAC6	histone deacetylase 6	Q9UBN7	ENSG00000094631	uc004dks.2	10013	HDAC6
MYO1C	myosin 1C	O00159	ENSG00000197879	uc002fso.4	4641	MYO1C

 

F-actin

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
ACTB	actin beta	P60709	ENSG00000075624	uc003sot.5	60	ACTB

 

20s supercomplex

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
NAPA	NSF attachment protein alpha	P54920	ENSG00000105402	uc002pha.3	8775	NAPA
NSF	N-ethylmaleimide sensitive factor	P46459	ENSG00000073969	uc002iku.4	4905	NSF

 

NOT IN PHALY

 

Symbol	Name	UniProt	ensembl	UCSC	NCBI gene	AmiGO
VTI1B	vesicle transport through interaction with t-SNAREs 1B	Q9UEU0	ENSG00000100568	uc001xjt.4	10490	VTI1B
STX6	syntaxin 6	O43752	ENSG00000135823	uc021pfr.3	10228	STX6
VAMP3	vesicle associated membrane protein 3	Q15836	ENSG00000049245	uc001aol.3	9341	VAMP3

 

New gene facts:

When we collect new gene facts from databases, we need to be able to annotate the source of a fact, independent of whether it has a pmid. I created a template for this purpose: {{DB|<database>|<ID>}}. For now, it only lists the database, but it will be straightforward to have the template create an actual hyperlink to the record - for a select set of databases.text2tsv.R on the GitHub repository has been modified accordingly.

 

• ATG13 [ATG13] (autophagy related 13) is a component of the ULK1 complex. Mutations in LC3 can destroy ATG13 interactions and reduce autophagosome formation. (UniProt:Q9H492) ATG13 interacts with LC3 via its LIR (LC3-interacting region). ATG13 is a member of the ULK1 complex which consists of ULK1 (formerly Atg1, unc-51 like autophagy activating kinase 1), ATG13, RB1CC1 (formerly Atg17 / FIP200, RB1 inducible coiled-coil 1), and ATG101. The Atg1 complex is activated under stress conditions by TORC1 and PKA.
• The ULK1 complex is a component of the autophagosome. The ULK1 complex integrates a large number of cellular systems: the mTOR pathway, AMPK as an effector of AMP homeostasis, growth factor pathways acting via TIP60, genotoxic stress response via PPM1D, protein biosynthesis, and response attenuation during prolonged starvation via the cullin E3 ligase .
• MAP1LC3B [MAP1LC3B] (microtubule associated protein 1 light chain 3 beta) is a component of the LC3-II system. LC3 beta and gamma are functionally equivalent homologues of MAP1LC3A (UCSC:uc002xaq.3).
• MAP1LC3C [MAP1LC3C] (microtubule associated protein 1 light chain 3 gamma) is a component of the LC3-II system. LC3 beta and gamma are functionally equivalent homologues of MAP1LC3A (UCSC:uc002xaq.3).
• SNAP23 [SNAP23] (synaptosome associated protein 23) is NOT IN PHALY. SNAP23 is a t-SNARE for general membrane fusion. (UniProt:O00161)
• SNAP25 [SNAP25] (synaptosome associated protein 25) is NOT IN PHALY. SNAP25 is a t-SNARE involved in neurotransmitter release at the synapse. (UniProt:P61266)
• STX1A [STX1A] (syntaxin 1A) is NOT IN PHALY. STX1A is involved in hormone and neurotransmitter exocytosis. (UniProt:Q16623)
• STX1B [STX1B] (syntaxin 1B) is NOT IN PHALY. STX1B is involved in docking of synaptic vesicles at presynaptic active zones. (UniProt:Q16623)
• STX2 [STX2] (syntaxin 2) is NOT IN PHALY. STX2 is essential for epithelial morphogenesis. (UniProt:P32856)
• STX3 [STX3] (syntaxin 3) is NOT IN PHALY. STX3 is involved in docking of synaptic vesicles at presynaptic active zones. (UniProt:Q13277)
• STX4 [STX4] (syntaxin 4) is NOT IN PHALY. STX3 is a plasma mebrane t-SNARE that is involved in docking of transport vesicles. (UniProt:Q12846)
• STX6 [STX6] (syntaxin 6) is NOT IN PHALY. STX6 is essential involved in vesicle trafficking. (UniProt:O43752)
• STX7 [STX7] (syntaxin 7) is NOT IN PHALY. STX7 is involved in homotypic fusion of endocytic organelles. (UniProt:O15400)
• STX8 [STX8] (syntaxin 8) is NOT IN PHALY. STX8 is involved in early-secretory retrograde transport. (UniProt:Q9UNK0)
• STX10 [STX10] (syntaxin 10) is NOT IN PHALY. STX10 is involved in vesicular transport from the late endosomes to the trans-Golgi network. (UniProt:O60499)
• STX11 [STX11] (syntaxin 11) is NOT IN PHALY. STX11 acts between the late endosome and the trans-Golgi network. (UniProt:O75558)
• STX12 [STX12] (syntaxin 12) is NOT IN PHALY. STX12 acts between the late endosome and the trans-Golgi network. (UniProt:Q86Y82)
• STX16 [STX16] (syntaxin 16) is NOT IN PHALY. STX16 is a t-SNARE localized to the trans-Golgi network. (UniProt:O14662)
• STX18 [STX18] (syntaxin 18) is NOT IN PHALY. STX18 is a SNARE that is involved in Golgi-derived retrograde transport vesicles. (UniProt:Q9P2W9)
• STX19 [STX19] (syntaxin 19) is NOT IN PHALY. STX19 is involved in in endosomal trafficking of the epidermal growth factor receptor (EGFR). (UniProt:Q8N4C7)

 

Genes added from network annotation

This includes genes discovered in the network neighbourhood of system components, in a database like STRING or IntAct, or in pathways such as KEGG or Reactome.

New gene facts

• SEC22B [SEC22B] (SEC22 homolog B, vesicle trafficking protein) is NOT IN PHALY. SEC22B is a high-confidence interactor in STRING, but it is a SNARE that is involved in retrograde transport from the Golgi to the ER. (UniProt:O75396)
• ATG4A [ATG4A] (autophagy related 4A cysteine peptidase) is a component of LC3-II. ATG4 proteins play a role in Atg8 protein PTM (priming for lipidation) and in delipidation for phagosome disassembly. (KEGG:hsa04140)
• ATG4B [ATG4B] (autophagy related 4B cysteine peptidase) is a component of LC3-II. ATG4 proteins play a role in Atg8 protein PTM (priming for lipidation) and in delipidation for phagosome disassembly. (KEGG:hsa04140)
• ATG4C [ATG4C] (autophagy related 4C cysteine peptidase) is a component of LC3-II. ATG4 proteins play a role in Atg8 protein PTM (priming for lipidation) and in delipidation for phagosome disassembly. (KEGG:hsa04140)
• ATG4D [ATG4D] (autophagy related 4D cysteine peptidase) is a component of LC3-II. ATG4 proteins play a role in Atg8 protein PTM (priming for lipidation) and in delipidation for phagosome disassembly. (KEGG:hsa04140)

 

Genes added from phenotype and behaviour

This includes genes annotated to a related phenotype in OMIM or the GWAS catalog.

 

Completing the Role Ontology

...

 

System Architecture

Sketch a system architecture.

 

System data

Format the system data for import into a system database. Details TBD.

 

---

JSON formatted data ...  (click to expand)

{"parameter":[{
"ID":"dame.left-7a1-9ff7-2582-3b5a-b2094984aaa2",
"typeID":"chop.cool-4d3-8407-c9d2-0b38-5b069be72da0",
"value":"2.1.1"}],

"type":[{
"ID":"chop.cool-4d3-8407-c9d2-0b38-5b069be72da0",
"name":"DBversion",
"description":"Version of the systems database schema",
"validation":"^\\\\d+\\\\.\\\\d+\\\\.\\\\d+$"
},
{
"ID":"suit.tang-e32-67a8-4e32-1abb-c9e75ce1f2c1",
"name":"componentType",
"description":"Type of the component: atomic or composed",
"validation":"^(atomic)|(composed)$"
},
{
"ID":"cash.mare-ecf-5799-0f92-19ce-514bce3b5276",
"name":"molType",
"description":"The type of an atomic component",
"validation":"^(protein)|(RNA)|(lipid)|(metabolite)|(concept)|(other)$"
},
{
"ID":"wail.help-74b-baea-9c82-2adb-86e613d00ea2",
"name":"xRefUniProt",
"description":"Cross-reference UniProt KB ID",
"validation":"^UniProt:[0-9A-Z_]+$"
},
{
"ID":"coup.thus-73e-1292-0442-a97f-825167430bb5",
"name":"xRefENST",
"description":"Cross-reference Ensembl Transcript ID",
"validation":"^ENST:\\\\d+$"
},
{
"ID":"when.lute-8f9-b1e1-0ce2-1bd7-e861591869fb",
"name":"xRefENSE",
"description":"Cross-reference Ensembl Exon ID",
"validation":"^ENSE:\\\\d+$"
},
{
"ID":"gems.bird-2b4-0370-b092-da6f-a1ca41435587",
"name":"xRefENSG",
"description":"Cross-reference Ensembl Gene ID",
"validation":"^ENSG:\\\\d+$"
},
{
"ID":"time.barn-768-97b6-7962-684c-6cbd7d366979",
"name":"xRefENSP",
"description":"Cross-reference Ensembl Protein ID",
"validation":"^ENSP:\\\\d+$"
},
{
"ID":"warm.mate-bad-125f-a2a2-4b13-edefc11e1df0",
"name":"xRefPMID",
"description":"PubMed ID",
"validation":"^PMID:\\\\d+$"
},
{
"ID":"ribs.bolt-da3-5f2e-3ae2-5940-0b361a01abff",
"name":"xRefHGNC",
"description":"HGNC symbol",
"validation":"^HGNC:.+$"
},
{
"ID":"know.palm-46d-6143-b892-184d-0d3a420d31db",
"name":"xRefRefSeq",
"description":"RefSeq ID",
"validation":"^RefSeq:.._\\\\d+(\\\\.\\\\d+)?$"
},
{
"ID":"mall.case-f26-4df1-e892-9b70-380b2672a009",
"name":"xRefUCSC",
"description":"UCSC ID",
"validation":"^UCSC:uc[0-9a-z]+(\\\\.\\\\d+)?$"
},
{
"ID":"cork.span-2a0-f809-4182-49e2-2b3ce58c8710",
"name":"xRefNCBIgene",
"description":"NCBI gene ID",
"validation":"^gene:\\\\d+$"
},
{
"ID":"coat.curl-eab-3beb-e8e2-4aae-5e0f2235619c",
"name":"xRefOMIM",
"description":"OMIM ID",
"validation":"^OMIM:\\\\d+$"
},
{
"ID":"logs.nice-b29-62f6-c1d2-29f4-87bdb7e996ab",
"name":"xRefPDB",
"description":"PDB ID with optional chain separated with \".\" or \"_\"",
"validation":"^PDB:[0-9][0-9A-Za-z]{3}([\\\\._][0-9A-Za-z])?$"
},
{
"ID":"snow.gram-8a2-cb70-96e2-daba-61933e196c9b",
"name":"genericNote",
"description":"Free-text annotation of an entity",
"validation":".+"
},
{
"ID":"pure.heal-c14-7e5a-65b2-ebbe-d822be29e26c",
"name":"historyNote",
"description":"Information on a superseded entity",
"validation":".+"
},
{
"ID":"seat.fate-150-9459-c452-3a15-98518ebcd683",
"name":"geneType",
"description":"Gene  type as defined by HGNC",
"validation":"^(immunoglobulin)|(lncRNA)|(miRNA)|(protein)|(protocadherin)|(RNA, cluster)|(RNA, misc)|(rRNA)|(scRNA)|(snoRNA)|(snRNA)|(TCR)|(tRNA)|(vtRNA)|(Y RNA)$"}],

"system":[{
"ID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"code":"PHALY",
"name":"Phagosome/Lysosome Fusion",
"def":"control and process of phagosome-lysosome docking and fusion.",
"description":"Phagosome-lysosome fusion is a key step in autophagy, the process in which a lysosome - a package of acidic, lytic enzymes - fuses to a phagosome that has enveloped some cargo, which is targeted for degradation and recycling. The fusion is a highly regulated process, involving the preparation of lipid microdomains, positioning of vesicles by dynein motors that move along the cytoskeleton, membrane anchored SNAREs that provide core docking functions, the facilitating CORVET, HOPS and BORC complexes, and precise regulation of fusion initiation at the protein level, the lipid level, and through the ionic context which involves calcium-selective voltage gated channels."
},
{
"ID":"skin.toll-8ab-a5d2-1202-eaf0-807d897969f0",
"code":"autophagosome",
"name":"autophagosome",
"def":"a phagosome that sequesters cell-internal material",
"description":"Autophagosomes digest cell-internal material for general maintenance and under nutrient stress conditions."
},
{
"ID":"rail.skid-d47-002b-68c2-0847-551c3015d524",
"code":"LC3-II",
"name":"LC3-II",
"def":"lipidated LC3",
"description":"Prenylated LC3 is membrane resident on phagosomes and lysosomes."
},
{
"ID":"stab.base-4c7-4edd-25d2-4bcc-4086ee82a3a7",
"code":"SNAP29-STX17 Qabc-SNARE",
"name":"SNAP29-STX17 Qabc-SNARE",
"def":"t-snare bundle",
"description":"Contains three of the four required helices on the target side."
},
{
"ID":"verb.wade-b97-7197-f292-bb4c-56a9ab1a5add",
"code":"Mon1-CCZ1",
"name":"Mon1-CCZ1 GEF complex",
"def":"GEF for Rab7",
"description":"Activates Rab7 by catalyzing the GDP-GTP exchange"
},
{
"ID":"pump.trap-67f-eb22-c5d2-4a6e-68673cb5afa3",
"code":"ULK1 complex",
"name":"ULK1 complex",
"def":"heterotrimeric nutrient status sensor complex",
"description":"The ULK1 complex integrates a large number of cellular systems: the mTOR pathway, AMPK as an effector of AMP homeostasis, growth factor pathways acting via TIP60, genotoxic stress response via PPM1D, protein biosynthesis, and response attenuation during prolonged starvation via the cullin E3 ligase."
},
{
"ID":"pant.balm-93f-c169-d342-a8fe-d88028fb890a",
"code":"lysosome",
"name":"lysosome",
"def":"a vesicle that contains acidic, lytic enzymes",
"description":"The cargo of the lysosome is evacuated into the phagosome after fusion and digests the phagosome's contents."
},
{
"ID":"root.boys-359-f424-0572-4bcd-19d6ff64c741",
"code":"SNAP29-STX17-VAMP8 SNARE-pin",
"name":"SNAP29-STX17-VAMP8 SNARE-pin",
"def":"four-helix bundle SNARE",
"description":"The SNARE pin is a trans-SNARE complex as it juxtaposes the membranes to be fused, and turns into a cis-SNARE complex after fusion."
},
{
"ID":"tier.dash-c42-4c22-ad72-6b4b-bfe470e4455f",
"code":"STX17bound",
"name":"Syntaxin 17 (membrane bound)",
"def":"Syntaxin 17 (membrane bound)",
"description":"Membrane bound form of the Q-SNARE syntaxin 17"
},
{
"ID":"deed.mead-d34-551d-1f82-4a65-a5cc8b9e745a",
"code":"RAB7active",
"name":"RAB7 (active)",
"def":"active, membrane bound RAB7",
"description":"The active (GTP bound) form of RAB7, prenylated and membrane bound."
},
{
"ID":"give.need-232-ddd4-b342-aaf0-041e2b87062a",
"code":"HOPS complex",
"name":"homotypic fusion and protein sorting complex",
"def":"a hexa-heterooligomeric membrane tethering complex (MTC complex)",
"description":"A tethering complex that bridges phagosome and lysosome via RAB7 and functions as a SNAREpin chaperone."
},
{
"ID":"stab.belt-ff1-c9fc-dcc2-da67-06c44a8d9005",
"code":"lipid rafts",
"name":"lipid rafts",
"def":"cholesterol enriched membrane subdomains",
"description":"Lipid raft subdomains are cholesterol rich patches in membranes that are foci of signalling activity."
},
{
"ID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"code":"PIK3C3 complex",
"name":"RUBCNL-UVRAG–BECN1,2–PIK3C3 complex",
"def":"PIK3C3 complex",
"description":"The PIK3C3 kinase complex creates phosphoinositide-3-phosphate at the phagosome-lysosome fusion site."
},
{
"ID":"rock.tend-392-4e0a-ae42-5a96-6ffdead1df8f",
"code":"PIKFYVE complex",
"name":"PIKFYVE complex",
"def":"PI(3)P-5 kinase",
"description":"PIKFYVE phosphorylates PI(3)P to PI(3,5)P2. Both an excess and a reduction of the PI(3)P to PI(3,5)P2 ratio inhibits fusion"
},
{
"ID":"fear.lead-daa-76b4-b832-29f8-48cb624ea900",
"code":"RAB7-RILP-dynein-dynactin complex",
"name":"RAB7-RILP-dynein-dynactin complex",
"def":"vesicle-cytoskeleton connector",
"description":"The RAB7-RILP-dynein-dynactin complex is responsible for minus-end transport of lysosomes along microtubules towards the MTOC, where most lysosomes are located."
},
{
"ID":"lull.slab-be7-27e1-df72-2959-b42fa71d83b2",
"code":"F-actin network",
"name":"actin filament network",
"def":"actin network",
"description":"A network of branched actin filaments. The branch points are constituted from the Arp2/3 complex."
},
{
"ID":"doll.fawn-529-099c-6462-fb0b-9ec626eef6a5",
"code":"F-actin",
"name":"filamentous actin",
"def":"actin filament",
"description":"F-actin is a filament that forms by polymerization of actin monomers."
},
{
"ID":"owls.gear-304-36d5-ff92-1913-0de755710d35",
"code":"20s supercomplex",
"name":"20s supercomplex",
"def":"SNARE unfoldase",
"description":"The 20s supercomplex forms around the cis-SNARE complex, by binding two to four molecules of alpha-SNAP and an NSF homohexamer to the cis-SNARE-pin"
},
{
"ID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"code":"NOT IN PHALY",
"name":"NOT IN PHALY",
"def":"External to PHALY",
"description":"Genes that are members of PHALY component protein families and/or interact with PHALY components but are not themselves a part of PHALY."}],

"systemComponent":[{
"ID":"bolt.bell-e18-2ff6-4872-58a9-2a619b9b335f",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"brew.main-b5c-4427-17f2-0a43-015f4f9486d1",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"input",
"notes":"Fusion is the process of joining the outer phagosomal membrane of the autophagosome  with the membrane of a lysosome (pmid:30115558).  The outer autophagosomal membrane (OAM) and the inner autophagosomal membrane (IAM) form by membrane fission after closure of the phagosomal sac (pmid:27885029)."
},
{
"ID":"rain.jade-116-4fc4-1ef2-aa6e-4d14417ef305",
"systemID":"skin.toll-8ab-a5d2-1202-eaf0-807d897969f0",
"componentID":"mild.spur-d4f-1dd4-3642-7ad1-b93e4b1b6357",
"evidenceType":"TAS",
"evidenceSource":"27885029",
"role":"location",
"notes":"The outer autophagosomal membrane (OAM) forms by membrane fission after closure of the phagosomal sac (pmid:27885029)."
},
{
"ID":"fuel.wool-319-ef94-b862-eb48-2e57de0d2b47",
"systemID":"skin.toll-8ab-a5d2-1202-eaf0-807d897969f0",
"componentID":"wolf.make-780-f3f4-2e42-781c-e985b856e937",
"evidenceType":"TAS",
"evidenceSource":"27885029",
"role":"location",
"notes":"The inner autophagosomal membrane (IAM) forms by membrane fission after closure of the phagosomal sac (pmid:27885029).  The IAM is degraded after lysosomal fusion and degradation of the IAM leads to immediate dissociation of STX17 from the cis-SNARE complex (pmid:27885029)."
},
{
"ID":"look.bred-be7-3c6c-4fe2-d9b7-828f6da0b6a4",
"systemID":"skin.toll-8ab-a5d2-1202-eaf0-807d897969f0",
"componentID":"calf.pane-5b5-127b-b3c2-b931-c79d4f9ded09",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"attachment",
"notes":"LC3-II (PE lipidated LC3) has been conjugated to the PE-enriched phagosome membrane and thereby serves as phagosome marker (pmid:30115558).  The LC3-II conjugate is produced by the Atg8 conjugation system (Atg7, Atg3, Atg5, Atg12, Atg16L1/2, Atg4A/B/C/D) (pmid:28939950).  Priming of the Atg8 conjugation system requires the Atg12 conjugating system (Atg12, Atg5, Atg7, Atg10) (pmid:28939950)."
},
{
"ID":"thin.meal-c1c-b556-3692-484b-e997f431469c",
"systemID":"rail.skid-d47-002b-68c2-0847-551c3015d524",
"componentID":"isle.gait-a82-1ff7-70b2-e810-fd2dd3c1c465",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"input",
"notes":"LC3 is a cytosolic protein that is conjugated to PE in the PE-enriched phagosome membrane in a stress response (pmid:30115558).  Conjugation of LC3 and PE involves a ubiquitin-like conjugation system (pmid:27146966)."
},
{
"ID":"gown.sign-01f-02b0-3ba2-fbbb-e443703bf2a3",
"systemID":"rail.skid-d47-002b-68c2-0847-551c3015d524",
"componentID":"stag.teas-702-efa2-8822-b9ae-4f7a179fa9c9",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"input",
"notes":"PE is the lipid anchor of LC3 in the phagosome membrane (pmid:30115558)."
},
{
"ID":"mink.foam-636-25ad-11e2-2bcf-c68dec8d56a1",
"systemID":"rail.skid-d47-002b-68c2-0847-551c3015d524",
"componentID":"gust.mice-439-a46b-71c2-1900-8fc7723c07bb",
"evidenceType":"TAS",
"evidenceSource":"KEGG:hsa04140",
"role":"transform",
"notes":"ATG4 proteins play a role in Atg8 protein PTM (priming for lipidation) and in delipidation for phagosome disassembly (KEGG:hsa04140}}"
},
{
"ID":"junk.each-74f-4b53-1612-3ae6-364828533626",
"systemID":"rail.skid-d47-002b-68c2-0847-551c3015d524",
"componentID":"core.crib-900-34d7-f252-1ae6-8593125d7d3f",
"evidenceType":"TAS",
"evidenceSource":"KEGG:hsa04140",
"role":"transform",
"notes":"ATG4 proteins play a role in Atg8 protein PTM (priming for lipidation) and in delipidation for phagosome disassembly (KEGG:hsa04140}}"
},
{
"ID":"silk.sock-773-5629-56f2-6a05-8512e3eb0f10",
"systemID":"rail.skid-d47-002b-68c2-0847-551c3015d524",
"componentID":"gang.sent-e39-e249-c2d2-8b56-3af299a9b19b",
"evidenceType":"TAS",
"evidenceSource":"KEGG:hsa04140",
"role":"transform",
"notes":"ATG4 proteins play a role in Atg8 protein PTM (priming for lipidation) and in delipidation for phagosome disassembly (KEGG:hsa04140}}"
},
{
"ID":"bark.mill-04f-e103-2702-3a18-e97e38c68767",
"systemID":"rail.skid-d47-002b-68c2-0847-551c3015d524",
"componentID":"bees.lone-c40-a77c-63b2-fafd-8486b1adf5c5",
"evidenceType":"TAS",
"evidenceSource":"KEGG:hsa04140",
"role":"transform",
"notes":"ATG4 proteins play a role in Atg8 protein PTM (priming for lipidation) and in delipidation for phagosome disassembly (KEGG:hsa04140}}"
},
{
"ID":"been.high-d45-3ffa-e232-b81e-afa6836a3187",
"systemID":"root.boys-359-f424-0572-4bcd-19d6ff64c741",
"componentID":"sign.bids-877-06f5-69c2-5a0f-ba6f1df4aca4",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"The SNAP29-STX17 Qabc-SNARE forms through the interaction of SNAP29 and STX17 in the phagosome membrane (pmid:30115558)."
},
{
"ID":"cult.moth-86e-fe5a-6c62-aaf7-8b864dad06ca",
"systemID":"stab.base-4c7-4edd-25d2-4bcc-4086ee82a3a7",
"componentID":"june.seas-24d-971c-f512-5826-33052e1e0ae3",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"SNAP29 is a Qa-SNARE (a t-SNARE) that localizes to the membrane in a lipidation independent manner through its STX17 interaction (pmid:30115558).  SNAP29 is held in a non-interacting state by O-GlcNAcylation with GlcNAC (pmid:25419848)."
},
{
"ID":"span.page-579-16b1-ffd2-3a0d-e19723671a57",
"systemID":"stab.base-4c7-4edd-25d2-4bcc-4086ee82a3a7",
"componentID":"sets.lips-81d-d3de-fce2-caf7-5b4393b8ea4b",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"prevent",
"notes":"O-GlcNAcylation of SNAP29 in nutrient-sufficient conditions inhibits the association of the SNAP29-STX17 Qabc-SNARE (pmid:30115558).  SNAP29 is O-GlcNAcylated by the promiscuous OGT (UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase) under nutrient-sufficient conditions and thus links the nutrient status sensing system with autophagic flux (pmid:25419848).  SNAP29 has its  O-GlcNAcetylation reversed by the N-acetyl-β-glucosaminidase OGA (O-GlcNAcase) (pmid:25419848)."
},
{
"ID":"laud.harm-f98-b9c9-11d2-0b43-fffda60215d6",
"systemID":"stab.base-4c7-4edd-25d2-4bcc-4086ee82a3a7",
"componentID":"mess.seal-1e4-158a-0e72-d8d5-ad944aaff957",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"Bound STX17 phosporylation on S2 is a key decision point for fusion to proceed; dephosphorylation relieves an inhibitory interaction with VPS33A and the phosphomimetic S2E mutant cannot form a SNARE bundle (pmid:30655294). STX17 has two glycine-zipper motif transmembrane domains that are required for membrane insertion (pmid:29420192)."
},
{
"ID":"prod.hemp-625-854e-4f92-f977-d044f65e6f66",
"systemID":"tier.dash-c42-4c22-ad72-6b4b-bfe470e4455f",
"componentID":"prod.bins-b67-7850-fca2-5bd0-9e214caf67c0",
"evidenceType":"TAS",
"evidenceSource":"29420192",
"role":"transform",
"notes":"STX17 is a Qa-SNARE which localizes to the phagosome by binding the phagosome membrane marker LC3-II via its LC3-interacting region (LIR) (pmid:30115558)."
},
{
"ID":"laud.chip-973-093d-4d12-b9f3-1248d590702d",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"pond.none-227-a5f6-2cc2-5ab0-f3d38b36d2a4",
"evidenceType":"TAS",
"evidenceSource":"27628032",
"role":"attachment",
"notes":"LAMP2 is an integral membrane protein. The LAMP-2A isoform has a lysosomal targeting signature sequence. The presence of LAMP2 is required for the binding  of STX17 (pmid:27628032)."
},
{
"ID":"mink.chin-b99-c186-d312-fa24-f951db653fd4",
"systemID":"tier.dash-c42-4c22-ad72-6b4b-bfe470e4455f",
"componentID":"stir.lids-10a-c2ff-94f2-88fe-cc259492b58b",
"evidenceType":"TAS",
"evidenceSource":"29420192",
"role":"prepare",
"notes":"IRGM forms a complex (an autophagosome recognition particle, ARP) with STX17 and the Atg8 homologues LC3 and GABARAPL1 that is responsible for phagosomal targeting of STX17. IRGM does not directly bind LC3. IRGM's active conformation is GTP bound. IRGM also has a role in autophagy initiation complexes, binding BECLIN1, ULK1 and ATG16L1, which is independent of STX17 binding (pmid:29420192)."
},
{
"ID":"sigh.food-1f7-1717-03b2-3baf-10ea36c3b372",
"systemID":"skin.toll-8ab-a5d2-1202-eaf0-807d897969f0",
"componentID":"reel.gull-3a8-71d1-6212-e9ec-fb252ff13105",
"evidenceType":"TAS",
"evidenceSource":"23645161",
"role":"attachment",
"notes":"RAB7 is a small GTPase that replaces RAB5 in maturing endosomes (pmid:23645161). RAB7 localization to the membrane requires '''prenylation''' (pmid:30115558).  RAB7 is held in an inactive, soluble state by GDI (ARHGDIA), this interaction - and membrane recruitment - is released by the Mon1-CCZ1 complex (pmid:30333976).  RAB7 is activated on the phagosome by the Mon1-CCZ1 GEF complex which localizes to the phagosome by Atg8 homologue protein binding (pmid:30115558)."
},
{
"ID":"poll.hope-4b2-7d07-4e52-884f-c2340590b760",
"systemID":"pant.balm-93f-c169-d342-a8fe-d88028fb890a",
"componentID":"reel.gull-3a8-71d1-6212-e9ec-fb252ff13105",
"evidenceType":"TAS",
"evidenceSource":"23645161",
"role":"attachment",
"notes":"RAB7 can be localized to the lysosome by interaction with active lysosomal proton pumping vacuolar-type ATPase (V-ATPase) (pmid:30717974).  In its active conformation, RAB7 can bind RILP to promote minus-end directed microtubular transport of the lysosome towards the MTOC (pmid:12944476)."
},
{
"ID":"keen.harm-699-f354-7dd2-6bf9-2df5c77c7076",
"systemID":"deed.mead-d34-551d-1f82-4a65-a5cc8b9e745a",
"componentID":"file.mime-4bf-2cfd-6e62-49f6-e5b1aefa698a",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"transform",
"notes":"The Mon1-CCZ1 GEF complex is a GEF that activates Rab7 by exchanging bound GDP (inactive form) to GTP (active form) (pmid:30115558).  It is found on both phagosome and lysosome membranes (pmid:30333976)."
},
{
"ID":"knot.dash-94f-dc9b-8252-5978-d3e1cfe76787",
"systemID":"verb.wade-b97-7197-f292-bb4c-56a9ab1a5add",
"componentID":"sage.wood-e9a-5934-c9d2-6aab-dca28ae194ba",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"MON1A is one of two proteins in the heterooligomeric Mon1-CCZ1 GEF complex (pmid:30115558)."
},
{
"ID":"dash.fool-60e-3441-5382-9ab7-f6f6c48c0d1f",
"systemID":"verb.wade-b97-7197-f292-bb4c-56a9ab1a5add",
"componentID":"knit.hiss-047-86fb-e0f2-4ad9-ebafcff9269d",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"CCZ1 is one of two proteins in the heterooligomeric Mon1-CCZ1 GEF complex (pmid:30115558)."
},
{
"ID":"kept.wigs-cef-5af9-38a2-d940-cb36fe33efaa",
"systemID":"verb.wade-b97-7197-f292-bb4c-56a9ab1a5add",
"componentID":"webs.laud-453-0049-6f12-59d2-c55101ab383b",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"localize",
"notes":"GABARAPL1 is a ubiquitin-like modifier that binds to the Mon1-CCZ1 GEF complex and localizes it to the autophagosome (pmid:30115558).  As a yeast Atg8 family homologue (like LC3), GABARAPL1 is a downstream effector of the mTOR pathway. Lipidation by phosphatidylethanolamine causes it to be enriched in the autophagosome membrane, where it serves as a scaffold to recruit other proteins to the membrane (pmid:30767700)."
},
{
"ID":"fail.camp-c66-f461-7382-a97d-c55140164ab9",
"systemID":"stab.base-4c7-4edd-25d2-4bcc-4086ee82a3a7",
"componentID":"wipe.bulk-ac5-33c4-a422-992b-15bbadd61344",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"enhance",
"notes":"EPG5 is a RAB7 effector that localizes to both the phagosome and the lysosome by RAB7 binding, and binds to and enhances the SNAP29-STX17 Qabc-SNARE, thus facilitating VAMP8 binding. Binding of EPG5 shifts STX17 affinity from SNAP25 (without EPG5) to SNAP29 (with EPG5). EPG5 mutations cause Vici syndrome (pmid:30115558)."
},
{
"ID":"vent.pane-a87-3e42-c542-b814-e5931d3c7e04",
"systemID":"pump.trap-67f-eb22-c5d2-4a6e-68673cb5afa3",
"componentID":"cage.back-649-14d7-fc22-58c5-21db5c35a36f",
"evidenceType":"TAS",
"evidenceSource":"24290141",
"role":"compose",
"notes":"Mutations in LC3 can destroy ATG13 interactions and reduce autophagosome formation (UniProt:Q9H492}}  ATG13 interacts with LC3 via its LIR (LC3-interacting region) (pmid:24290141).  ATG13 is a member of the ULK1 complex which consists of ULK1 (formerly Atg1, unc-51 like autophagy activating kinase 1), ATG13, RB1CC1 (formerly Atg17 / FIP200, RB1 inducible coiled-coil 1), and ATG101 (pmid:24290141)."
},
{
"ID":"spin.seam-e1a-ac2b-0332-69d5-3fc0ad54b43b",
"systemID":"skin.toll-8ab-a5d2-1202-eaf0-807d897969f0",
"componentID":"safe.bent-d50-883d-efc2-c947-81c5fc7d0fde",
"evidenceType":"TAS",
"evidenceSource":"24290141",
"role":"transform",
"notes":"The ULK1 complex consists of ULK1 (formerly Atg1, unc-51 like autophagy activating kinase 1), ATG13, RB1CC1 (formerly Atg17 / FIP200, RB1 inducible coiled-coil 1), and ATG101 (pmid:24290141). The ULK1 complex integrates a large number of cellular systems: the mTOR pathway, AMPK as an effector of AMP homeostasis, growth factor pathways acting via TIP60, genotoxic stress response via PPM1D, protein biosynthesis, and response attenuation during prolonged starvation via the cullin E3 ligase (pmid:29233870).  The ULK1 complex is activated under stress conditions  by TORC1 and PKA, it is thus a sensor of nutrient signals that activates autophagy (pmid:24290141)."
},
{
"ID":"barn.live-4fe-7833-6702-2acb-a43a8dfbd622",
"systemID":"rail.skid-d47-002b-68c2-0847-551c3015d524",
"componentID":"grog.cold-1e7-3859-a5e2-e917-bc2c0001dad2",
"evidenceType":"TAS",
"evidenceSource":"UCSC:uc002xaq.3",
"role":"input",
"notes":"LC3 beta and gamma are functionally equivalent homologues of MAP1LC3A (UCSC:uc002xaq.3}}."
},
{
"ID":"rich.make-64b-cd9e-97c2-585c-5da155a6e05d",
"systemID":"rail.skid-d47-002b-68c2-0847-551c3015d524",
"componentID":"wasp.deal-c61-5011-f0b2-6b87-b52b5f0c7b44",
"evidenceType":"TAS",
"evidenceSource":"UCSC:uc002xaq.3",
"role":"input",
"notes":"LC3 beta and gamma are functionally equivalent homologues of MAP1LC3A (UCSC:uc002xaq.3}}."
},
{
"ID":"harp.peek-c1b-2c35-54f2-e9a3-3c3330b418d1",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"flip.glad-f50-9299-e452-8978-24620d230bdc",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"input",
"notes":"Fusion is the process of joining the outer phagosomal membrane of the phagosome with the membrane of a lysosome (pmid:30115558)."
},
{
"ID":"fine.urge-c89-006b-e822-fa5a-8510ff8201ba",
"systemID":"pant.balm-93f-c169-d342-a8fe-d88028fb890a",
"componentID":"harp.thaw-f3d-f0e0-0622-0b87-ffc3a9aef0e2",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"attachment",
"notes":"LAMP1 is an integral membrane protein that is a lysosomal marker (pmid:30115558)."
},
{
"ID":"fast.clay-29f-fef8-d7c2-5b33-0b07d578df97",
"systemID":"root.boys-359-f424-0572-4bcd-19d6ff64c741",
"componentID":"toes.rods-c61-ca74-9b72-ca0c-96cfe2a82869",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"VAMP8 is a component of the lysosome membrane. VAMP8 is the single v-SNARE (an R-SNARE) that is recruited into the Qabc-SNARE complex for fusion. This SNARE \"pairing\" forms a membrane-bridging trans-SNARE complex, the SNAP29-STX17-VAMP8 SNAREpin. Localization of VAMP8 to the lysosome is dependent on active RAB21 (pmid:30115558). RAB21 activation by SBF2 (a guanine nucleotide exchange factor for GTPases) under starvation conditions is an interface to nutrient sensing (pmid:25648148)."
},
{
"ID":"roar.golf-fec-1919-dc82-1a9e-f976fa4d8011",
"systemID":"pant.balm-93f-c169-d342-a8fe-d88028fb890a",
"componentID":"cave.gull-aac-32e6-43a2-4975-812d31591dfa",
"evidenceType":"TAS",
"evidenceSource":"30240735",
"role":"compose",
"notes":"The v-SNARE VAMP7 has been considered to be characteristic of secretory lysosomes, i.e. not PHALY (pmid:30240735).  However, VAMP7 interacts with the VPS33A domain of HOPS complex and has been found to be able to initiate fusion with the SNAP29-STX17 Qabc-SNARE by FRET (pmid:30655294).  VAMP7 is part of the SNARE-pin with STX4 and SNAP23 in secretory lysosomes (pmid:28471021).  VAMP7 has an autoinhibitory longin domain that VAMP8 does not have (pmid:26567219)."
},
{
"ID":"bids.mane-e66-dd34-a102-3889-a8b1f9bf3937",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"cone.nail-78b-a797-60a2-1a71-4b6973f63bfa",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"integrate",
"notes":"Binding of the SNAP29-STX17 Qabc-SNARE with VAMP8 forms the initial SNAP29-STX17-VAMP8 SNARE-pin which bridges the phagosome and the lysosome.  This trans-SNARE complex (membrane bridging) is the fusion initiator which ultimately leads to \"zippering\" - membrane apposition, lipid mixing, pore-formation, membrane bilayer fusion, which results in the formation of the cis-SNARE complex (inserted into a single membrane), and bringing the cis-SNARE pin into a alpha-SNAP binding competent conformation (pmid:30115558).  (pmid:25581794)."
},
{
"ID":"pint.free-64c-6e51-c3f2-69b5-11e5e9bae248",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"coat.dean-37b-7c8c-b692-581e-548b259def46",
"evidenceType":"TAS",
"evidenceSource":"23878393",
"role":"transform",
"notes":"ATG14 stimulates BECN1 phosphorylation (pmid:23878393).  ATG14 regulates the PIK3C3 complex (pmid:25686604). ATG14 binds to and stabilizes the SNAP29-STX17 Qabc-SNARE on the membrane (pmid:25686604).  ATG14 homooligomers have a membrane-tethering function via their BATS domains (Barkor autophagosome targeting sequence), which is enhanced in membranes with low curvature and high PI(3)P (pmid:25686604)."
},
{
"ID":"mode.ants-6b8-b09c-1b82-19fa-99f37c57d40c",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"hits.kite-345-8536-8682-8aa8-5da04b7a4ff8",
"evidenceType":"TAS",
"evidenceSource":"23645161",
"role":"locate",
"notes":"The HOPS complex is a hexa-heterooligomeric membrane tethering complex (MTC complex) that bridges two membranes containing RAB7 molecules in active conformation. It bridges vesicle and target membranes via its Rab7 binding domains and acts as a SNARE chaperone via a SNARE binding domain. It is the major \"clamping\" factor in SNARE mediated fusion (pmid:23645161).  The chaperoning function is crucial for topologically correct assembly of the trans-SNARE-pin, and prevention of reassembly of a cis-SNARE complex after SNARE disassembly by NSF-SNAP (pmid:27301672).   The BORC complex recruits the HOPS complex to the lysosomal membrane. The BORC complex functions by interacting with kinesins and determining the position of the lysosome by regulating the balance of (+)-end and (-)-end microtubular transport. One of its effectors is Arl8. The BORC complex comprises BLOC1S1, BLOC1S2, SNAPIN, KXD1, BORCS5, BORCS6, BORCS7, and BORCS8 (pmid:25898167)."
},
{
"ID":"drum.team-041-4d03-84e2-9a2d-35f6006313c8",
"systemID":"give.need-232-ddd4-b342-aaf0-041e2b87062a",
"componentID":"thru.fort-62b-f289-e932-b910-85ed42d6588b",
"evidenceType":"TAS",
"evidenceSource":"23645161",
"role":"compose",
"notes":"VPS16 provides part of the SNARE-pin interaction interface (pmid:23645161)."
},
{
"ID":"vise.docs-2fb-1c10-3bd2-f843-a04f72566d3e",
"systemID":"give.need-232-ddd4-b342-aaf0-041e2b87062a",
"componentID":"meet.high-e7f-67d6-4fa2-8ae0-1a5338569f23",
"evidenceType":"TAS",
"evidenceSource":"23645161",
"role":"compose",
"notes":"VPS33 provides part of the SNARE-pin interaction interface (pmid:23645161).  VPS33A is an SM protein (Sec1/Munc18 protein) which stabilizes the nascent SNARE bundle by interacting with both v-SNARES and t-SNARES (pmid:30655294).  VPS33A interacts with a \"closed form of STX17 (pmid:30655294)."
},
{
"ID":"knit.boar-c8c-bc2e-1a42-8aa6-6c55154fdf27",
"systemID":"give.need-232-ddd4-b342-aaf0-041e2b87062a",
"componentID":"wave.deem-5c8-d6ef-d192-5920-be2617eaa320",
"evidenceType":"TAS",
"evidenceSource":"23645161",
"role":"compose",
"notes":"VPS18 does not interact with the SNARE-pin (pmid:23645161)."
},
{
"ID":"whey.loop-081-3926-40c2-790c-a564baaaf74a",
"systemID":"give.need-232-ddd4-b342-aaf0-041e2b87062a",
"componentID":"hook.take-193-7c5c-b3b2-ba68-9b26aeb88e4f",
"evidenceType":"TAS",
"evidenceSource":"23645161",
"role":"compose",
"notes":"VPS11 does not interact with the SNARE-pin (pmid:23645161)."
},
{
"ID":"cure.newt-cb8-b736-af42-8b73-e6c3a794928e",
"systemID":"give.need-232-ddd4-b342-aaf0-041e2b87062a",
"componentID":"soak.have-ead-d696-4292-8a1c-c6bd6dab86d8",
"evidenceType":"TAS",
"evidenceSource":"23645161",
"role":"compose",
"notes":"VPS41 provides one of two Rab7 interaction interfaces (pmid:23645161)."
},
{
"ID":"page.thug-7a0-e1af-6542-a95a-588432e9a518",
"systemID":"give.need-232-ddd4-b342-aaf0-041e2b87062a",
"componentID":"leap.code-1e6-a805-9e82-88da-dc3c7a9b0939",
"evidenceType":"TAS",
"evidenceSource":"23645161",
"role":"compose",
"notes":"VPS39 provides one of two Rab7 interaction interfaces (pmid:23645161)."
},
{
"ID":"than.bulk-206-8a9a-52b2-59b7-356f2320f718",
"systemID":"skin.toll-8ab-a5d2-1202-eaf0-807d897969f0",
"componentID":"runs.ploy-bfc-c454-45d2-dbdf-7adcde1b3758",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"location",
"notes":"Lipid rafts are required for autophagic flux and play a role in the fusion event (pmid:30115558)."
},
{
"ID":"vent.soup-82d-42d7-e732-f9e6-90bc94db939e",
"systemID":"pant.balm-93f-c169-d342-a8fe-d88028fb890a",
"componentID":"runs.ploy-bfc-c454-45d2-dbdf-7adcde1b3758",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"location",
"notes":"Lipid rafts are required for autophagic flux and play a role in the fusion event (pmid:30115558)."
},
{
"ID":"says.feud-17f-0711-e972-08cf-861f38cc0ac3",
"systemID":"stab.belt-ff1-c9fc-dcc2-da67-06c44a8d9005",
"componentID":"thin.brew-e9c-fa09-4462-290d-797babf87586",
"evidenceType":"TAS",
"evidenceSource":"30747526",
"role":"compose",
"notes":"Cholesterol provides specific binding domains and increases membrane thickness and stiffness (pmid:30747526)."
},
{
"ID":"tick.rift-bf4-6d24-0f62-ea0c-eaaa877f8500",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"hugs.stub-676-67ee-a7d2-a8a3-cff6ea1a60f0",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"localize",
"notes":"OSBPL1A is a RAB7-GTP effector. In active form it interacts with cholesterol in lipd rafts through its ORD domain. This interaction recruits PLEKHM1 and through it the HOPS complex. In the absence of cholesterol, OSBPL1A interacts with VAPA via its FFAT domain (pmid:30115558).  This inhibits PLEKHM1 binding to RAB7, whereupon PLEKHM1 and RILP recruit HOPS complex (pmid:27283760).  The ER-bound VAPA protein can be bound by OSBPL1A via its FFAT domain.This interaction creates contact sites between the ER and the phagosome, which inhibits membrane tethers, microtubular transport, and  stalls the fusion process (pmid:30115558)."
},
{
"ID":"eats.milk-5b2-be25-3eb2-6810-55b1d69bfd3f",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"pays.leap-4b7-35ce-5aa2-aa05-c93631a533c4",
"evidenceType":"TAS",
"evidenceSource":"30704899",
"role":"integrate",
"notes":"The PIK3C3 complex creates phosphoinositide-3-phosphate at the phagosome-lysosome fusion site. It integrates a number of general (GPCR) signalling pathways (pmid:30704899)."
},
{
"ID":"gene.fled-c70-8829-0302-5b08-b703cf387b8a",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"word.film-fb9-d0d6-4ef2-6982-9e517633e41f",
"evidenceType":"TAS",
"evidenceSource":"29089378",
"role":"compose",
"notes":"PIK3C3 (also: Vps34) produces phosphatidylinositol-3-phosphate (PI(3)P) from PI (pmid:29089378)."
},
{
"ID":"beds.twig-f65-6c43-bff2-5b21-4bdb173c9aeb",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"note.shin-85d-2c29-5bf2-abcd-506232a14b8d",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"UVRAG increases RAB7 concentration in maturing endosomes. It provides an interface to the MTORC1 complex: phosporylation of UVRAG by MTORC1 causes it to sequester with RUBCN, away from the HOPS complex (pmid:30115558)."
},
{
"ID":"same.prey-2cc-fac9-ab82-78e2-ce291c12a486",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"walk.next-cee-da9e-3802-5970-688389626c3b",
"evidenceType":"TAS",
"evidenceSource":"25086043",
"role":"compose",
"notes":"NRBF2 inhibts PIK3C3 activity and thus reduces PI(3)P levels (pmid:25086043)."
},
{
"ID":"runs.odds-b47-3aaa-45a2-dbcd-63b8c85b8f1c",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"pies.slip-a4b-a984-7722-cac5-86ccadd86a1d",
"evidenceType":"TAS",
"evidenceSource":"18326940",
"role":"compose",
"notes":"PK3R4 (also called Vps15) is a protein kinase that regulates PIK3C3 (pmid:18326940)."
},
{
"ID":"debt.robe-aae-1366-13b2-0849-b6435d0d81cc",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"bore.vain-cbb-04d5-bfc2-c8cf-bf964f752fc8",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"RUBCN sequesters UVRAG away from the HOPS complex (pmid:30115558)."
},
{
"ID":"gait.slap-41a-2472-1e42-9ae0-67023bef60fa",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"toll.fell-e8c-8b22-1082-7bb0-8ce383ade0ea",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"RUBCNL (Pacer, protein associated with UVRAG as autophagy enhancer) releases UVRAG from RUBCN (pmid:30115558). . RUBCNL also anchors PI3KC3 as well as HOPS to STX17. Its phosphorylation by mTORC1 integrates the mTOR pathway (active mTOR shuts down RUBCNL enhancement of the system); its acetylation by TIP60 integrates the GSK3-TIP60 pathway (pmid:30704899)."
},
{
"ID":"ties.barn-f4c-7730-3322-5bf9-0aa47eea15cc",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"swim.doom-f60-b92a-d092-4ae6-535916d7ac3a",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"BECN1 (Beclin1) is a core component of the RUBCNL-UVRAG–BECN1,2–PIK3C3 complex (pmid:30115558).  Phosphorylation of BECN1 is stimulated by ATG14 (pmid:23878393)."
},
{
"ID":"caps.chat-62a-f55b-a6f2-ab48-ace5fc572d05",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"hens.sang-044-e09f-a102-a9b6-63a33e9f8e2e",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"PLEKHM1 (Pleckstrin homology domain-containing family M member 1) is a multivalent adaptor that enhances HOPS complex / LC3 (Atg8) interactions in a RAB7 dependent way (pmid:30115558)."
},
{
"ID":"oaks.next-f5a-15d1-0e52-7b5b-6c43f86a688b",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"wake.stop-028-e0d1-dbd2-39dc-24af09d1894d",
"evidenceType":"TAS",
"evidenceSource":"29089378",
"role":"output",
"notes":"PI(3)P interfaces with many signalling pathways. It is produced at the phagosome by PIK3C3 in the PIK3C3 complex, and is further phosphorylated to PI(3,5)P by PIKfyve after dissociation of PIK3C3 (pmid:29089378).  Degradation of PI(3)P to PI on phagosomes reduces autophagy (pmid:27340123)."
},
{
"ID":"bone.gage-392-a7ea-a602-1834-b69324a5b3ac",
"systemID":"stub.sigh-a47-a0a5-b7c2-c832-1a2bcec5753f",
"componentID":"give.toad-b23-1014-6712-9b1f-d76f1abe9aae",
"evidenceType":"TAS",
"evidenceSource":"29089378",
"role":"input",
"notes":"PI is phosphorylated at the phagosome toPI(3)P by PIK3C3 in the PIK3C3 complex. Degradation of PI(3)P to PI on phagosomes reduces autophagy (pmid:27340123)."
},
{
"ID":"care.myth-84b-8f47-aae2-7840-957ac3c7d9c5",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"mole.heel-580-b3cf-ec42-7b8e-33a0504c5b5b",
"evidenceType":"TAS",
"evidenceSource":"27340123",
"role":"set",
"notes":"INPP5E decreases lysosomal phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2)  and increases PI(3)P and is required for the fusion event. Both an excess and a reduction of the PI(3)P to PI(3,5)P2 ratio inhibits fusion (pmid:27340123)."
},
{
"ID":"fill.howl-085-d857-3782-c998-bd6d034f3ef6",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"cell.raft-364-a39c-6362-abe2-797a0dcf9276",
"evidenceType":"TAS",
"evidenceSource":"28302928",
"role":"set",
"notes":"The PIKFYVE complex controls PI(3,5)P2 levels and consists of PIKFYVE, FIG4, VAC14 (ArPIKfyve), and WIPI1 (pmid:28302928)."
},
{
"ID":"else.pine-dbf-9c59-a5c2-2a78-86671c651f80",
"systemID":"rock.tend-392-4e0a-ae42-5a96-6ffdead1df8f",
"componentID":"turn.need-3fe-2bc6-1312-7923-3dd66b25371f",
"evidenceType":"TAS",
"evidenceSource":"27340123",
"role":"set",
"notes":"PIKFYVE phosphorylates PI(3)P to PI(3,5)P2. Both an excess and a reduction of the PI(3)P to PI(3,5)P2 ratio inhibits fusion (pmid:27340123)."
},
{
"ID":"lamp.swap-83a-e9dd-fb22-28f8-a7ceefcedae1",
"systemID":"rock.tend-392-4e0a-ae42-5a96-6ffdead1df8f",
"componentID":"team.flex-712-75fe-9e02-a999-9aded07a24cb",
"evidenceType":"TAS",
"evidenceSource":"29089378",
"role":"output",
"notes":"(PI(3,5)P2) is produced by the action of PIKFYVE on PI3P (pmid:29089378).  PI(3,5)P2 counteracts cortactin mediated actin filament stabilization on lysosomes; actin on the lysosome surface is required for fusion (pmid:27340123)."
},
{
"ID":"sock.peak-cc3-f027-59d2-4902-d552d6d0337d",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"rang.torn-8e1-1ff3-4bc2-7962-137d0835f74a",
"evidenceType":"TAS",
"evidenceSource":"27283760",
"role":"locate",
"notes":"The RAB7-RILP-dynein-dynactin complex is responsible for minus-end transport of lysosomes along microtubules towards the MTOC, where most lysosomes are located (pmid:27283760)."
},
{
"ID":"damp.snip-5f5-cdcf-4d42-7b0b-61870a6323ec",
"systemID":"fear.lead-daa-76b4-b832-29f8-48cb624ea900",
"componentID":"prep.used-3a0-36b4-c5e2-eb17-df6d634b8277",
"evidenceType":"TAS",
"evidenceSource":"12944476",
"role":"compose",
"notes":"RILP associates with RAB7-GTP; the complex promotes dynein-dynactin association with the membrane and subsequent transport (pmid:12944476)."
},
{
"ID":"trip.mill-1c2-4adf-30d2-db77-b8850e3f60b2",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"head.maps-b51-5222-9e02-9a83-317947b0f03d",
"evidenceType":"TAS",
"evidenceSource":"27146966",
"role":"location",
"notes":"A cortactin dependent, remodelled, local filamentous actin network between the phagosome and the lysosome promotes fusion (pmid:27146966)."
},
{
"ID":"cast.warm-784-8365-e2c2-2866-2ece261021a2",
"systemID":"lull.slab-be7-27e1-df72-2959-b42fa71d83b2",
"componentID":"pair.flaw-425-1875-ed02-dbf9-277bb04e893e",
"evidenceType":"TAS",
"evidenceSource":"27146966",
"role":"compose",
"notes":"CTTN is a branch-stabilizing interactor that remodels the F-actin network, which is a fusion requirement by recruiting the ARP2/3 complex to the fusion site (pmid:27146966)."
},
{
"ID":"cake.shoe-56c-e70f-78b2-0871-9521ca8461a4",
"systemID":"lull.slab-be7-27e1-df72-2959-b42fa71d83b2",
"componentID":"grub.luck-728-4d5c-02c2-d923-9232b842de40",
"evidenceType":"TAS",
"evidenceSource":"27146966",
"role":"locate",
"notes":"HDAC6, a ubiquitin binding deacylase, recruits CTTN to the autophagosome (pmid:27146966)."
},
{
"ID":"gaps.miss-5a3-38cc-f972-6a1a-6c9c7c35cfc8",
"systemID":"lull.slab-be7-27e1-df72-2959-b42fa71d83b2",
"componentID":"mens.lack-87b-d4b4-a3a2-9aa7-752a2b098f4d",
"evidenceType":"TAS",
"evidenceSource":"27146966",
"role":"compose",
"notes":"The actin-nucleator ARP2/3 complex is a seven-subunit complex that can nucleate actin-filament branchpoints to establish a network. It stimulates the local assembly of an F-actin network for efficient fusion. It consists of ARP2, ARP3, ARPC1, ARPC2, ARPC3, ARPC4, and ARPC5 (pmid:27146966)."
},
{
"ID":"ears.wide-f7a-3e36-0262-eae4-41de1c812c2d",
"systemID":"lull.slab-be7-27e1-df72-2959-b42fa71d83b2",
"componentID":"stub.tile-0e5-909f-6942-8bce-c38696a2d4a0",
"evidenceType":"TAS",
"evidenceSource":"27146966",
"role":"compose",
"notes":"F-actin is a filament of ACTB (G-actin) monomers which is a scaffold for myosin-motors like the fusion-promoting MYO1C myosin to move on (pmid:27146966)."
},
{
"ID":"worm.raft-766-5b1e-b712-a894-a0fa20c4fa92",
"systemID":"doll.fawn-529-099c-6462-fb0b-9ec626eef6a5",
"componentID":"dare.bans-b1a-0594-e102-badf-d8b373f431b7",
"evidenceType":"TAS",
"evidenceSource":"27146966",
"role":"compose",
"notes":"The cytoplasmic, soluble globular G-actin polymerizes in to a filamentous form: F-actin (pmid:27146966)."
},
{
"ID":"hunt.sand-38e-9c6d-20c2-2b59-041e13f8d9d7",
"systemID":"lull.slab-be7-27e1-df72-2959-b42fa71d83b2",
"componentID":"thin.pier-e5c-032e-e622-8ae1-e5d46bfe78ac",
"evidenceType":"TAS",
"evidenceSource":"27146966",
"role":"locate",
"notes":"MYO1C is a monomeric class I myosin, which associates with cholesterol lipid rafts. It contains a PH domain that binds specifically to PI(4,5)P2. It is a \"slow\" motor, ideal for translocating heavy cargos, not tethering, and thus is able to move lipid rafts from storage compartments to their site of action (pmid:27146966)."
},
{
"ID":"tell.take-da1-2b0e-1082-09f0-5eaf46754632",
"systemID":"lull.slab-be7-27e1-df72-2959-b42fa71d83b2",
"componentID":"fees.yarn-c6a-179d-4952-4918-5bccc8330297",
"evidenceType":"TAS",
"evidenceSource":"30692198",
"role":"attachment",
"notes":"PI(4,5)P2 clusters at lipid rafts in a cholesterol and Ca2+ dependent fashion. These clusters bind the ARP2/3 complex (pmid:30692198)."
},
{
"ID":"foul.lung-999-21ee-1602-1865-4ee3b84d42d0",
"systemID":"root.boys-359-f424-0572-4bcd-19d6ff64c741",
"componentID":"some.fled-330-0e4c-4362-fa2b-6ca9b43a1075",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"compose",
"notes":"Ca2+ is required to stabilize the SNAREpin (pmid:30115558)."
},
{
"ID":"mail.wren-16e-362d-d2d2-6bf3-61ca2d3517aa",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"bead.hour-c64-88c8-a1f2-993f-723284239b26",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"input",
"notes":"The lysosome resident population of voltage-gated calcium channel CACNA1A is required for calcium efflux from the lysosome for the fusion event (pmid:30115558)."
},
{
"ID":"rust.peat-984-967c-1192-d9b0-b6d090102ed4",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"pour.bugs-bdb-0abf-e892-e885-9c20e949c76a",
"evidenceType":"TAS",
"evidenceSource":"30700546",
"role":"transmit",
"notes":"From three to six SNAP29-STX17-VAMP8 SNARE-pins form a mechanically coupled SNAREpin team in a rigid membrane (cholesterol lipid-raft) which accelerates fusion by four orders of magnitude (pmid:30700546)."
},
{
"ID":"says.lull-fe4-2d88-d912-a98c-57cd3eaedadf",
"systemID":"root.boys-359-f424-0572-4bcd-19d6ff64c741",
"componentID":"vise.hash-35f-ead8-99d2-2947-9ab8f6561c13",
"evidenceType":"TAS",
"evidenceSource":"25581794",
"role":"decompose",
"notes":"The 20s supercomplex forms around the cis-SNARE complex, by binding two to four molecules of alpha-SNAP and an NSF homohexamer to the cis-SNARE-pin (pmid:25581794)."
},
{
"ID":"dove.rust-d29-c0b5-e052-580e-987747841192",
"systemID":"owls.gear-304-36d5-ff92-1913-0de755710d35",
"componentID":"suit.leak-8bf-2889-5ca2-f9ed-9e91f9b1d069",
"evidenceType":"TAS",
"evidenceSource":"25581794",
"role":"compose",
"notes":"Two to four molecules of cytoplasmic alpha-SNAP wrap around the cis-SNARE-pin to form a SNAP-SNARE subcomplex (pmid:25581794)."
},
{
"ID":"duct.arch-552-5563-80a2-a86f-0ba12ac82042",
"systemID":"owls.gear-304-36d5-ff92-1913-0de755710d35",
"componentID":"chip.lend-5df-d630-ef52-dbc7-59aaa7c71494",
"evidenceType":"TAS",
"evidenceSource":"25581794",
"role":"compose",
"notes":"NSF is a cytoplasmic AAA+ ATPase that binds to the SNAP-SNARE subcomplex in an ATP-bound state. Subsequent ATP hydrolysis induces major conformational rearrangements of NSF that disassociate the SNARE-pin into individual constituent molecules. Nucleotide exchange presumably disassociates the remaining NSF-SNAP subcomplex, and allows the cycle to restart (pmid:25581794)."
},
{
"ID":"laud.flop-bab-1dfa-db02-1b60-9da8e3bd25f8",
"systemID":"deed.mead-d34-551d-1f82-4a65-a5cc8b9e745a",
"componentID":"lawn.gong-987-4d18-70e2-692b-749431f5af5b",
"evidenceType":"TAS",
"evidenceSource":"30333976",
"role":"inactivate",
"notes":"TBC1D2 (Armus) is a RAB7 specific GAP that activates hydrolysis of RAB7 bound GTP to GDP and thus catalyzes conversion of RAB7 to its inactive state (pmid:30333976)."
},
{
"ID":"cove.pray-ec1-5534-3992-39a2-c772a8808378",
"systemID":"sled.bets-e87-946c-4ed2-8b81-171d499085d6",
"componentID":"lamb.hull-aec-9fb5-f932-99b1-e85db79ee1b9",
"evidenceType":"TAS",
"evidenceSource":"Unpublished",
"role":"external",
"notes":"NOT IN PHALY genes are related to PHALY system components, but are demonstrably not part of PHALY (Unpublished}}"
},
{
"ID":"lend.cool-80b-a405-3312-6819-cef6da560b74",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"muse.jobs-c24-59c5-a362-f8f0-f6f8e26f964d",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"external",
"notes":"The t-SNARE VTI1B may work in a pathway that is parallel to STX17, in pathogen containing autophagosomes or recycling endosomes (pmid:30115558)."
},
{
"ID":"laud.dent-a0e-307a-dcf2-6a5e-04a14c070e67",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"cubs.rice-546-05aa-1d52-9a4f-09507cdf1d5f",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"external",
"notes":"The t-SNARE STX6 is the interaction partner of VTI1B (pmid:30115558)."
},
{
"ID":"rice.saws-b50-ebc2-5e92-9baf-6c6608493d11",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"drum.fell-823-079f-8062-5a36-452d68d5c393",
"evidenceType":"TAS",
"evidenceSource":"30115558",
"role":"external",
"notes":"The v-SNARE VAMP3 forms a SNAREpin with the  VTI1B-STX6 complex (pmid:30115558)."
},
{
"ID":"kick.beam-399-f82c-9642-2b34-6fe7940831a2",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"owls.turn-c44-bab3-d632-28ff-69b1af2d31a3",
"evidenceType":"TAS",
"evidenceSource":"UniProt:O00161",
"role":"external",
"notes":"SNAP23 is a t-SNARE for general membrane fusion (UniProt:O00161}}"
},
{
"ID":"coal.thru-f1c-3841-1f42-49c7-0d6c2c2e2f2b",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"gall.fees-89f-514f-32d2-cb4d-9c7ceadaad1e",
"evidenceType":"TAS",
"evidenceSource":"UniProt:P61266",
"role":"external",
"notes":"SNAP25 is a t-SNARE involved in neurotransmitter release at the synapse (UniProt:P61266}}"
},
{
"ID":"yawn.sits-ab8-02f0-a3c2-8ae0-5ff796b54c97",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"bout.join-dc8-84fe-4c12-fb23-3f7afee2f8d0",
"evidenceType":"TAS",
"evidenceSource":"UniProt:Q16623",
"role":"external",
"notes":"STX1A is involved in hormone and neurotransmitter exocytosis (UniProt:Q16623}}"
},
{
"ID":"veil.size-110-f429-1f12-98b8-36a8b28a978a",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"clan.mash-3f2-bd57-f332-2b3b-cf1f03acf736",
"evidenceType":"TAS",
"evidenceSource":"UniProt:Q16623",
"role":"external",
"notes":"STX1B is involved in docking of synaptic vesicles at presynaptic active zones (UniProt:Q16623}}"
},
{
"ID":"term.time-fd8-d7d9-3782-0aa4-fc612a22b0ab",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"trim.male-e1d-1978-2b02-eafb-6b5591cb1d79",
"evidenceType":"TAS",
"evidenceSource":"UniProt:P32856",
"role":"external",
"notes":"STX2 is essential for epithelial morphogenesis (UniProt:P32856}}"
},
{
"ID":"flee.file-ee7-fb71-b6e2-b895-5d5234454ca7",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"path.tuck-be6-c1fd-5df2-1b55-0ccae7f59b0e",
"evidenceType":"TAS",
"evidenceSource":"UniProt:Q13277",
"role":"external",
"notes":"STX3 is involved in docking of synaptic vesicles at presynaptic active zones (UniProt:Q13277}}"
},
{
"ID":"cook.tend-286-439f-dc22-e8b2-aff44cb2f068",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"frog.nose-1d4-17a3-a1f2-6a2b-a535ba4ba518",
"evidenceType":"TAS",
"evidenceSource":"UniProt:Q12846",
"role":"external",
"notes":"STX3 is a plasma mebrane t-SNARE that is involved in docking of transport vesicles (UniProt:Q12846}}"
},
{
"ID":"grab.thus-b6e-c3b5-b612-28c5-3b8bc9482c07",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"cubs.rice-546-05aa-1d52-9a4f-09507cdf1d5f",
"evidenceType":"TAS",
"evidenceSource":"UniProt:O43752",
"role":"external",
"notes":"STX6 is essential involved in vesicle trafficking (UniProt:O43752}}"
},
{
"ID":"junk.ride-9ae-3d32-4002-a87d-3cff81bdedc5",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"rugs.raid-f56-17e3-0dc2-39c8-7acc151dfe7d",
"evidenceType":"TAS",
"evidenceSource":"UniProt:O15400",
"role":"external",
"notes":"STX7 is involved in homotypic fusion of endocytic organelles (UniProt:O15400}}"
},
{
"ID":"tale.wind-340-cbff-20d2-5acb-28412f0d472f",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"mash.yawn-fa3-12cb-9ad2-797f-db540783b7db",
"evidenceType":"TAS",
"evidenceSource":"UniProt:Q9UNK0",
"role":"external",
"notes":"STX8 is involved in early-secretory retrograde transport (UniProt:Q9UNK0}}"
},
{
"ID":"kind.math-7ce-0d76-58c2-488f-cbd2da03575e",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"from.snip-78c-4de9-dc02-abcf-c80a48851217",
"evidenceType":"TAS",
"evidenceSource":"UniProt:O60499",
"role":"external",
"notes":"STX10 is  involved in vesicular transport from the late endosomes to the trans-Golgi network (UniProt:O60499}}"
},
{
"ID":"fawn.bulk-5aa-78a1-e992-884b-54830177189f",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"dome.calf-07a-cff6-ebc2-4899-6c254e4ab7bb",
"evidenceType":"TAS",
"evidenceSource":"UniProt:O75558",
"role":"external",
"notes":"STX11 acts between the late endosome and the trans-Golgi network (UniProt:O75558}}"
},
{
"ID":"cans.salt-119-4cfe-1292-aad1-7ac77c865d26",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"golf.park-56f-a5db-f132-0b74-34887708dee8",
"evidenceType":"TAS",
"evidenceSource":"UniProt:Q86Y82",
"role":"external",
"notes":"STX12 acts between the late endosome and the trans-Golgi network (UniProt:Q86Y82}}"
},
{
"ID":"goat.fact-735-d9db-0bf2-89ea-fa951cf6ae42",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"asks.drop-bfd-7feb-4d92-4b5f-8fffd85deea1",
"evidenceType":"TAS",
"evidenceSource":"UniProt:O14662",
"role":"external",
"notes":"STX16 is a t-SNARE localized to the trans-Golgi network (UniProt:O14662}}"
},
{
"ID":"yard.plus-ae5-f711-3c12-f81d-620053869882",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"cook.mile-c28-9ec7-a532-dba9-e4ea0774f8fd",
"evidenceType":"TAS",
"evidenceSource":"UniProt:Q9P2W9",
"role":"external",
"notes":"STX18 is a SNARE that is involved in Golgi-derived retrograde transport vesicles (UniProt:Q9P2W9}}"
},
{
"ID":"cone.tent-73a-bc7f-cf82-984e-30d02923d9ed",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"deep.sift-2e6-95e6-fa32-aa4b-bf00f510f54e",
"evidenceType":"TAS",
"evidenceSource":"UniProt:Q8N4C7",
"role":"external",
"notes":"STX19 is involved in in endosomal trafficking of the epidermal growth factor receptor (EGFR) (UniProt:Q8N4C7}}"
},
{
"ID":"deed.each-bbc-d18b-3d42-1a8f-ec4d4a7c7617",
"systemID":"rash.stir-fe0-1bb3-ae62-28f8-4e6cab1e945b",
"componentID":"watt.bind-8c1-752c-61c2-3ab3-7734965c6621",
"evidenceType":"TAS",
"evidenceSource":"UniProt:O75396",
"role":"external",
"notes":"SEC22B is a high-confidence interactor in STRING, but it is a SNARE that is involved in retrograde transport from the Golgi to the ER (UniProt:O75396}}"}],

"component":[{
"ID":"brew.main-b5c-4427-17f2-0a43-015f4f9486d1",
"code":"autophagosome",
"componentType":"composed"
},
{
"ID":"mild.spur-d4f-1dd4-3642-7ad1-b93e4b1b6357",
"code":"OAM",
"componentType":"atomic"
},
{
"ID":"wolf.make-780-f3f4-2e42-781c-e985b856e937",
"code":"IAM",
"componentType":"atomic"
},
{
"ID":"calf.pane-5b5-127b-b3c2-b931-c79d4f9ded09",
"code":"LC3-II",
"componentType":"composed"
},
{
"ID":"isle.gait-a82-1ff7-70b2-e810-fd2dd3c1c465",
"code":"LC3",
"componentType":"atomic"
},
{
"ID":"stag.teas-702-efa2-8822-b9ae-4f7a179fa9c9",
"code":"PE",
"componentType":"atomic"
},
{
"ID":"sign.bids-877-06f5-69c2-5a0f-ba6f1df4aca4",
"code":"SNAP29-STX17 Qabc-SNARE",
"componentType":"composed"
},
{
"ID":"june.seas-24d-971c-f512-5826-33052e1e0ae3",
"code":"SNAP29",
"componentType":"atomic"
},
{
"ID":"sets.lips-81d-d3de-fce2-caf7-5b4393b8ea4b",
"code":"GlcNAC",
"componentType":"atomic"
},
{
"ID":"mess.seal-1e4-158a-0e72-d8d5-ad944aaff957",
"code":"STX17bound",
"componentType":"composed"
},
{
"ID":"prod.bins-b67-7850-fca2-5bd0-9e214caf67c0",
"code":"STX17free",
"componentType":"atomic"
},
{
"ID":"pond.none-227-a5f6-2cc2-5ab0-f3d38b36d2a4",
"code":"LAMP2",
"componentType":"atomic"
},
{
"ID":"stir.lids-10a-c2ff-94f2-88fe-cc259492b58b",
"code":"IRGM",
"componentType":"atomic"
},
{
"ID":"reel.gull-3a8-71d1-6212-e9ec-fb252ff13105",
"code":"RAB7active",
"componentType":"composed"
},
{
"ID":"doll.club-c20-7172-ace2-5a9c-145dd3ff8e41",
"code":"RAB7",
"componentType":"atomic"
},
{
"ID":"file.mime-4bf-2cfd-6e62-49f6-e5b1aefa698a",
"code":"Mon1-CCZ1",
"componentType":"composed"
},
{
"ID":"sage.wood-e9a-5934-c9d2-6aab-dca28ae194ba",
"code":"MON1A",
"componentType":"atomic"
},
{
"ID":"knit.hiss-047-86fb-e0f2-4ad9-ebafcff9269d",
"code":"CCZ1",
"componentType":"atomic"
},
{
"ID":"webs.laud-453-0049-6f12-59d2-c55101ab383b",
"code":"GABARAPL1",
"componentType":"atomic"
},
{
"ID":"wipe.bulk-ac5-33c4-a422-992b-15bbadd61344",
"code":"EPG5",
"componentType":"atomic"
},
{
"ID":"cage.back-649-14d7-fc22-58c5-21db5c35a36f",
"code":"ATG13",
"componentType":"atomic"
},
{
"ID":"safe.bent-d50-883d-efc2-c947-81c5fc7d0fde",
"code":"ULK1 complex",
"componentType":"composed"
},
{
"ID":"grog.cold-1e7-3859-a5e2-e917-bc2c0001dad2",
"code":"MAP1LC3B",
"componentType":"atomic"
},
{
"ID":"wasp.deal-c61-5011-f0b2-6b87-b52b5f0c7b44",
"code":"MAP1LC3C",
"componentType":"atomic"
},
{
"ID":"flip.glad-f50-9299-e452-8978-24620d230bdc",
"code":"lysosome",
"componentType":"composed"
},
{
"ID":"harp.thaw-f3d-f0e0-0622-0b87-ffc3a9aef0e2",
"code":"LAMP1",
"componentType":"atomic"
},
{
"ID":"toes.rods-c61-ca74-9b72-ca0c-96cfe2a82869",
"code":"VAMP8",
"componentType":"atomic"
},
{
"ID":"cave.gull-aac-32e6-43a2-4975-812d31591dfa",
"code":"VAMP7",
"componentType":"atomic"
},
{
"ID":"cone.nail-78b-a797-60a2-1a71-4b6973f63bfa",
"code":"SNAP29-STX17-VAMP8 SNARE-pin",
"componentType":"composed"
},
{
"ID":"coat.dean-37b-7c8c-b692-581e-548b259def46",
"code":"ATG14",
"componentType":"atomic"
},
{
"ID":"hits.kite-345-8536-8682-8aa8-5da04b7a4ff8",
"code":"HOPS complex",
"componentType":"composed"
},
{
"ID":"thru.fort-62b-f289-e932-b910-85ed42d6588b",
"code":"VPS16",
"componentType":"atomic"
},
{
"ID":"meet.high-e7f-67d6-4fa2-8ae0-1a5338569f23",
"code":"VPS33A",
"componentType":"atomic"
},
{
"ID":"wave.deem-5c8-d6ef-d192-5920-be2617eaa320",
"code":"VPS18",
"componentType":"atomic"
},
{
"ID":"hook.take-193-7c5c-b3b2-ba68-9b26aeb88e4f",
"code":"VPS11",
"componentType":"atomic"
},
{
"ID":"soak.have-ead-d696-4292-8a1c-c6bd6dab86d8",
"code":"VPS41",
"componentType":"atomic"
},
{
"ID":"leap.code-1e6-a805-9e82-88da-dc3c7a9b0939",
"code":"VPS39",
"componentType":"atomic"
},
{
"ID":"runs.ploy-bfc-c454-45d2-dbdf-7adcde1b3758",
"code":"lipid rafts",
"componentType":"composed"
},
{
"ID":"thin.brew-e9c-fa09-4462-290d-797babf87586",
"code":"cholesterol",
"componentType":"atomic"
},
{
"ID":"hugs.stub-676-67ee-a7d2-a8a3-cff6ea1a60f0",
"code":"OSBPL1A",
"componentType":"atomic"
},
{
"ID":"pays.leap-4b7-35ce-5aa2-aa05-c93631a533c4",
"code":"PIK3C3 complex",
"componentType":"composed"
},
{
"ID":"word.film-fb9-d0d6-4ef2-6982-9e517633e41f",
"code":"PIK3C3",
"componentType":"atomic"
},
{
"ID":"note.shin-85d-2c29-5bf2-abcd-506232a14b8d",
"code":"UVRAG",
"componentType":"atomic"
},
{
"ID":"walk.next-cee-da9e-3802-5970-688389626c3b",
"code":"NRBF2",
"componentType":"atomic"
},
{
"ID":"pies.slip-a4b-a984-7722-cac5-86ccadd86a1d",
"code":"PIK3R4",
"componentType":"atomic"
},
{
"ID":"bore.vain-cbb-04d5-bfc2-c8cf-bf964f752fc8",
"code":"RUBCN",
"componentType":"atomic"
},
{
"ID":"toll.fell-e8c-8b22-1082-7bb0-8ce383ade0ea",
"code":"RUBCNL",
"componentType":"atomic"
},
{
"ID":"swim.doom-f60-b92a-d092-4ae6-535916d7ac3a",
"code":"BECN1",
"componentType":"atomic"
},
{
"ID":"hens.sang-044-e09f-a102-a9b6-63a33e9f8e2e",
"code":"PLEKHM1",
"componentType":"atomic"
},
{
"ID":"give.toad-b23-1014-6712-9b1f-d76f1abe9aae",
"code":"PI",
"componentType":"atomic"
},
{
"ID":"wake.stop-028-e0d1-dbd2-39dc-24af09d1894d",
"code":"PI(3)P",
"componentType":"atomic"
},
{
"ID":"team.flex-712-75fe-9e02-a999-9aded07a24cb",
"code":"PI(3,5)P2",
"componentType":"atomic"
},
{
"ID":"mole.heel-580-b3cf-ec42-7b8e-33a0504c5b5b",
"code":"INPP5E",
"componentType":"atomic"
},
{
"ID":"cell.raft-364-a39c-6362-abe2-797a0dcf9276",
"code":"PIKFYVE complex",
"componentType":"composed"
},
{
"ID":"turn.need-3fe-2bc6-1312-7923-3dd66b25371f",
"code":"PIKFYVE",
"componentType":"atomic"
},
{
"ID":"rang.torn-8e1-1ff3-4bc2-7962-137d0835f74a",
"code":"RAB7-RILP-dynein-dynactin complex",
"componentType":"composed"
},
{
"ID":"prep.used-3a0-36b4-c5e2-eb17-df6d634b8277",
"code":"RILP",
"componentType":"atomic"
},
{
"ID":"head.maps-b51-5222-9e02-9a83-317947b0f03d",
"code":"F-actin network",
"componentType":"composed"
},
{
"ID":"pair.flaw-425-1875-ed02-dbf9-277bb04e893e",
"code":"CTTN",
"componentType":"atomic"
},
{
"ID":"grub.luck-728-4d5c-02c2-d923-9232b842de40",
"code":"HDAC6",
"componentType":"atomic"
},
{
"ID":"mens.lack-87b-d4b4-a3a2-9aa7-752a2b098f4d",
"code":"ARP2/3 complex",
"componentType":"composed"
},
{
"ID":"stub.tile-0e5-909f-6942-8bce-c38696a2d4a0",
"code":"F-actin",
"componentType":"composed"
},
{
"ID":"dare.bans-b1a-0594-e102-badf-d8b373f431b7",
"code":"ACTB",
"componentType":"atomic"
},
{
"ID":"thin.pier-e5c-032e-e622-8ae1-e5d46bfe78ac",
"code":"MYO1C",
"componentType":"atomic"
},
{
"ID":"fees.yarn-c6a-179d-4952-4918-5bccc8330297",
"code":"PI(4,5)P2",
"componentType":"atomic"
},
{
"ID":"some.fled-330-0e4c-4362-fa2b-6ca9b43a1075",
"code":"Ca2+",
"componentType":"atomic"
},
{
"ID":"bead.hour-c64-88c8-a1f2-993f-723284239b26",
"code":"CACNA1A",
"componentType":"atomic"
},
{
"ID":"pour.bugs-bdb-0abf-e892-e885-9c20e949c76a",
"code":"SNAREpin team",
"componentType":"atomic"
},
{
"ID":"vise.hash-35f-ead8-99d2-2947-9ab8f6561c13",
"code":"20s supercomplex",
"componentType":"composed"
},
{
"ID":"suit.leak-8bf-2889-5ca2-f9ed-9e91f9b1d069",
"code":"alpha-SNAP",
"componentType":"atomic"
},
{
"ID":"chip.lend-5df-d630-ef52-dbc7-59aaa7c71494",
"code":"NSF",
"componentType":"atomic"
},
{
"ID":"lawn.gong-987-4d18-70e2-692b-749431f5af5b",
"code":"TBC1D2",
"componentType":"atomic"
},
{
"ID":"lamb.hull-aec-9fb5-f932-99b1-e85db79ee1b9",
"code":"NOT IN PHALY",
"componentType":"composed"
},
{
"ID":"muse.jobs-c24-59c5-a362-f8f0-f6f8e26f964d",
"code":"VTI1B",
"componentType":"atomic"
},
{
"ID":"drum.fell-823-079f-8062-5a36-452d68d5c393",
"code":"VAMP3",
"componentType":"atomic"
},
{
"ID":"bout.join-dc8-84fe-4c12-fb23-3f7afee2f8d0",
"code":"STX1A",
"componentType":"atomic"
},
{
"ID":"clan.mash-3f2-bd57-f332-2b3b-cf1f03acf736",
"code":"STX1B",
"componentType":"atomic"
},
{
"ID":"trim.male-e1d-1978-2b02-eafb-6b5591cb1d79",
"code":"STX2",
"componentType":"atomic"
},
{
"ID":"path.tuck-be6-c1fd-5df2-1b55-0ccae7f59b0e",
"code":"STX3",
"componentType":"atomic"
},
{
"ID":"frog.nose-1d4-17a3-a1f2-6a2b-a535ba4ba518",
"code":"STX4",
"componentType":"atomic"
},
{
"ID":"cubs.rice-546-05aa-1d52-9a4f-09507cdf1d5f",
"code":"STX6",
"componentType":"atomic"
},
{
"ID":"rugs.raid-f56-17e3-0dc2-39c8-7acc151dfe7d",
"code":"STX7",
"componentType":"atomic"
},
{
"ID":"mash.yawn-fa3-12cb-9ad2-797f-db540783b7db",
"code":"STX8",
"componentType":"atomic"
},
{
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"ID":"blot.tape-372-a2cd-fc22-09d1-f0430b98cb5b",
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"ID":"hush.keys-e56-8024-1352-dbe3-67dc93cc2c35",
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"ID":"burn.sure-463-5a92-b302-487b-8d543ee5ca04",
"name":"microtubule associated protein 1 light chain 3 alpha",
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},
{
"ID":"cell.lynx-b0d-c61f-4442-ca86-6056262af5a0",
"name":"phosphatidylethanolamine",
"moleculeType":"lipid",
"structure":"TBD"
},
{
"ID":"ease.same-d07-2587-0d12-da22-eb93b7b06519",
"name":"synaptosome associated protein 29",
"moleculeType":"protein",
"structure":"TBD"
},
{
"ID":"fate.swat-de5-9446-e762-a817-4a170cb5d0e1",
"name":"N-acetyl-glucosamine",
"moleculeType":"metabolite",
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"name":"Syntaxin 17",
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"structure":"TBD"
},
{
"ID":"hugs.dump-30b-76ba-ef62-890d-91d464502746",
"name":"lysosomal associated membrane protein 2",
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"structure":"TBD"
},
{
"ID":"cats.eggs-597-296a-edb2-4bd5-b7f7cc29ff4b",
"name":"immunity related GTPase M",
"moleculeType":"protein",
"structure":"TBD"
},
{
"ID":"grip.paid-df1-2830-0552-3839-4ddd6865e612",
"name":"RAB7A, member RAS oncogene family",
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"structure":"TBD"
},
{
"ID":"grim.folk-88b-3e9e-72a2-c869-e9c2b85c8cf5",
"name":"MON1 homolog A, secretory trafficking associated",
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},
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"ID":"mole.hymn-e25-7fe0-6682-0b8f-1bdbae452dae",
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},
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},
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"ID":"does.mane-3fb-4cff-b792-4921-adc353d5e286",
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},
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"ID":"pear.calf-f86-1558-b222-bb6d-9e90aeefe6a4",
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"ID":"bits.bets-cf6-2b15-6112-d832-abb95ee40b8a",
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},
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"structure":"TBD"
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"ID":"door.cure-3a0-ed59-c782-0a74-186630532fa4",
"name":"Barkor, beclin 1-associated autophagy-related key regulator",
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},
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"ID":"gems.chin-e26-1247-e7c2-6bf0-78e6b51d7217",
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},
{
"ID":"maze.both-289-f20d-c9d2-b82f-6edab5e48a43",
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"ID":"what.hits-b3a-ffe2-d672-ba66-20a1a0355ae2",
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},
{
"ID":"fake.wild-8e8-3a08-cf62-8914-2629716216eb",
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{
"ID":"coil.chat-de0-7f57-6db2-cbeb-125d6e727efc",
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},
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"ID":"wink.past-19d-8100-1172-690b-7c620504b665",
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"name":"Oxysterol binding protein like 1A",
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"ID":"meet.hoop-63e-b993-1f82-9b63-86f3d21b30a5",
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"ID":"fail.here-eb8-61b1-8db2-9aeb-b4c201371609",
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"ID":"sane.fins-dd5-3c12-cd82-3b7b-b1e21bcd3849",
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"ID":"guts.slug-006-6241-5832-5a94-c1db346306e2",
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"ID":"talk.weld-3e8-ba6c-19b2-aa18-3b11c9137a0e",
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},
{
"ID":"mite.gems-7d8-2798-dd02-581a-b202e2d6c657",
"symbol":"STX12",
"name":"syntaxin 12"
},
{
"ID":"snip.hoop-bf2-a3c8-d2c2-6b24-f492eebca97e",
"symbol":"STX16",
"name":"syntaxin 16"
},
{
"ID":"dash.arms-612-6244-dc22-8a41-e6020da03bb7",
"symbol":"STX18",
"name":"syntaxin 18"
},
{
"ID":"ends.pump-b58-a995-ca62-3afa-d8eabcccf566",
"symbol":"STX19",
"name":"syntaxin 19"
},
{
"ID":"rise.rail-b97-a9b1-d852-39d4-ba1e66a68310",
"symbol":"SEC22B",
"name":"SEC22 homolog B, vesicle trafficking protein"
},
{
"ID":"melt.span-184-b3c0-c902-a8cf-6579894682a2",
"symbol":"ATG4A",
"name":"autophagy related 4A cysteine peptidase"
},
{
"ID":"june.neat-93c-537f-8202-5b27-873449a7ce28",
"symbol":"ATG4B",
"name":"autophagy related 4B cysteine peptidase"
},
{
"ID":"rail.rail-357-d5a2-0dd2-aaab-ec0c435af6fa",
"symbol":"ATG4C",
"name":"autophagy related 4C cysteine peptidase"
},
{
"ID":"wise.hive-648-cfb0-f042-281c-27c30eea6a21",
"symbol":"ATG4D",
"name":"autophagy related 4D cysteine peptidase"
},
{
"ID":"hash.cute-394-0fe5-5102-2bd5-c3c87ec06919",
"symbol":"SNAP23",
"name":"synaptosome associated protein 23"
},
{
"ID":"foil.tune-b62-896e-7112-5995-bd865236a222",
"symbol":"SNAP25",
"name":"synaptosome associated protein 25"}],

"note":[{
"ID":"hoop.soul-75e-c6bb-f7a2-2a71-c78d21456ce1",
"targetID":"isle.gait-a82-1ff7-70b2-e810-fd2dd3c1c465",
"typeID":"snow.gram-8a2-cb70-96e2-daba-61933e196c9b",
"note":"LC3 is a member of the Atg8 protein family (pmid:30115558)."
},
{
"ID":"whey.gang-44f-deb3-ce72-3b35-ab092c467c34",
"targetID":"webs.laud-453-0049-6f12-59d2-c55101ab383b",
"typeID":"snow.gram-8a2-cb70-96e2-daba-61933e196c9b",
"note":"GABARAPL1 is a member of the Atg8 protein family (pmid:30115558)."
},
{
"ID":"shot.beds-878-03b0-1b22-fa9f-5cdfa307a978",
"targetID":"thru.fort-62b-f289-e932-b910-85ed42d6588b",
"typeID":"snow.gram-8a2-cb70-96e2-daba-61933e196c9b",
"note":"VPS16 (Vacuolar Protein Sorting) is one of the four subunits that are common to the HOPS complex and the CORVET complex (pmid:23645161)."
},
{
"ID":"used.your-5a8-1c69-6722-0946-a9f99f70dc0d",
"targetID":"meet.high-e7f-67d6-4fa2-8ae0-1a5338569f23",
"typeID":"snow.gram-8a2-cb70-96e2-daba-61933e196c9b",
"note":"VPS33 (Vacuolar Protein Sorting) is one of the four subunits that are common to the HOPS complex and the CORVET complex (pmid:23645161)."
},
{
"ID":"boat.lots-2b1-6f69-8ca2-783d-a49dec5a64a0",
"targetID":"wave.deem-5c8-d6ef-d192-5920-be2617eaa320",
"typeID":"snow.gram-8a2-cb70-96e2-daba-61933e196c9b",
"note":"VPS18 (Vacuolar Protein Sorting) is one of the four subunits that are common to the HOPS complex and the CORVET complex (pmid:23645161)."
},
{
"ID":"fans.trap-e6e-982b-1092-7802-d8d06fd4cd6c",
"targetID":"hook.take-193-7c5c-b3b2-ba68-9b26aeb88e4f",
"typeID":"snow.gram-8a2-cb70-96e2-daba-61933e196c9b",
"note":"VPS11 (Vacuolar Protein Sorting) is one of the four subunits that are common to the HOPS complex and the CORVET complex (pmid:23645161)."
},
{
"ID":"fate.tell-bc9-74e6-c1e2-6b50-789076344e05",
"targetID":"soak.have-ead-d696-4292-8a1c-c6bd6dab86d8",
"typeID":"snow.gram-8a2-cb70-96e2-daba-61933e196c9b",
"note":"VPS41 (Vacuolar Protein Sorting) is one of the two subunits that are specific to the HOPS complex (pmid:23645161)."
},
{
"ID":"saws.care-2f8-34f8-b092-2a17-fedc96ecf116",
"targetID":"leap.code-1e6-a805-9e82-88da-dc3c7a9b0939",
"typeID":"snow.gram-8a2-cb70-96e2-daba-61933e196c9b",
"note":"VPS39 (Vacuolar Protein Sorting) is one of the two subunits that are specific to the HOPS complex (pmid:23645161)."}]}

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References

 

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