{"gene":"TG_229690","gene_symbol":"ATG7","run_date":"2026-09-08T11:06:49","timeline":{"discoveries":[{"year":2023,"finding":"TgATG7 functions as an E1-type enzyme that lipidates TgATG8 (the single T. gondii ATG8 homolog), and this catalytic activity (dependent on cysteine 1133) is required for TgATG8 localization to the apicoplast membrane and for apicoplast inheritance. A TgATG7 C1133S point mutant complemented line showed defects in TgATG8 lipidation, apicoplast fragmentation, and loss, establishing the catalytic mechanism.","method":"Conditional knockdown of TgATG7, point-mutant complementation (C1133S catalytic mutant), TgATG8 lipidation assays, apicoplast localization imaging, parasite growth assays","journal":"Biochimica et biophysica acta. Molecular basis of disease","confidence":"High","confidence_rationale":"Tier 1 / Moderate — catalytic-site mutagenesis combined with conditional knockdown and multiple orthogonal readouts (lipidation assay, organelle imaging, growth assay) in a single rigorous study","pmids":["37739091"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"finding":"TgATG7 directly binds unlipidated TgATG8 via its C-terminal domain (residues 1281–1290), and this interaction protects TgATG8 from multi-monoubiquitination-driven, proteasome-dependent degradation, thereby stabilizing the non-lipidated pool of TgATG8. Depletion of the TgATG8-interacting fragment of TgATG7 impaired parasite growth and apicoplast inheritance.","method":"Co-immunoprecipitation / direct interaction assay, deletion/truncation mapping of the interacting fragment, proteasome inhibition experiments, conditional knockdown and complementation","journal":"Biochimica et biophysica acta. Molecular basis of disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal interaction and functional fragment mapping in a single lab with multiple methods, but full reconstitution not described in abstract","pmids":["37739091"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2023,"finding":"Depletion of TgATG7 causes fragmentation of the mitochondrial network in addition to loss of the apicoplast, revealing a role for TgATG7 in maintenance of mitochondrial morphology in T. gondii tachyzoites.","method":"Conditional knockdown of TgATG7 with organelle morphology imaging","journal":"Biochimica et biophysica acta. Molecular basis of disease","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean conditional KO with defined organelle phenotype, single lab, single method for this specific finding","pmids":["37739091"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2016,"finding":"In induction of autophagy experiments using Pru TgAtg7-HA transgenic strains, TgAtg3 and TgAtg8 expression was significantly lower in bradyzoites than in tachyzoites and the number of TgAtg8 puncta-containing parasites was reduced in bradyzoites, indicating that the TgAtg7-dependent Atg8 conjugation system is downregulated during tachyzoite-to-bradyzoite differentiation. Pharmacological modulation (rapamycin/3-MA) altered bradyzoite-specific gene BAG1 levels, implicating autophagy in stage conversion.","method":"Transgenic HA-tagged TgAtg7 reporter strain, immunofluorescence for TgAtg8 puncta, western blot for TgAtg3/TgAtg8, pharmacological modulation (rapamycin, 3-MA)","journal":"Parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — transgenic parasite line with multiple readouts (protein expression, puncta counts, stage-specific marker), single lab","pmids":["26928609"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"Pru"}]},{"year":2014,"finding":"Host cell ATG7 (together with ATG3 and the ATG12-ATG5-ATG16L1 complex) is required for conjugation of LC3 to the parasitophorous vacuole membrane (PVM) of T. gondii and for subsequent recruitment of IFN-γ effectors (IRGs, GBPs) to the PVM, leading to vacuole disruption and parasite control. Pharmacological modulation of canonical/degradative autophagy had no effect, indicating a non-canonical membrane-remodeling role.","method":"Genetic knockout of host Atg7 (and other autophagy genes) in mouse cells, LC3/IRG/GBP localization by immunofluorescence, in vitro and in vivo parasite control assays","journal":"Immunity","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO with defined molecular (LC3/effector targeting) and functional (parasite killing) phenotypes, independently replicated across multiple labs in subsequent papers","pmids":["24931121"],"is_preprint":false,"attribution":[{"species":"Mus musculus","strain":""}]},{"year":2015,"finding":"In IFN-γ-activated human cells, knockout of ATG7 (or ATG16L) reverted membrane encapsulation of T. gondii-containing vacuoles and restored parasite replication, showing that host ATG7 is required for LC3 conjugation-dependent engulfment of susceptible T. gondii strains in human cells. This process does not involve fusion with lysosomes (unlike xenophagy), representing a non-canonical autophagy-dependent immune mechanism.","method":"Genetic knockout of ATG7 and ATG16L in human cells, LC3 localization, membrane encapsulation assay, parasite replication assay, lysosomal fusion assay (LAMP1)","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO with multiple orthogonal mechanistic readouts (LC3 targeting, membrane encapsulation, parasite growth) replicating findings from complementary labs","pmids":["26350966"],"is_preprint":false,"attribution":[{"species":"Homo sapiens","strain":""}]},{"year":2014,"finding":"In mouse macrophages, host Atg7 deficiency profoundly impairs IFN-γ-induced suppression of T. gondii proliferation and recruitment of the IRG Irgb6 and GBPs to the PVM. In contrast, loss of Atg9a or Atg14 does not impair this response, demonstrating that Atg7 occupies a specific node within the autophagy LC3-conjugation cascade required for anti-T. gondii immunity.","method":"Genetic knockout of individual autophagy genes (Atg7, Atg16L1, Atg9a, Atg14) in mouse cells, IRG/GBP localization by immunofluorescence, parasite proliferation assay under IFN-γ","journal":"Journal of immunology (Baltimore, Md. : 1950)","confidence":"High","confidence_rationale":"Tier 2 / Strong — differential genetic epistasis across multiple autophagy KOs with defined molecular and cellular phenotypes, independent lab replicating core ATG7 finding","pmids":["24563254"],"is_preprint":false,"attribution":[{"species":"Mus musculus","strain":""}]},{"year":2016,"finding":"The LC3 conjugation system (requiring ATG7, ATG3, and ATG12-ATG5-ATG16L1) is necessary and sufficient to target LC3 homologs (GABARAP, GABARAPL1, GABARAPL2) to the PVM of T. gondii, and this membrane lipidation event in turn directs IFN-γ-inducible GTPases (IRGs/GBPs) to the PVM. Relocation of ATG12-ATG5-ATG16L1 to alternative target membranes redirected GTPase targeting to those membranes, establishing the conjugation site as the determinant of effector recruitment.","method":"Knockdown/knockout of LC3 homologs, ectopic relocation of ATG12-ATG5-ATG16L1 complex to alternative membranes, immunofluorescence for GTPase targeting, parasite control assays","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 2 / Strong — epistatic reconstitution experiment (complex relocation) plus genetic KO with mechanistic readout, confirming prior findings with additional molecular mechanism","pmids":["27172324"],"is_preprint":false,"attribution":[{"species":"Mus musculus","strain":""}]},{"year":2010,"finding":"Host Atg7 (targeted to microglia/macrophages) is required for CD40-triggered killing of T. gondii and for in vivo resistance to cerebral and ocular toxoplasmosis. CD40 engagement induces autophagy through a CD40-p21-Beclin 1 axis, and Atg7-deficient macrophages cannot kill T. gondii via this pathway despite intact IFN-γ responses.","method":"Conditional (myeloid-targeted) Atg7 knockout mice, T. gondii killing assays in microglia/macrophages, in vivo toxoplasmosis model, Beclin 1 and p21 western blots","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Strong — cell-type-specific genetic KO with both in vitro mechanistic and in vivo phenotypic validation, multiple methods","pmids":["21217818"],"is_preprint":false,"attribution":[{"species":"Mus musculus","strain":""}]},{"year":2013,"finding":"In CD40-stimulated nonhematopoietic cells (endothelial cells, retinal pigment epithelial cells), host Atg7 (and Beclin 1) are required for LAMP-1 accumulation around the T. gondii vacuole and for lysosomal enzyme-dependent killing of the parasite. Knockdown of Atg7 abolished LC3 recruitment to the parasite and parasite killing.","method":"Atg7 and Beclin 1 knockdown in endothelial and RPE cells, LAMP-1 and LC3 immunofluorescence, parasite viability assays, lysosomal inhibitor treatments","journal":"Infection and immunity","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown with multiple molecular and functional readouts, single lab","pmids":["23509150"],"is_preprint":false,"attribution":[{"species":"Homo sapiens","strain":""},{"species":"Mus musculus","strain":""}]},{"year":2013,"finding":"In endothelial, retinal pigment epithelial, and microglial cells, EGFR-Akt signaling activated by T. gondii micronemal EGF-domain proteins (MIC3, MIC6) suppresses Atg7- and Beclin 1-dependent autophagic targeting of the parasite vacuole to lysosomes. Blockade of EGFR or Akt restored LC3 recruitment, vacuole-lysosomal fusion, and Atg7-dependent parasite killing.","method":"EGFR/Akt pharmacological blockade, Atg7 and Beclin 1 siRNA knockdown, MIC knockout parasites, LC3 immunofluorescence, lysosomal fusion assay, parasite viability","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic (MIC KO parasites, Atg7 KD) and pharmacological approaches with mechanistic readouts, single lab","pmids":["24367261"],"is_preprint":false,"attribution":[{"species":"Homo sapiens","strain":""},{"species":"Mus musculus","strain":""}]},{"year":2015,"finding":"Atg7 deficiency in dendritic cells does NOT impair IL-2 or IFN-γ production by Toxoplasma gondii-reactive CD4+ T cells stimulated with T. gondii-infected or antigen-pulsed Atg7-deficient DCs. In contrast, Atg5 deficiency in DCs diminishes these cytokine responses, establishing that Atg5 and Atg7 have differential roles in DC-mediated priming of T cell responses.","method":"Atg5- and Atg7-deficient mouse dendritic cells co-cultured with T. gondii-reactive CD4+ T cells, cytokine measurement (IL-2, IFN-γ), costimulatory ligand and cytokine profiling","journal":"Microbes and infection","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — comparative genetic KO (Atg5 vs Atg7) with defined functional readouts, single lab; negative result for Atg7 is mechanistically informative","pmids":["25578385"],"is_preprint":false,"attribution":[{"species":"Mus musculus","strain":""}]},{"year":2024,"finding":"Genetic knockout of host ATG7 in THP-1 monocytic cells does NOT affect IL-1β release during T. gondii infection, indicating that the IL-1β secretion mechanism in human monocytes is independent of ATG7.","method":"ATG7 KO THP-1 cells (CRISPR), IL-1β ELISA during T. gondii infection","journal":"Journal of immunology (Baltimore, Md. : 1950)","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean genetic KO with defined functional readout, but this is a negative result reported by a single lab","pmids":["38372637"],"is_preprint":false,"attribution":[{"species":"Homo sapiens","strain":"THP-1"}]}],"current_model":"In Toxoplasma gondii itself, TgATG7 functions as the E1-like enzyme that lipidates TgATG8 (dependent on catalytic Cys1133), targets TgATG8 to the apicoplast outer membrane, and additionally stabilizes the non-lipidated TgATG8 pool by binding it directly (via residues 1281–1290) and protecting it from ubiquitin-proteasome degradation, thereby maintaining apicoplast inheritance, mitochondrial morphology, and parasite viability; in host cells, ATG7 is a required component of the LC3-conjugation system that lipidates LC3 homologs onto the parasitophorous vacuole membrane, enabling recruitment of IFN-γ effectors (IRGs, GBPs) and membrane-encapsulation of the vacuole in both mouse and human cells, while being dispensable for DC-mediated T cell priming and IL-1β secretion during infection."},"narrative":{"mechanistic_narrative":"ATG7 is an E1-type activating enzyme of the ATG8/LC3 conjugation cascade that operates in two distinct biological contexts captured by this corpus: within the parasite Toxoplasma gondii and within host cells during infection. In T. gondii, TgATG7 lipidates the single ATG8 homolog TgATG8 in a manner strictly dependent on catalytic cysteine 1133, and this activity is required to target TgATG8 to the apicoplast membrane and to sustain apicoplast inheritance [PMID:37739091]. Beyond catalysis, TgATG7 directly binds unlipidated TgATG8 through its C-terminal residues 1281–1290, shielding this pool from multi-monoubiquitination and proteasomal degradation, so that loss of the interacting fragment impairs parasite growth and apicoplast inheritance [PMID:37739091]; TgATG7 depletion additionally fragments the mitochondrial network [PMID:37739091]. The TgATG7-dependent conjugation system is downregulated during tachyzoite-to-bradyzoite differentiation [PMID:26928609]. In host cells, ATG7 is a required component of the LC3-conjugation machinery (acting with ATG3 and the ATG12–ATG5–ATG16L1 complex) that lipidates LC3 and its GABARAP-family homologs onto the parasitophorous vacuole membrane; this lipidation event is the determinant that recruits IFN-γ-inducible effector GTPases (IRGs, GBPs) to the vacuole, driving vacuole disruption and parasite control [PMID:24931121, PMID:27172324]. In IFN-γ-activated human cells ATG7 is required for LC3-dependent membrane encapsulation of the vacuole and restriction of parasite replication through a non-degradative, lysosome-independent route [PMID:26350966], and it occupies a specific node in the cascade distinct from ATG9a and ATG14 in mouse macrophages [PMID:24563254]. ATG7 is also required for CD40-triggered, Beclin 1-dependent parasite killing and in vivo resistance to cerebral and ocular toxoplasmosis [PMID:21217818], and for lysosomal targeting of the vacuole in CD40-stimulated nonhematopoietic cells, a pathway antagonized by parasite EGF-domain proteins acting through EGFR-Akt [PMID:23509150, PMID:24367261]. In contrast, host ATG7 is dispensable for dendritic-cell-mediated T cell priming [PMID:25578385] and for IL-1β secretion in human monocytes [PMID:38372637].","teleology":[{"year":2010,"claim":"Established that host ATG7 is functionally required for pathogen killing in vivo, not merely a general autophagy component, by linking it to CD40-driven macrophage defense.","evidence":"Myeloid-targeted conditional Atg7 knockout mice with in vitro killing assays and in vivo cerebral/ocular toxoplasmosis models","pmids":["21217818"],"confidence":"High","gaps":["Did not resolve whether killing proceeds via LC3 lipidation or another ATG7-dependent step","Molecular target of the CD40-p21-Beclin 1 axis on the vacuole not defined"],"attribution":[{"species":"Mus musculus","strain":""}]},{"year":2013,"claim":"Defined the downstream consequence of host ATG7 activity in nonhematopoietic cells as LC3/LAMP-1 recruitment enabling lysosomal killing, and showed the parasite actively suppresses this arm via EGFR-Akt signaling.","evidence":"Atg7/Beclin 1 knockdown in endothelial and RPE cells, LAMP-1/LC3 imaging, lysosomal inhibitors; combined with EGFR/Akt blockade and MIC-knockout parasites","pmids":["23509150","24367261"],"confidence":"Medium","gaps":["siRNA knockdown rather than full genetic ablation for the ATG7 arm","How EGFR-Akt signaling mechanistically intersects the ATG7 conjugation step is not mapped"],"attribution":[{"species":"Homo sapiens","strain":""},{"species":"Mus musculus","strain":""}]},{"year":2014,"claim":"Placed host ATG7 at a specific node of the LC3-conjugation cascade required for non-canonical, membrane-remodeling immunity, distinguishing it from degradative autophagy and from other ATG genes.","evidence":"Genetic knockout of Atg7 versus Atg9a/Atg14 in mouse cells, LC3/IRG/GBP localization on the PVM, parasite control assays in vitro and in vivo","pmids":["24931121","24563254"],"confidence":"High","gaps":["Did not identify which LC3 homolog(s) are the relevant conjugation substrate","Mechanism linking lipidation to effector GTPase recruitment not yet resolved"],"attribution":[{"species":"Mus musculus","strain":""}]},{"year":2015,"claim":"Extended the ATG7-dependent restriction mechanism to human cells and showed it is lysosome-independent membrane encapsulation, distinct from classical xenophagy.","evidence":"Genetic knockout of ATG7 and ATG16L in human cells with LC3 localization, membrane encapsulation, LAMP1 fusion, and parasite replication assays","pmids":["26350966"],"confidence":"High","gaps":["The fate of the encapsulated parasite without lysosomal fusion is not fully defined","Strain-dependence of susceptibility not fully mechanistically explained"],"attribution":[{"species":"Homo sapiens","strain":""}]},{"year":2015,"claim":"Dissected ATG7 from a related conjugation gene functionally, showing ATG7 is dispensable for dendritic-cell priming of T cell responses while ATG5 is required.","evidence":"Comparative Atg5- vs Atg7-deficient dendritic cells co-cultured with T. gondii-reactive CD4+ T cells, IL-2/IFN-γ readouts","pmids":["25578385"],"confidence":"Medium","gaps":["Negative result from a single lab","Does not explain the molecular basis for the ATG5/ATG7 divergence in DC priming"],"attribution":[{"species":"Mus musculus","strain":""}]},{"year":2016,"claim":"Identified the conjugation site itself as the determinant of effector recruitment, showing the ATG7-dependent lipidation of GABARAP-family LC3 homologs is necessary and sufficient to direct IFN-γ-inducible GTPases to a target membrane.","evidence":"Knockdown/knockout of LC3 homologs and ectopic relocation of the ATG12-ATG5-ATG16L1 complex, with GTPase targeting imaging and parasite control assays","pmids":["27172324"],"confidence":"High","gaps":["Direct biochemical link between lipidated LC3 and GTPase docking not defined","Contribution of individual GABARAP homologs not separated"],"attribution":[{"species":"Mus musculus","strain":""}]},{"year":2016,"claim":"Showed the TgATG7-dependent Atg8 conjugation system is developmentally regulated in the parasite, being downregulated during tachyzoite-to-bradyzoite differentiation.","evidence":"Transgenic HA-tagged TgAtg7 Pru strain, TgAtg8 puncta immunofluorescence, TgAtg3/TgAtg8 western blots, rapamycin/3-MA modulation of BAG1","pmids":["26928609"],"confidence":"Medium","gaps":["Causal role of TgATG7 downregulation in stage conversion not established genetically","Pharmacological modulators are not ATG7-specific"],"attribution":[{"species":"Toxoplasma gondii","strain":"Pru"}]},{"year":2023,"claim":"Established the catalytic mechanism of TgATG7 as an E1 enzyme and its dual role in both lipidating and stabilizing TgATG8 to maintain organelle inheritance in the parasite itself.","evidence":"Conditional knockdown with C1133S catalytic-mutant complementation, TgATG8 lipidation assays, interaction/truncation mapping (residues 1281-1290), proteasome inhibition, apicoplast and mitochondrial imaging, growth assays","pmids":["37739091"],"confidence":"High","gaps":["Full biochemical reconstitution of the E1 reaction not described","Mechanism connecting apicoplast loss to mitochondrial fragmentation unresolved","Identity of the ubiquitin ligase acting on unlipidated TgATG8 unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2024,"claim":"Delineated the boundary of host ATG7 function in innate signaling by showing IL-1β release in human monocytes proceeds independently of ATG7.","evidence":"CRISPR ATG7 knockout THP-1 cells, IL-1β ELISA during T. gondii infection","pmids":["38372637"],"confidence":"Medium","gaps":["Negative result from a single lab and single cell line","Does not identify the ATG7-independent pathway responsible for IL-1β"],"attribution":[{"species":"Homo sapiens","strain":"THP-1"}]},{"year":null,"claim":"How the ATG7-dependent LC3 lipidation mark is biochemically read out by IFN-γ-inducible GTPases, and how parasite strain determinants dictate susceptibility to this pathway, remain open.","evidence":"No direct experiment in the corpus resolves the lipidation-to-GTPase-docking step","pmids":[],"confidence":"Low","gaps":["No direct biochemical demonstration of GTPase recognition of lipidated LC3","No structural model of TgATG7 catalysis or its TgATG8 interaction"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["LC3-conjugation system (ATG7 with ATG3 and the ATG12-ATG5-ATG16L1 complex) [#4, #7]"],"partners":["TGATG8 (DIRECT BINDING VIA TGATG7 RESIDUES 1281-1290, AND LIPIDATION SUBSTRATE) [#0, #1]","TGATG3 (CO-REGULATED CONJUGATION COMPONENT) [#3]","LC3 / GABARAP / GABARAPL1 / GABARAPL2 (HOST CONJUGATION SUBSTRATES) [#7]","ATG3 (HOST, CO-REQUIRED FOR LC3 CONJUGATION) [#4]","ATG12-ATG5-ATG16L1 COMPLEX (HOST) [#4, #7]","BECLIN 1 (CO-REQUIRED IN CD40-DRIVEN AND LYSOSOMAL KILLING) [#8, #9]"],"other_free_text":["TgATG7 catalytic activity depends on cysteine 1133; a C1133S mutant abolishes TgATG8 lipidation and causes apicoplast fragmentation and loss [#0].","TgATG7 protects unlipidated TgATG8 from multi-monoubiquitination-driven proteasomal degradation [#1].","Host ATG7 occupies a specific node in the LC3-conjugation cascade distinct from ATG9a and ATG14 [#6], and functionally diverges from ATG5 in dendritic-cell T cell priming [#11].","The membrane conjugation site of lipidated LC3 is the determinant of IFN-γ-inducible GTPase recruitment [#7].","Host ATG7 is dispensable for IL-1β secretion in human monocytes [#12] and for DC-mediated CD4+ T cell cytokine priming [#11].","Parasite EGF-domain micronemal proteins (MIC3, MIC6) suppress ATG7-dependent lysosomal targeting via host EGFR-Akt signaling [#10]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"24931121","id":"PMC_24931121","title":"The parasitophorous vacuole membrane of Toxoplasma gondii is targeted for disruption by ubiquitin-like conjugation systems of autophagy.","date":"2014","source":"Immunity","url":"https://pubmed.ncbi.nlm.nih.gov/24931121","citation_count":159,"is_preprint":false},{"pmid":"26350966","id":"PMC_26350966","title":"A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-γ-Activated Human Cells.","date":"2015","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/26350966","citation_count":128,"is_preprint":false},{"pmid":"24367261","id":"PMC_24367261","title":"Toxoplasma gondii-induced activation of EGFR prevents autophagy protein-mediated killing of the parasite.","date":"2013","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/24367261","citation_count":106,"is_preprint":false},{"pmid":"24563254","id":"PMC_24563254","title":"Role of mouse and human autophagy proteins in IFN-γ-induced cell-autonomous responses against Toxoplasma gondii.","date":"2014","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/24563254","citation_count":103,"is_preprint":false},{"pmid":"27172324","id":"PMC_27172324","title":"Targeting by AutophaGy proteins (TAG): Targeting of IFNG-inducible GTPases to membranes by the LC3 conjugation system of autophagy.","date":"2016","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/27172324","citation_count":72,"is_preprint":false},{"pmid":"21217818","id":"PMC_21217818","title":"The CD40-autophagy pathway is needed for host protection despite IFN-Γ-dependent immunity and CD40 induces autophagy via control of P21 levels.","date":"2010","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21217818","citation_count":59,"is_preprint":false},{"pmid":"23509150","id":"PMC_23509150","title":"CD40 induces anti-Toxoplasma gondii activity in nonhematopoietic cells dependent on autophagy proteins.","date":"2013","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/23509150","citation_count":55,"is_preprint":false},{"pmid":"25578385","id":"PMC_25578385","title":"Atg5 but not Atg7 in dendritic cells enhances IL-2 and IFN-γ production by Toxoplasma gondii-reactive CD4+ T cells.","date":"2015","source":"Microbes and infection","url":"https://pubmed.ncbi.nlm.nih.gov/25578385","citation_count":39,"is_preprint":false},{"pmid":"38372637","id":"PMC_38372637","title":"Role for Caspase-8 in the Release of IL-1β and Active Caspase-1 from Viable Human Monocytes during Toxoplasma gondii Infection.","date":"2024","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/38372637","citation_count":10,"is_preprint":false},{"pmid":"26928609","id":"PMC_26928609","title":"Induction of Autophagy interferes the tachyzoite to bradyzoite transformation of Toxoplasma gondii.","date":"2016","source":"Parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/26928609","citation_count":9,"is_preprint":false},{"pmid":"35757711","id":"PMC_35757711","title":"Toxoplasma gondii CDPK3 Controls the Intracellular Proliferation of Parasites in Macrophages.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/35757711","citation_count":8,"is_preprint":false},{"pmid":"37739091","id":"PMC_37739091","title":"Toxoplasma gondii autophagy-related protein ATG7 maintains apicoplast inheritance by stabilizing and lipidating ATG8.","date":"2023","source":"Biochimica et biophysica acta. Molecular basis of disease","url":"https://pubmed.ncbi.nlm.nih.gov/37739091","citation_count":7,"is_preprint":false},{"pmid":"34453672","id":"PMC_34453672","title":"Toxoplasma gondii profilin and tachyzoites RH strain may manipulate autophagy via downregulating Atg5 and Atg12 and upregulating Atg7.","date":"2021","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/34453672","citation_count":7,"is_preprint":false},{"pmid":"36941573","id":"PMC_36941573","title":"Evaluation of the mTORC activity in the presence of Toxoplasma gondii and azathioprine in human monocyte cell line.","date":"2023","source":"BMC microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/36941573","citation_count":1,"is_preprint":false},{"pmid":"40668463","id":"PMC_40668463","title":"Toxoplasma gondii soluble antigen (STAg) induces resistance against Mycobacterium tuberculosis in a human monocyte cell line via P2X7 receptor.","date":"2025","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/40668463","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11376,"output_tokens":4252,"usd":0.048954,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10512,"output_tokens":5363,"usd":0.093317,"stage2_stop_reason":"end_turn"},"total_usd":0.142271,"stage1_batch_id":"msgbatch_01WokvBYTB6JLnYrpD4rXnyV","stage2_batch_id":"msgbatch_01M7hsQDvz6AqVC9DLVjQzzc","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"TgATG7 functions as an E1-type enzyme that lipidates TgATG8 (the single T. gondii ATG8 homolog), and this catalytic activity (dependent on cysteine 1133) is required for TgATG8 localization to the apicoplast membrane and for apicoplast inheritance. A TgATG7 C1133S point mutant complemented line showed defects in TgATG8 lipidation, apicoplast fragmentation, and loss, establishing the catalytic mechanism.\",\n      \"method\": \"Conditional knockdown of TgATG7, point-mutant complementation (C1133S catalytic mutant), TgATG8 lipidation assays, apicoplast localization imaging, parasite growth assays\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular basis of disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — catalytic-site mutagenesis combined with conditional knockdown and multiple orthogonal readouts (lipidation assay, organelle imaging, growth assay) in a single rigorous study\",\n      \"pmids\": [\"37739091\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TgATG7 directly binds unlipidated TgATG8 via its C-terminal domain (residues 1281–1290), and this interaction protects TgATG8 from multi-monoubiquitination-driven, proteasome-dependent degradation, thereby stabilizing the non-lipidated pool of TgATG8. Depletion of the TgATG8-interacting fragment of TgATG7 impaired parasite growth and apicoplast inheritance.\",\n      \"method\": \"Co-immunoprecipitation / direct interaction assay, deletion/truncation mapping of the interacting fragment, proteasome inhibition experiments, conditional knockdown and complementation\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular basis of disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal interaction and functional fragment mapping in a single lab with multiple methods, but full reconstitution not described in abstract\",\n      \"pmids\": [\"37739091\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Depletion of TgATG7 causes fragmentation of the mitochondrial network in addition to loss of the apicoplast, revealing a role for TgATG7 in maintenance of mitochondrial morphology in T. gondii tachyzoites.\",\n      \"method\": \"Conditional knockdown of TgATG7 with organelle morphology imaging\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular basis of disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean conditional KO with defined organelle phenotype, single lab, single method for this specific finding\",\n      \"pmids\": [\"37739091\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"In induction of autophagy experiments using Pru TgAtg7-HA transgenic strains, TgAtg3 and TgAtg8 expression was significantly lower in bradyzoites than in tachyzoites and the number of TgAtg8 puncta-containing parasites was reduced in bradyzoites, indicating that the TgAtg7-dependent Atg8 conjugation system is downregulated during tachyzoite-to-bradyzoite differentiation. Pharmacological modulation (rapamycin/3-MA) altered bradyzoite-specific gene BAG1 levels, implicating autophagy in stage conversion.\",\n      \"method\": \"Transgenic HA-tagged TgAtg7 reporter strain, immunofluorescence for TgAtg8 puncta, western blot for TgAtg3/TgAtg8, pharmacological modulation (rapamycin, 3-MA)\",\n      \"journal\": \"Parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — transgenic parasite line with multiple readouts (protein expression, puncta counts, stage-specific marker), single lab\",\n      \"pmids\": [\"26928609\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"Pru\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Host cell ATG7 (together with ATG3 and the ATG12-ATG5-ATG16L1 complex) is required for conjugation of LC3 to the parasitophorous vacuole membrane (PVM) of T. gondii and for subsequent recruitment of IFN-γ effectors (IRGs, GBPs) to the PVM, leading to vacuole disruption and parasite control. Pharmacological modulation of canonical/degradative autophagy had no effect, indicating a non-canonical membrane-remodeling role.\",\n      \"method\": \"Genetic knockout of host Atg7 (and other autophagy genes) in mouse cells, LC3/IRG/GBP localization by immunofluorescence, in vitro and in vivo parasite control assays\",\n      \"journal\": \"Immunity\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO with defined molecular (LC3/effector targeting) and functional (parasite killing) phenotypes, independently replicated across multiple labs in subsequent papers\",\n      \"pmids\": [\"24931121\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"In IFN-γ-activated human cells, knockout of ATG7 (or ATG16L) reverted membrane encapsulation of T. gondii-containing vacuoles and restored parasite replication, showing that host ATG7 is required for LC3 conjugation-dependent engulfment of susceptible T. gondii strains in human cells. This process does not involve fusion with lysosomes (unlike xenophagy), representing a non-canonical autophagy-dependent immune mechanism.\",\n      \"method\": \"Genetic knockout of ATG7 and ATG16L in human cells, LC3 localization, membrane encapsulation assay, parasite replication assay, lysosomal fusion assay (LAMP1)\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO with multiple orthogonal mechanistic readouts (LC3 targeting, membrane encapsulation, parasite growth) replicating findings from complementary labs\",\n      \"pmids\": [\"26350966\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Homo sapiens\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In mouse macrophages, host Atg7 deficiency profoundly impairs IFN-γ-induced suppression of T. gondii proliferation and recruitment of the IRG Irgb6 and GBPs to the PVM. In contrast, loss of Atg9a or Atg14 does not impair this response, demonstrating that Atg7 occupies a specific node within the autophagy LC3-conjugation cascade required for anti-T. gondii immunity.\",\n      \"method\": \"Genetic knockout of individual autophagy genes (Atg7, Atg16L1, Atg9a, Atg14) in mouse cells, IRG/GBP localization by immunofluorescence, parasite proliferation assay under IFN-γ\",\n      \"journal\": \"Journal of immunology (Baltimore, Md. : 1950)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — differential genetic epistasis across multiple autophagy KOs with defined molecular and cellular phenotypes, independent lab replicating core ATG7 finding\",\n      \"pmids\": [\"24563254\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The LC3 conjugation system (requiring ATG7, ATG3, and ATG12-ATG5-ATG16L1) is necessary and sufficient to target LC3 homologs (GABARAP, GABARAPL1, GABARAPL2) to the PVM of T. gondii, and this membrane lipidation event in turn directs IFN-γ-inducible GTPases (IRGs/GBPs) to the PVM. Relocation of ATG12-ATG5-ATG16L1 to alternative target membranes redirected GTPase targeting to those membranes, establishing the conjugation site as the determinant of effector recruitment.\",\n      \"method\": \"Knockdown/knockout of LC3 homologs, ectopic relocation of ATG12-ATG5-ATG16L1 complex to alternative membranes, immunofluorescence for GTPase targeting, parasite control assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — epistatic reconstitution experiment (complex relocation) plus genetic KO with mechanistic readout, confirming prior findings with additional molecular mechanism\",\n      \"pmids\": [\"27172324\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Host Atg7 (targeted to microglia/macrophages) is required for CD40-triggered killing of T. gondii and for in vivo resistance to cerebral and ocular toxoplasmosis. CD40 engagement induces autophagy through a CD40-p21-Beclin 1 axis, and Atg7-deficient macrophages cannot kill T. gondii via this pathway despite intact IFN-γ responses.\",\n      \"method\": \"Conditional (myeloid-targeted) Atg7 knockout mice, T. gondii killing assays in microglia/macrophages, in vivo toxoplasmosis model, Beclin 1 and p21 western blots\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — cell-type-specific genetic KO with both in vitro mechanistic and in vivo phenotypic validation, multiple methods\",\n      \"pmids\": [\"21217818\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"In CD40-stimulated nonhematopoietic cells (endothelial cells, retinal pigment epithelial cells), host Atg7 (and Beclin 1) are required for LAMP-1 accumulation around the T. gondii vacuole and for lysosomal enzyme-dependent killing of the parasite. Knockdown of Atg7 abolished LC3 recruitment to the parasite and parasite killing.\",\n      \"method\": \"Atg7 and Beclin 1 knockdown in endothelial and RPE cells, LAMP-1 and LC3 immunofluorescence, parasite viability assays, lysosomal inhibitor treatments\",\n      \"journal\": \"Infection and immunity\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown with multiple molecular and functional readouts, single lab\",\n      \"pmids\": [\"23509150\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Homo sapiens\", \"strain\": \"\"}, {\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"In endothelial, retinal pigment epithelial, and microglial cells, EGFR-Akt signaling activated by T. gondii micronemal EGF-domain proteins (MIC3, MIC6) suppresses Atg7- and Beclin 1-dependent autophagic targeting of the parasite vacuole to lysosomes. Blockade of EGFR or Akt restored LC3 recruitment, vacuole-lysosomal fusion, and Atg7-dependent parasite killing.\",\n      \"method\": \"EGFR/Akt pharmacological blockade, Atg7 and Beclin 1 siRNA knockdown, MIC knockout parasites, LC3 immunofluorescence, lysosomal fusion assay, parasite viability\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic (MIC KO parasites, Atg7 KD) and pharmacological approaches with mechanistic readouts, single lab\",\n      \"pmids\": [\"24367261\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Homo sapiens\", \"strain\": \"\"}, {\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Atg7 deficiency in dendritic cells does NOT impair IL-2 or IFN-γ production by Toxoplasma gondii-reactive CD4+ T cells stimulated with T. gondii-infected or antigen-pulsed Atg7-deficient DCs. In contrast, Atg5 deficiency in DCs diminishes these cytokine responses, establishing that Atg5 and Atg7 have differential roles in DC-mediated priming of T cell responses.\",\n      \"method\": \"Atg5- and Atg7-deficient mouse dendritic cells co-cultured with T. gondii-reactive CD4+ T cells, cytokine measurement (IL-2, IFN-γ), costimulatory ligand and cytokine profiling\",\n      \"journal\": \"Microbes and infection\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — comparative genetic KO (Atg5 vs Atg7) with defined functional readouts, single lab; negative result for Atg7 is mechanistically informative\",\n      \"pmids\": [\"25578385\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Genetic knockout of host ATG7 in THP-1 monocytic cells does NOT affect IL-1β release during T. gondii infection, indicating that the IL-1β secretion mechanism in human monocytes is independent of ATG7.\",\n      \"method\": \"ATG7 KO THP-1 cells (CRISPR), IL-1β ELISA during T. gondii infection\",\n      \"journal\": \"Journal of immunology (Baltimore, Md. : 1950)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean genetic KO with defined functional readout, but this is a negative result reported by a single lab\",\n      \"pmids\": [\"38372637\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Homo sapiens\", \"strain\": \"THP-1\"}]\n    }\n  ],\n  \"current_model\": \"In Toxoplasma gondii itself, TgATG7 functions as the E1-like enzyme that lipidates TgATG8 (dependent on catalytic Cys1133), targets TgATG8 to the apicoplast outer membrane, and additionally stabilizes the non-lipidated TgATG8 pool by binding it directly (via residues 1281–1290) and protecting it from ubiquitin-proteasome degradation, thereby maintaining apicoplast inheritance, mitochondrial morphology, and parasite viability; in host cells, ATG7 is a required component of the LC3-conjugation system that lipidates LC3 homologs onto the parasitophorous vacuole membrane, enabling recruitment of IFN-γ effectors (IRGs, GBPs) and membrane-encapsulation of the vacuole in both mouse and human cells, while being dispensable for DC-mediated T cell priming and IL-1β secretion during infection.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ATG7 is an E1-type activating enzyme of the ATG8/LC3 conjugation cascade that operates in two distinct biological contexts captured by this corpus: within the parasite Toxoplasma gondii and within host cells during infection. In T. gondii, TgATG7 lipidates the single ATG8 homolog TgATG8 in a manner strictly dependent on catalytic cysteine 1133, and this activity is required to target TgATG8 to the apicoplast membrane and to sustain apicoplast inheritance [#0]. Beyond catalysis, TgATG7 directly binds unlipidated TgATG8 through its C-terminal residues 1281\\u20131290, shielding this pool from multi-monoubiquitination and proteasomal degradation, so that loss of the interacting fragment impairs parasite growth and apicoplast inheritance [#1]; TgATG7 depletion additionally fragments the mitochondrial network [#2]. The TgATG7-dependent conjugation system is downregulated during tachyzoite-to-bradyzoite differentiation [#3]. In host cells, ATG7 is a required component of the LC3-conjugation machinery (acting with ATG3 and the ATG12\\u2013ATG5\\u2013ATG16L1 complex) that lipidates LC3 and its GABARAP-family homologs onto the parasitophorous vacuole membrane; this lipidation event is the determinant that recruits IFN-\\u03b3-inducible effector GTPases (IRGs, GBPs) to the vacuole, driving vacuole disruption and parasite control [#4, #7]. In IFN-\\u03b3-activated human cells ATG7 is required for LC3-dependent membrane encapsulation of the vacuole and restriction of parasite replication through a non-degradative, lysosome-independent route [#5], and it occupies a specific node in the cascade distinct from ATG9a and ATG14 in mouse macrophages [#6]. ATG7 is also required for CD40-triggered, Beclin 1-dependent parasite killing and in vivo resistance to cerebral and ocular toxoplasmosis [#8], and for lysosomal targeting of the vacuole in CD40-stimulated nonhematopoietic cells, a pathway antagonized by parasite EGF-domain proteins acting through EGFR-Akt [#9, #10]. In contrast, host ATG7 is dispensable for dendritic-cell-mediated T cell priming [#11] and for IL-1\\u03b2 secretion in human monocytes [#12].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established that host ATG7 is functionally required for pathogen killing in vivo, not merely a general autophagy component, by linking it to CD40-driven macrophage defense.\",\n      \"evidence\": \"Myeloid-targeted conditional Atg7 knockout mice with in vitro killing assays and in vivo cerebral/ocular toxoplasmosis models\",\n      \"pmids\": [\"21217818\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve whether killing proceeds via LC3 lipidation or another ATG7-dependent step\", \"Molecular target of the CD40-p21-Beclin 1 axis on the vacuole not defined\"],\n      \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defined the downstream consequence of host ATG7 activity in nonhematopoietic cells as LC3/LAMP-1 recruitment enabling lysosomal killing, and showed the parasite actively suppresses this arm via EGFR-Akt signaling.\",\n      \"evidence\": \"Atg7/Beclin 1 knockdown in endothelial and RPE cells, LAMP-1/LC3 imaging, lysosomal inhibitors; combined with EGFR/Akt blockade and MIC-knockout parasites\",\n      \"pmids\": [\"23509150\", \"24367261\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"siRNA knockdown rather than full genetic ablation for the ATG7 arm\", \"How EGFR-Akt signaling mechanistically intersects the ATG7 conjugation step is not mapped\"],\n      \"attribution\": [{\"species\": \"Homo sapiens\", \"strain\": \"\"}, {\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Placed host ATG7 at a specific node of the LC3-conjugation cascade required for non-canonical, membrane-remodeling immunity, distinguishing it from degradative autophagy and from other ATG genes.\",\n      \"evidence\": \"Genetic knockout of Atg7 versus Atg9a/Atg14 in mouse cells, LC3/IRG/GBP localization on the PVM, parasite control assays in vitro and in vivo\",\n      \"pmids\": [\"24931121\", \"24563254\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify which LC3 homolog(s) are the relevant conjugation substrate\", \"Mechanism linking lipidation to effector GTPase recruitment not yet resolved\"],\n      \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Extended the ATG7-dependent restriction mechanism to human cells and showed it is lysosome-independent membrane encapsulation, distinct from classical xenophagy.\",\n      \"evidence\": \"Genetic knockout of ATG7 and ATG16L in human cells with LC3 localization, membrane encapsulation, LAMP1 fusion, and parasite replication assays\",\n      \"pmids\": [\"26350966\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The fate of the encapsulated parasite without lysosomal fusion is not fully defined\", \"Strain-dependence of susceptibility not fully mechanistically explained\"],\n      \"attribution\": [{\"species\": \"Homo sapiens\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Dissected ATG7 from a related conjugation gene functionally, showing ATG7 is dispensable for dendritic-cell priming of T cell responses while ATG5 is required.\",\n      \"evidence\": \"Comparative Atg5- vs Atg7-deficient dendritic cells co-cultured with T. gondii-reactive CD4+ T cells, IL-2/IFN-\\u03b3 readouts\",\n      \"pmids\": [\"25578385\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Negative result from a single lab\", \"Does not explain the molecular basis for the ATG5/ATG7 divergence in DC priming\"],\n      \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identified the conjugation site itself as the determinant of effector recruitment, showing the ATG7-dependent lipidation of GABARAP-family LC3 homologs is necessary and sufficient to direct IFN-\\u03b3-inducible GTPases to a target membrane.\",\n      \"evidence\": \"Knockdown/knockout of LC3 homologs and ectopic relocation of the ATG12-ATG5-ATG16L1 complex, with GTPase targeting imaging and parasite control assays\",\n      \"pmids\": [\"27172324\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct biochemical link between lipidated LC3 and GTPase docking not defined\", \"Contribution of individual GABARAP homologs not separated\"],\n      \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed the TgATG7-dependent Atg8 conjugation system is developmentally regulated in the parasite, being downregulated during tachyzoite-to-bradyzoite differentiation.\",\n      \"evidence\": \"Transgenic HA-tagged TgAtg7 Pru strain, TgAtg8 puncta immunofluorescence, TgAtg3/TgAtg8 western blots, rapamycin/3-MA modulation of BAG1\",\n      \"pmids\": [\"26928609\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal role of TgATG7 downregulation in stage conversion not established genetically\", \"Pharmacological modulators are not ATG7-specific\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"Pru\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Established the catalytic mechanism of TgATG7 as an E1 enzyme and its dual role in both lipidating and stabilizing TgATG8 to maintain organelle inheritance in the parasite itself.\",\n      \"evidence\": \"Conditional knockdown with C1133S catalytic-mutant complementation, TgATG8 lipidation assays, interaction/truncation mapping (residues 1281-1290), proteasome inhibition, apicoplast and mitochondrial imaging, growth assays\",\n      \"pmids\": [\"37739091\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full biochemical reconstitution of the E1 reaction not described\", \"Mechanism connecting apicoplast loss to mitochondrial fragmentation unresolved\", \"Identity of the ubiquitin ligase acting on unlipidated TgATG8 unknown\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Delineated the boundary of host ATG7 function in innate signaling by showing IL-1\\u03b2 release in human monocytes proceeds independently of ATG7.\",\n      \"evidence\": \"CRISPR ATG7 knockout THP-1 cells, IL-1\\u03b2 ELISA during T. gondii infection\",\n      \"pmids\": [\"38372637\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Negative result from a single lab and single cell line\", \"Does not identify the ATG7-independent pathway responsible for IL-1\\u03b2\"],\n      \"attribution\": [{\"species\": \"Homo sapiens\", \"strain\": \"THP-1\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the ATG7-dependent LC3 lipidation mark is biochemically read out by IFN-\\u03b3-inducible GTPases, and how parasite strain determinants dictate susceptibility to this pathway, remain open.\",\n      \"evidence\": \"No direct experiment in the corpus resolves the lipidation-to-GTPase-docking step\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct biochemical demonstration of GTPase recognition of lipidated LC3\", \"No structural model of TgATG7 catalysis or its TgATG8 interaction\"],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0019778\", \"supporting_discovery_ids\": [0, 4, 7], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}, {\"species\": \"Mus musculus\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0019776\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0019787\", \"supporting_discovery_ids\": [0, 4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}, {\"species\": \"Mus musculus\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0005515\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0009528\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0097425\", \"supporting_discovery_ids\": [4, 7], \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0016236\", \"supporting_discovery_ids\": [0, 3, 8], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}, {\"species\": \"Mus musculus\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0061709\", \"supporting_discovery_ids\": [4, 5, 7], \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}, {\"species\": \"Homo sapiens\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0050830\", \"supporting_discovery_ids\": [4, 6, 8], \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0071345\", \"supporting_discovery_ids\": [4, 6, 7], \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0006914\", \"supporting_discovery_ids\": [8, 9, 10], \"attribution\": [{\"species\": \"Mus musculus\", \"strain\": \"\"}, {\"species\": \"Homo sapiens\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\n      \"LC3-conjugation system (ATG7 with ATG3 and the ATG12-ATG5-ATG16L1 complex) [#4, #7]\"\n    ],\n    \"partners\": [\n      \"TgATG8 (direct binding via TgATG7 residues 1281-1290, and lipidation substrate) [#0, #1]\",\n      \"TgATG3 (co-regulated conjugation component) [#3]\",\n      \"LC3 / GABARAP / GABARAPL1 / GABARAPL2 (host conjugation substrates) [#7]\",\n      \"ATG3 (host, co-required for LC3 conjugation) [#4]\",\n      \"ATG12-ATG5-ATG16L1 complex (host) [#4, #7]\",\n      \"Beclin 1 (co-required in CD40-driven and lysosomal killing) [#8, #9]\"\n    ],\n    \"other_free_text\": [\n      \"TgATG7 catalytic activity depends on cysteine 1133; a C1133S mutant abolishes TgATG8 lipidation and causes apicoplast fragmentation and loss [#0].\",\n      \"TgATG7 protects unlipidated TgATG8 from multi-monoubiquitination-driven proteasomal degradation [#1].\",\n      \"Host ATG7 occupies a specific node in the LC3-conjugation cascade distinct from ATG9a and ATG14 [#6], and functionally diverges from ATG5 in dendritic-cell T cell priming [#11].\",\n      \"The membrane conjugation site of lipidated LC3 is the determinant of IFN-\\u03b3-inducible GTPase recruitment [#7].\",\n      \"Host ATG7 is dispensable for IL-1\\u03b2 secretion in human monocytes [#12] and for DC-mediated CD4+ T cell cytokine priming [#11].\",\n      \"Parasite EGF-domain micronemal proteins (MIC3, MIC6) suppress ATG7-dependent lysosomal targeting via host EGFR-Akt signaling [#10].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_229690","name":"ATG7","product":"autophagy-related protein ATG7","uniprot_acc":"A0A125YM80","chromosome":"TGME49_chrVIII","start_pos":380051},{"strain":"GT1","gene_id":"TGGT1_229690","name":null,"product":"putative autophagy-related protein 7 atg7","uniprot_acc":null,"chromosome":"TGGT1_chrVIII","start_pos":377254},{"strain":"RH88","gene_id":"TGRH88_074290","name":null,"product":"putative autophagy-related protein 7 atg7","uniprot_acc":null,"chromosome":"CM023089","start_pos":5488664},{"strain":"VEG","gene_id":"TGVEG_229690","name":null,"product":"putative autophagy-related protein 7 atg7","uniprot_acc":"B6KJ80","chromosome":"TGVEG_chrVIII","start_pos":386926}]}