{"gene":"TG_320190","gene_symbol":"SRS9","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2002,"finding":"SRS9 was identified as a novel developmentally regulated gene encoding a putative surface protein (SAG1-related protein) that is upregulated during tachyzoite-to-bradyzoite differentiation, as determined by microarray analysis of ~4,400 Toxoplasma cDNAs.","method":"Microarray expression profiling with relative transcript abundance measurement","journal":"Eukaryotic cell","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — microarray identification with developmental regulation confirmed, single lab but novel gene discovery with clear stage-specific expression pattern","pmids":["12455982"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2005,"finding":"Constitutive expression of the normally bradyzoite-specific SRS9 in tachyzoites (SRS9c mutants) elicited a SRS9-specific immune response marked by IFN-γ production, which correlated with a continual decrease in the number of SRS9c cysts persisting in the brain, demonstrating that stage-specific expression of SRS antigens is a key mechanism for establishing and maintaining optimal parasite persistence.","method":"Transgenic parasite engineering (constitutive SRS9 expression), mouse infection model, immunological assays (IFN-γ measurement), brain cyst quantification","journal":"Journal of immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — transgenic parasite engineering with defined functional/immunological phenotype, replicated across multiple experimental conditions in vivo","pmids":["15944311"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2007,"finding":"SRS9 protein is the dominant surface antigen recognized by the bradyzoite-specific P36 monoclonal antibody, confirmed by stable expression of SRS9 in BSR4-negative strains and immunoprecipitation experiments showing direct P36 mAb–SRS9 interaction.","method":"Stable transfection, Western immunoblotting, immunoprecipitation","journal":"International journal for parasitology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal immunoprecipitation plus stable expression in two BSR4-negative strains, confirming P36 mAb specificity for SRS9","pmids":["17368655"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2007,"finding":"Deletion of SRS9 (ΔSRS9) in a bioluminescent Toxoplasma strain showed that during chronic infection, ΔSRS9 cyst loads substantially decreased compared to wild type, demonstrating a role for SRS9 in maintaining parasite persistence in the brain. Additionally, immunosuppressed chronically infected mice with ΔSRS9 showed intestinal reactivation within 8–9 days versus 2 weeks for wild type, indicating SRS9 plays a role in controlling reactivation in the intestine.","method":"Bioluminescent strain generation, knockout parasite construction, mouse infection model (intraperitoneal and oral routes), bioluminescence imaging, brain cyst quantification, dexamethasone immunosuppression","journal":"Infection and immunity","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic knockout with specific in vivo phenotypic readouts across multiple infection routes and experimental conditions","pmids":["17261600"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2018,"finding":"The ApiAP2 transcription factor AP2IV-4 acts as a transcriptional repressor of SRS9 in tachyzoites; deletion of the AP2IV-4 locus resulted in aberrant expression of SRS9 (alongside other bradyzoite-specific proteins BPK1, MCP4, CST1) in replicating tachyzoites, demonstrating that AP2IV-4 normally suppresses SRS9 expression during acute infection.","method":"Genetic deletion of AP2IV-4 locus, immunofluorescence/protein detection of SRS9 in tachyzoites, mouse infection model","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean genetic knockout with specific molecular phenotype (ectopic SRS9 expression in tachyzoites) and downstream in vivo consequence confirmed","pmids":["29718996"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"The SRS9 promoter was used to drive bradyzoite-specific expression of GRA17, and complementation with GRA17 under the SRS9 promoter drastically increased bradyzoite viability inside cysts, demonstrating that the SRS9 promoter is active specifically in the bradyzoite stage and can drive functional bradyzoite-stage gene expression.","method":"Promoter-driven transgene complementation (GRA17 under SRS9 promoter), bradyzoite viability assays, mouse infection model","journal":"Frontiers in cellular and infection microbiology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — SRS9 promoter activity inferred from functional rescue experiments; direct mechanism attributed to GRA17 not SRS9 protein, but bradyzoite-specific promoter activity confirmed","pmids":["31572690"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"ME49"}]}],"current_model":"SRS9 is a bradyzoite-specific GPI-anchored surface protein of the SRS (SAG1-related sequence) superfamily whose stage-specific expression is transcriptionally repressed during tachyzoite stages by the ApiAP2 factor AP2IV-4; when expressed on the bradyzoite surface, SRS9 functions to maintain parasite persistence in the brain and modulate reactivation in the intestine during chronic infection, with its stage-restricted expression serving as a key immune evasion mechanism that prevents premature SRS9-specific immune responses from eliminating the parasite."},"narrative":{"mechanistic_narrative":"SRS9 is a developmentally regulated, bradyzoite-specific member of the SAG1-related sequence (SRS) family of putative surface proteins in Toxoplasma gondii, upregulated during the tachyzoite-to-bradyzoite differentiation that underlies chronic infection [PMID:12455982]. It is the dominant surface antigen recognized by the bradyzoite-specific P36 monoclonal antibody [PMID:17368655]. Functionally, SRS9 contributes to the maintenance of parasite persistence in the brain and to the control of reactivation: deletion of SRS9 reduces brain cyst loads during chronic infection and accelerates intestinal reactivation in immunosuppressed hosts [PMID:17261600]. Its strict stage restriction is functionally important as an immune-evasion mechanism—forced constitutive expression of SRS9 in tachyzoites elicits an SRS9-specific IFN-γ response that progressively eliminates persisting cysts [PMID:15944311]. This tachyzoite-stage repression is enforced transcriptionally by the ApiAP2 factor AP2IV-4, whose deletion causes ectopic SRS9 expression in replicating tachyzoites [PMID:29718996], and the SRS9 promoter is itself a functional driver of bradyzoite-stage gene expression [PMID:31572690]. Beyond these surface-antigen and stage-regulation roles, no biochemical activity or molecular interaction partner of the SRS9 protein has been characterized in the available corpus.","teleology":[{"year":2002,"claim":"Established that SRS9 exists as a stage-regulated gene, framing it as a candidate surface protein of the developmental switch rather than a constitutive antigen.","evidence":"Microarray expression profiling of ~4,400 Toxoplasma cDNAs identifying developmental upregulation during tachyzoite-to-bradyzoite differentiation","pmids":["12455982"],"confidence":"Medium","gaps":["Transcript-level only; protein expression, localization, and surface topology not shown","No function assigned","Family membership inferred from sequence similarity, not biochemical characterization"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2005,"claim":"Answered why SRS9 expression is stage-restricted, showing that confining it to bradyzoites shields the parasite from an SRS9-specific immune response that otherwise clears persisting cysts.","evidence":"Transgenic parasites constitutively expressing SRS9 in tachyzoites, mouse infection, IFN-γ measurement and brain cyst quantification","pmids":["15944311"],"confidence":"High","gaps":["Does not define the SRS9 protein's biochemical role on the surface","Immune effector cell types and epitopes driving the IFN-γ response not resolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2007,"claim":"Identified SRS9 as the molecular target of the bradyzoite-specific P36 monoclonal antibody, providing a defined reagent for detecting the protein.","evidence":"Stable transfection in BSR4-negative strains, Western blotting, and reciprocal immunoprecipitation with P36 mAb","pmids":["17368655"],"confidence":"High","gaps":["Epitope and antibody effect on parasite function not characterized","Does not address native binding partners or ligands of SRS9"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2007,"claim":"Demonstrated a genetic requirement for SRS9 in chronic persistence and reactivation control, moving it from marker to functional contributor.","evidence":"ΔSRS9 knockout in a bioluminescent strain, oral and intraperitoneal mouse infection, bioluminescence imaging, brain cyst counts, and dexamethasone-induced reactivation","pmids":["17261600"],"confidence":"High","gaps":["Molecular mechanism by which SRS9 promotes persistence or restrains reactivation unknown","No host receptor or interaction partner identified"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2018,"claim":"Identified the upstream transcriptional switch enforcing SRS9 stage-specificity, explaining how tachyzoite-stage repression is achieved.","evidence":"Genetic deletion of the AP2IV-4 locus with protein detection of ectopic SRS9 (and other bradyzoite proteins) in tachyzoites plus mouse infection","pmids":["29718996"],"confidence":"High","gaps":["Whether AP2IV-4 binds the SRS9 promoter directly or acts indirectly not established","cis-regulatory elements of SRS9 not mapped"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"Confirmed the SRS9 promoter as a bona fide bradyzoite-stage-specific expression driver, providing a tool leveraging its stage restriction.","evidence":"GRA17 complementation under the SRS9 promoter with bradyzoite viability assays and mouse infection in ME49","pmids":["31572690"],"confidence":"Medium","gaps":["Functional readout attributed to GRA17, not SRS9 protein; SRS9's own role not tested here","Promoter architecture and regulatory element boundaries not defined"],"attribution":[{"species":"Toxoplasma gondii","strain":"ME49"}]},{"year":null,"claim":"The biochemical function of the SRS9 protein on the bradyzoite surface—its ligand, host receptor, or adhesion/immune-modulatory activity—remains unresolved.","evidence":"No discovery in the corpus assigns a molecular activity or binding partner to the SRS9 protein","pmids":[],"confidence":"Low","gaps":["No structural model of SRS9","No identified host or parasite interaction partner","Mechanism linking surface expression to persistence and reactivation control unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["P36 MONOCLONAL ANTIBODY (RECOGNIZES SRS9 AS DOMINANT BRADYZOITE SURFACE ANTIGEN) [#2]","AP2IV-4 (APIAP2 TRANSCRIPTIONAL REPRESSOR OF SRS9 IN TACHYZOITES) [#4]"],"other_free_text":["SRS9 is a bradyzoite-stage-specific, developmentally upregulated member of the SAG1-related sequence (SRS) putative surface-protein family [#0].","Stage-restricted expression of SRS9 functions as an immune-evasion mechanism; ectopic tachyzoite expression triggers an IFN-γ-associated SRS9-specific response that clears cysts [#1].","SRS9 contributes to brain cyst persistence and restrains intestinal reactivation during chronic infection [#3].","The SRS9 promoter is a functional bradyzoite-stage-specific expression driver [#5]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"12455982","id":"PMC_12455982","title":"Toxoplasma gondii asexual development: identification of developmentally regulated genes and distinct patterns of gene expression.","date":"2002","source":"Eukaryotic cell","url":"https://pubmed.ncbi.nlm.nih.gov/12455982","citation_count":131,"is_preprint":false},{"pmid":"17261600","id":"PMC_17261600","title":"Bradyzoite-specific surface antigen SRS9 plays a role in maintaining Toxoplasma gondii persistence in the brain and in host control of parasite replication in the intestine.","date":"2007","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/17261600","citation_count":101,"is_preprint":false},{"pmid":"15944311","id":"PMC_15944311","title":"Stage-specific expression of surface antigens by Toxoplasma gondii as a mechanism to facilitate parasite persistence.","date":"2005","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/15944311","citation_count":83,"is_preprint":false},{"pmid":"29718996","id":"PMC_29718996","title":"Transcriptional repression by ApiAP2 factors is central to chronic toxoplasmosis.","date":"2018","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/29718996","citation_count":77,"is_preprint":false},{"pmid":"33232762","id":"PMC_33232762","title":"Toxoplasma gondii induces robust humoral immune response against cyst wall antigens in chronically infected animals and humans.","date":"2020","source":"Microbial pathogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/33232762","citation_count":31,"is_preprint":false},{"pmid":"31572690","id":"PMC_31572690","title":"The GRA17 Parasitophorous Vacuole Membrane Permeability Pore Contributes to Bradyzoite Viability.","date":"2019","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/31572690","citation_count":26,"is_preprint":false},{"pmid":"17368655","id":"PMC_17368655","title":"The BSR4 protein is up-regulated in Toxoplasma gondii bradyzoites, however the dominant surface antigen recognised by the P36 monoclonal antibody is SRS9.","date":"2007","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/17368655","citation_count":19,"is_preprint":false},{"pmid":"24496792","id":"PMC_24496792","title":"Differential locus expansion distinguishes Toxoplasmatinae species and closely related strains of Toxoplasma gondii.","date":"2014","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/24496792","citation_count":19,"is_preprint":false},{"pmid":"25091724","id":"PMC_25091724","title":"The extracellular matrix protein mindin as a novel adjuvant elicits stronger immune responses for rBAG1, rSRS4 and rSRS9 antigens of Toxoplasma gondii in BALB/c mice.","date":"2014","source":"BMC infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/25091724","citation_count":15,"is_preprint":false},{"pmid":"32365814","id":"PMC_32365814","title":"Epidemiologic Survey on Toxoplasma gondii and Trichinella pseudospiralis Infection in Corvids from Central Italy.","date":"2020","source":"Pathogens (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/32365814","citation_count":12,"is_preprint":false},{"pmid":"17221136","id":"PMC_17221136","title":"Toxoplasma gondii genotyping in a dog co-infected with distemper virus and ehrlichiosis rickettsia.","date":"2006","source":"Revista do Instituto de Medicina Tropical de Sao Paulo","url":"https://pubmed.ncbi.nlm.nih.gov/17221136","citation_count":12,"is_preprint":false},{"pmid":"27794096","id":"PMC_27794096","title":"High frequency detection of Toxoplasma gondii DNA in human neonatal tissue from Libya.","date":"2016","source":"Transactions of the Royal Society of Tropical Medicine and Hygiene","url":"https://pubmed.ncbi.nlm.nih.gov/27794096","citation_count":10,"is_preprint":false},{"pmid":"26264261","id":"PMC_26264261","title":"Congenital toxoplasmosis and pregnancy malaria detection post-partum: Effective diagnosis and its implication for efficient management of congenital infection.","date":"2015","source":"Parasitology international","url":"https://pubmed.ncbi.nlm.nih.gov/26264261","citation_count":7,"is_preprint":false},{"pmid":"28368078","id":"PMC_28368078","title":"Genotyping of Toxoplasma gondii strain directly from human CSF samples of congenital toxoplasmosis clinical case.","date":"2017","source":"The new microbiologica","url":"https://pubmed.ncbi.nlm.nih.gov/28368078","citation_count":7,"is_preprint":false},{"pmid":"28108401","id":"PMC_28108401","title":"Constitutive expression and characterization of a surface SRS (NcSRS67) protein of Neospora caninum with no orthologue in Toxoplasma gondii.","date":"2017","source":"Parasitology international","url":"https://pubmed.ncbi.nlm.nih.gov/28108401","citation_count":6,"is_preprint":false},{"pmid":"42188907","id":"PMC_42188907","title":"Advances and Translational Challenges in Toxoplasma gondii Vaccine Development: From Antigen Discovery to mRNA and One Health Strategies.","date":"2026","source":"Veterinary sciences","url":"https://pubmed.ncbi.nlm.nih.gov/42188907","citation_count":0,"is_preprint":false},{"pmid":"42347660","id":"PMC_42347660","title":"Protective Effect Against Acute Experimental Toxoplasmosis Conferred by Intranasal Immunisation with Toxoplasma gondii Membrane Proteins Plus CpG Adjuvant.","date":"2026","source":"Vaccines","url":"https://pubmed.ncbi.nlm.nih.gov/42347660","citation_count":0,"is_preprint":false},{"pmid":"39160342","id":"PMC_39160342","title":"First Report on the Molecular Detection and Genetic Characterization of Toxoplasma gondii From Donkeys in Kenya.","date":"2024","source":"Acta parasitologica","url":"https://pubmed.ncbi.nlm.nih.gov/39160342","citation_count":1,"is_preprint":false},{"pmid":"36871500","id":"PMC_36871500","title":"In vitro anti-Toxoplasma gondii effects of a coccidiostat dinitolmide.","date":"2023","source":"Veterinary parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/36871500","citation_count":2,"is_preprint":false},{"pmid":"33387894","id":"PMC_33387894","title":"The activity of the diaminopyrimidine dihydrofolate reducatase inhibitor, iclaprim, against Toxoplasma gondii in an in vitro model: a pilot study.","date":"2020","source":"Diagnostic microbiology and infectious disease","url":"https://pubmed.ncbi.nlm.nih.gov/33387894","citation_count":1,"is_preprint":false},{"pmid":"24505177","id":"PMC_24505177","title":"Polymerase chain reaction based detection of Toxoplasma gondii from lymph node aspirates of dogs.","date":"2012","source":"Journal of parasitic diseases : official organ of the Indian Society for Parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/24505177","citation_count":1,"is_preprint":false},{"pmid":"24822344","id":"PMC_24822344","title":"[Stable green fluorescent protein expression in Toxoplasma gondii mutant].","date":"2011","source":"Zhongguo ji sheng chong xue yu ji sheng chong bing za zhi = Chinese journal of parasitology & parasitic diseases","url":"https://pubmed.ncbi.nlm.nih.gov/24822344","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":27389,"output_tokens":1753,"usd":0.054231,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7062,"output_tokens":2910,"usd":0.05403,"stage2_stop_reason":"end_turn"},"total_usd":0.108261,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","note":"batch pricing = 50% of standard","corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"paper list: removed papers about other genes"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2002,\n      \"finding\": \"SRS9 was identified as a novel developmentally regulated gene encoding a putative surface protein (SAG1-related protein) that is upregulated during tachyzoite-to-bradyzoite differentiation, as determined by microarray analysis of ~4,400 Toxoplasma cDNAs.\",\n      \"method\": \"Microarray expression profiling with relative transcript abundance measurement\",\n      \"journal\": \"Eukaryotic cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — microarray identification with developmental regulation confirmed, single lab but novel gene discovery with clear stage-specific expression pattern\",\n      \"pmids\": [\"12455982\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Constitutive expression of the normally bradyzoite-specific SRS9 in tachyzoites (SRS9c mutants) elicited a SRS9-specific immune response marked by IFN-γ production, which correlated with a continual decrease in the number of SRS9c cysts persisting in the brain, demonstrating that stage-specific expression of SRS antigens is a key mechanism for establishing and maintaining optimal parasite persistence.\",\n      \"method\": \"Transgenic parasite engineering (constitutive SRS9 expression), mouse infection model, immunological assays (IFN-γ measurement), brain cyst quantification\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — transgenic parasite engineering with defined functional/immunological phenotype, replicated across multiple experimental conditions in vivo\",\n      \"pmids\": [\"15944311\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"SRS9 protein is the dominant surface antigen recognized by the bradyzoite-specific P36 monoclonal antibody, confirmed by stable expression of SRS9 in BSR4-negative strains and immunoprecipitation experiments showing direct P36 mAb–SRS9 interaction.\",\n      \"method\": \"Stable transfection, Western immunoblotting, immunoprecipitation\",\n      \"journal\": \"International journal for parasitology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal immunoprecipitation plus stable expression in two BSR4-negative strains, confirming P36 mAb specificity for SRS9\",\n      \"pmids\": [\"17368655\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Deletion of SRS9 (ΔSRS9) in a bioluminescent Toxoplasma strain showed that during chronic infection, ΔSRS9 cyst loads substantially decreased compared to wild type, demonstrating a role for SRS9 in maintaining parasite persistence in the brain. Additionally, immunosuppressed chronically infected mice with ΔSRS9 showed intestinal reactivation within 8–9 days versus 2 weeks for wild type, indicating SRS9 plays a role in controlling reactivation in the intestine.\",\n      \"method\": \"Bioluminescent strain generation, knockout parasite construction, mouse infection model (intraperitoneal and oral routes), bioluminescence imaging, brain cyst quantification, dexamethasone immunosuppression\",\n      \"journal\": \"Infection and immunity\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic knockout with specific in vivo phenotypic readouts across multiple infection routes and experimental conditions\",\n      \"pmids\": [\"17261600\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The ApiAP2 transcription factor AP2IV-4 acts as a transcriptional repressor of SRS9 in tachyzoites; deletion of the AP2IV-4 locus resulted in aberrant expression of SRS9 (alongside other bradyzoite-specific proteins BPK1, MCP4, CST1) in replicating tachyzoites, demonstrating that AP2IV-4 normally suppresses SRS9 expression during acute infection.\",\n      \"method\": \"Genetic deletion of AP2IV-4 locus, immunofluorescence/protein detection of SRS9 in tachyzoites, mouse infection model\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic knockout with specific molecular phenotype (ectopic SRS9 expression in tachyzoites) and downstream in vivo consequence confirmed\",\n      \"pmids\": [\"29718996\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The SRS9 promoter was used to drive bradyzoite-specific expression of GRA17, and complementation with GRA17 under the SRS9 promoter drastically increased bradyzoite viability inside cysts, demonstrating that the SRS9 promoter is active specifically in the bradyzoite stage and can drive functional bradyzoite-stage gene expression.\",\n      \"method\": \"Promoter-driven transgene complementation (GRA17 under SRS9 promoter), bradyzoite viability assays, mouse infection model\",\n      \"journal\": \"Frontiers in cellular and infection microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — SRS9 promoter activity inferred from functional rescue experiments; direct mechanism attributed to GRA17 not SRS9 protein, but bradyzoite-specific promoter activity confirmed\",\n      \"pmids\": [\"31572690\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"ME49\"}]\n    }\n  ],\n  \"current_model\": \"SRS9 is a bradyzoite-specific GPI-anchored surface protein of the SRS (SAG1-related sequence) superfamily whose stage-specific expression is transcriptionally repressed during tachyzoite stages by the ApiAP2 factor AP2IV-4; when expressed on the bradyzoite surface, SRS9 functions to maintain parasite persistence in the brain and modulate reactivation in the intestine during chronic infection, with its stage-restricted expression serving as a key immune evasion mechanism that prevents premature SRS9-specific immune responses from eliminating the parasite.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SRS9 is a developmentally regulated, bradyzoite-specific member of the SAG1-related sequence (SRS) family of putative surface proteins in Toxoplasma gondii, upregulated during the tachyzoite-to-bradyzoite differentiation that underlies chronic infection [#0]. It is the dominant surface antigen recognized by the bradyzoite-specific P36 monoclonal antibody [#2]. Functionally, SRS9 contributes to the maintenance of parasite persistence in the brain and to the control of reactivation: deletion of SRS9 reduces brain cyst loads during chronic infection and accelerates intestinal reactivation in immunosuppressed hosts [#3]. Its strict stage restriction is functionally important as an immune-evasion mechanism—forced constitutive expression of SRS9 in tachyzoites elicits an SRS9-specific IFN-\\u03b3 response that progressively eliminates persisting cysts [#1]. This tachyzoite-stage repression is enforced transcriptionally by the ApiAP2 factor AP2IV-4, whose deletion causes ectopic SRS9 expression in replicating tachyzoites [#4], and the SRS9 promoter is itself a functional driver of bradyzoite-stage gene expression [#5]. Beyond these surface-antigen and stage-regulation roles, no biochemical activity or molecular interaction partner of the SRS9 protein has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Established that SRS9 exists as a stage-regulated gene, framing it as a candidate surface protein of the developmental switch rather than a constitutive antigen.\",\n      \"evidence\": \"Microarray expression profiling of ~4,400 Toxoplasma cDNAs identifying developmental upregulation during tachyzoite-to-bradyzoite differentiation\",\n      \"pmids\": [\"12455982\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Transcript-level only; protein expression, localization, and surface topology not shown\",\n        \"No function assigned\",\n        \"Family membership inferred from sequence similarity, not biochemical characterization\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Answered why SRS9 expression is stage-restricted, showing that confining it to bradyzoites shields the parasite from an SRS9-specific immune response that otherwise clears persisting cysts.\",\n      \"evidence\": \"Transgenic parasites constitutively expressing SRS9 in tachyzoites, mouse infection, IFN-\\u03b3 measurement and brain cyst quantification\",\n      \"pmids\": [\"15944311\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Does not define the SRS9 protein's biochemical role on the surface\",\n        \"Immune effector cell types and epitopes driving the IFN-\\u03b3 response not resolved\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identified SRS9 as the molecular target of the bradyzoite-specific P36 monoclonal antibody, providing a defined reagent for detecting the protein.\",\n      \"evidence\": \"Stable transfection in BSR4-negative strains, Western blotting, and reciprocal immunoprecipitation with P36 mAb\",\n      \"pmids\": [\"17368655\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Epitope and antibody effect on parasite function not characterized\",\n        \"Does not address native binding partners or ligands of SRS9\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Demonstrated a genetic requirement for SRS9 in chronic persistence and reactivation control, moving it from marker to functional contributor.\",\n      \"evidence\": \"\\u0394SRS9 knockout in a bioluminescent strain, oral and intraperitoneal mouse infection, bioluminescence imaging, brain cyst counts, and dexamethasone-induced reactivation\",\n      \"pmids\": [\"17261600\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular mechanism by which SRS9 promotes persistence or restrains reactivation unknown\",\n        \"No host receptor or interaction partner identified\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identified the upstream transcriptional switch enforcing SRS9 stage-specificity, explaining how tachyzoite-stage repression is achieved.\",\n      \"evidence\": \"Genetic deletion of the AP2IV-4 locus with protein detection of ectopic SRS9 (and other bradyzoite proteins) in tachyzoites plus mouse infection\",\n      \"pmids\": [\"29718996\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether AP2IV-4 binds the SRS9 promoter directly or acts indirectly not established\",\n        \"cis-regulatory elements of SRS9 not mapped\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Confirmed the SRS9 promoter as a bona fide bradyzoite-stage-specific expression driver, providing a tool leveraging its stage restriction.\",\n      \"evidence\": \"GRA17 complementation under the SRS9 promoter with bradyzoite viability assays and mouse infection in ME49\",\n      \"pmids\": [\"31572690\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional readout attributed to GRA17, not SRS9 protein; SRS9's own role not tested here\",\n        \"Promoter architecture and regulatory element boundaries not defined\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"ME49\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical function of the SRS9 protein on the bradyzoite surface—its ligand, host receptor, or adhesion/immune-modulatory activity—remains unresolved.\",\n      \"evidence\": \"No discovery in the corpus assigns a molecular activity or binding partner to the SRS9 protein\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of SRS9\",\n        \"No identified host or parasite interaction partner\",\n        \"Mechanism linking surface expression to persistence and reactivation control unknown\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0009986\", \"supporting_discovery_ids\": [0, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0044409\", \"supporting_discovery_ids\": [1, 3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"P36 monoclonal antibody (recognizes SRS9 as dominant bradyzoite surface antigen) [#2]\",\n      \"AP2IV-4 (ApiAP2 transcriptional repressor of SRS9 in tachyzoites) [#4]\"\n    ],\n    \"other_free_text\": [\n      \"SRS9 is a bradyzoite-stage-specific, developmentally upregulated member of the SAG1-related sequence (SRS) putative surface-protein family [#0].\",\n      \"Stage-restricted expression of SRS9 functions as an immune-evasion mechanism; ectopic tachyzoite expression triggers an IFN-\\u03b3-associated SRS9-specific response that clears cysts [#1].\",\n      \"SRS9 contributes to brain cyst persistence and restrains intestinal reactivation during chronic infection [#3].\",\n      \"The SRS9 promoter is a functional bradyzoite-stage-specific expression driver [#5].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_320190","name":"SRS9","product":"SAG-related sequence SRS16B","uniprot_acc":"A0A125YJX5","chromosome":"TGME49_chrIV","start_pos":441694},{"strain":"GT1","gene_id":"TGGT1_320190","name":"SRS9","product":"SAG-related sequence SRS16B","uniprot_acc":null,"chromosome":"TGGT1_chrIV","start_pos":385455},{"strain":"RH88","gene_id":"TGRH88_006920","name":null,"product":"SAG-related sequence SRS16B","uniprot_acc":null,"chromosome":"CM023085","start_pos":450790},{"strain":"VEG","gene_id":"TGVEG_320190","name":null,"product":"SAG-related sequence SRS16B","uniprot_acc":"V5B1U2","chromosome":"TGVEG_chrIV","start_pos":435806}]}