IFI30

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0016667 oxidoreductase activity, acting on a sulfur group of donors	IBA GO_REF:0000033	ACCEPT	Summary: GILT is established as a lysosomal thiol reductase with a thioredoxin-like CXXC active site that catalyzes disulfide bond reduction. This IBA annotation is well-supported by phylogenetic evidence and experimental data across species. Reason: This annotation accurately captures the core molecular function of GILT. The enzyme reduces disulfide bonds in the endolysosomal pathway using its CXXC active site motif. PMID:10639150 demonstrated the thiol reductase activity experimentally. PMID:17142755 confirmed that the thiol reductase activity of GILT is its essential function in MHC class II-restricted Ag processing. The IBA annotation based on phylogenetic inference is consistent with this experimental evidence. Supporting Evidence: PMID:10639150 We describe here a lysosomal thiol reductase optimally active at low pH and capable of catalyzing disulfide bond reduction both in vivo and in vitro. The active site, determined by mutagenesis, consists of a pair of cysteine residues separated by two amino acids, similar to other enzymes of the thioredoxin family. PMID:17142755 These studies demonstrate that the thiol reductase activity of GILT is its essential function in MHC class II-restricted Ag processing. file:human/IFI30/IFI30-deep-research-falcon.md GILT is a lysosomal thiol reductase that enzymatically reduces disulfide bonds of endocytosed proteins, facilitating antigen processing; described as the primary/only known reductase in the endocytic/lysosomal compartment.
GO:0005764 lysosome	IBA GO_REF:0000033	ACCEPT	Summary: GILT localizes to lysosomes via mannose-6-phosphate receptor-mediated trafficking. This is a core localization supported by multiple experimental studies. Reason: Lysosomal localization is a fundamental aspect of GILT function, enabling its activity at the acidic pH optimal for disulfide reduction. PMID:10639150 demonstrated mannose 6-phosphate receptor-mediated delivery. PMID:3136170 showed punctate fluorescence pattern in monocytes consistent with a vesicular subcellular location. The IBA annotation is well-supported. Supporting Evidence: PMID:10639150 After delivery into the endosomal/lysosomal system by the mannose 6-phosphate receptor, N- and C-terminal prosequences are removed. PMID:3136170 Indirect immunofluorescence microscopy reveals a punctate fluorescence pattern in monocytes consistent with a vesicular subcellular location. file:human/IFI30/IFI30-deep-research-falcon.md Localizes to the endocytic/MHC class II loading compartments (late endosomes/lysosomes) and shows maximal activity at acidic endolysosomal pH.
GO:0002376 immune system process	IEA GO_REF:0000043	MARK AS OVER ANNOTATED	Summary: This is a very broad GO term derived from UniProt keyword mapping. While GILT does function in immunity, a more specific annotation (MHC class II antigen processing) already exists and is more informative. Reason: The term "immune system process" (GO:0002376) is too general and uninformative. GILT's specific immune function is in antigen processing and presentation, which is already captured by the more specific annotations to GO:0019886 (MHC class II antigen presentation) and GO:0042590 (MHC class I cross-presentation). The automated IEA from UniProt keyword mapping is technically correct but redundant with more specific annotations that better characterize GILT's role. Supporting Evidence: PMID:10639150 The enzyme is expressed constitutively in antigen-presenting cells and induced by IFN-gamma in other cell types, suggesting a potentially important role in antigen processing.
GO:0005576 extracellular region	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: GILT can be secreted as a disulfide-linked dimer, particularly by activated macrophages. This is a secondary localization, not the primary site of function. Reason: While GILT is primarily a lysosomal enzyme, the precursor form can be secreted as a disulfide-linked dimer. PMID:3136170 demonstrated that IP-30 is either secreted or converted intracellularly. The deep research notes that a minor disulfide-linked dimeric precursor can be secreted by activated macrophages and retains activity. However, the primary functional site is the lysosome, so this should be marked as non-core. Supporting Evidence: PMID:3136170 a 30-kDa polypeptide (referred to as IP-30) is either secreted or converted intracellularly into a 25-kDa protein file:human/IFI30/IFI30-deep-research-falcon.md A minor disulfide-linked dimeric precursor can be secreted by activated macrophages and retains activity
GO:0005764 lysosome	IEA GO_REF:0000120	ACCEPT	Summary: Duplicate annotation with IBA and IDA evidence. Lysosomal localization is well-supported and this IEA is consistent with experimental evidence. Reason: This IEA annotation is consistent with the IBA and IDA annotations for the same term. Duplicates with different evidence codes are acceptable in GO annotation as they represent independent lines of evidence. The combined automated method (GO_REF:0000120) correctly predicts lysosomal localization based on ortholog data (mouse GILT) and UniProt subcellular location vocabulary. Supporting Evidence: PMID:10639150 Enzymatic reduction of disulfide bonds in lysosomes: characterization of a gamma-interferon-inducible lysosomal thiol reductase (GILT).
GO:0016491 oxidoreductase activity	IEA GO_REF:0000043	ACCEPT	Summary: This is a parent term of the more specific GO:0016667 annotation. While correct, it is redundant with the more specific child term. Reason: This IEA annotation from UniProt keyword mapping is technically correct - GILT is an oxidoreductase. While GO:0016667 (oxidoreductase activity, acting on a sulfur group of donors) is more specific and informative, having the broader parent term from IEA is acceptable as it represents an independent inference pathway. The annotation is not wrong, just less specific than the experimental annotations. Supporting Evidence: PMID:10639150 We describe here a lysosomal thiol reductase optimally active at low pH and capable of catalyzing disulfide bond reduction both in vivo and in vitro.
GO:0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	IEA GO_REF:0000002	ACCEPT	Summary: This InterPro-based annotation is highly specific and accurately describes GILT's enzymatic function - reducing disulfide bonds using its thioredoxin-like active site. Reason: GO:0016671 is a child of GO:0016667 and specifies that the acceptor is a disulfide bond, which is precisely what GILT does. This is the most specific MF term applicable to GILT's catalytic activity. The InterPro domain (IPR004911 - Interferon-induced_GILT) correctly predicts this function. PMID:10639150 demonstrated experimentally that GILT reduces disulfide bonds in protein substrates. Supporting Evidence: PMID:10639150 Proteins internalized into the endocytic pathway are usually degraded. Efficient proteolysis requires denaturation, induced by acidic conditions within lysosomes, and reduction of inter- and intrachain disulfide bonds.
GO:0005515 protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	REMOVE	Summary: High-throughput interactome study detected GILT interactions with NOTCH2NLA and KRTAP4-12. These are from systematic Y2H screening but lack functional context. Reason: The term "protein binding" (GO:0005515) is uninformative and does not add value to GILT's functional annotation. PMID:25416956 is a large-scale proteome-wide interactome mapping study that used Y2H to detect binary protein-protein interactions. The interactions with NOTCH2NLA and KRTAP4-12 detected in this screen lack biological context and validation. These interactions do not inform us about GILT's function. Generic "protein binding" annotations from high-throughput screens without functional validation should be removed as they do not meet quality standards for informative annotations. Supporting Evidence: PMID:25416956 A proteome-scale map of the human interactome network.
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	REMOVE	Summary: HuRI reference interactome study detected GILT interaction with TGM1 (transglutaminase 1). This is another high-throughput Y2H finding without functional validation. Reason: PMID:32296183 is the HuRI reference map of the human binary protein interactome, presenting protein-protein interactions from systematic Y2H screening. The detected interaction between GILT and TGM1 lacks functional validation and biological context. TGM1 is a keratinocyte transglutaminase involved in epidermal differentiation, and there is no obvious functional connection to GILT's role in antigen processing. Generic "protein binding" annotations from these high-throughput screens are uninformative and should be removed. If a more specific binding function were characterized, that would be informative, but "protein binding" alone provides no functional insight. Supporting Evidence: PMID:32296183 Apr 8. A reference map of the human binary protein interactome.
GO:0042590 antigen processing and presentation of exogenous peptide antigen via MHC class I	IEA GO_REF:0000107	ACCEPT	Summary: GILT facilitates MHC class I cross-presentation by reducing disulfide bonds in exogenous antigens. This annotation is transferred from mouse ortholog evidence. Reason: GILT's role in cross-presentation is documented in the literature. The deep research document notes that reduction by GILT can enhance transfer of endocytosed disulfide-containing antigens into the cytosol for class I cross-presentation. The UniProt function annotation states GILT also facilitates MHC class I-restricted recognition of exogenous antigens containing disulfide bonds. The IEA from Ensembl Compara ortholog transfer is supported by this biological understanding. Supporting Evidence: file:human/IFI30/IFI30-deep-research-falcon.md Reduction by GILT can enhance transfer of endocytosed disulfide-containing antigens into the cytosol for class I cross-presentation in certain settings.
GO:0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	IMP PMID:10639150 Enzymatic reduction of disulfide bonds in lysosomes: charact...	ACCEPT	Summary: Direct experimental demonstration of GILT's disulfide reductase activity using mutant phenotype analysis of the CXXC active site cysteines. Reason: PMID:10639150 is the seminal paper characterizing GILT's enzymatic function. The IMP (Inferred from Mutant Phenotype) evidence code is appropriate because the authors demonstrated that mutation of either Cys-72 or Cys-75 in the CXXC motif abolishes reductase activity. The abstract states the active site, determined by mutagenesis, consists of a pair of cysteine residues separated by two amino acids. This is strong experimental evidence for GO:0016671. Supporting Evidence: PMID:10639150 The active site, determined by mutagenesis, consists of a pair of cysteine residues separated by two amino acids, similar to other enzymes of the thioredoxin family.
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II	TAS Reactome:R-HSA-2132295	ACCEPT	Summary: GILT's role in MHC class II antigen processing is its primary biological function. Reactome pathway annotation is well-supported by primary literature. Reason: This is a core function of GILT. The Reactome pathway R-HSA-2132295 describes MHC class II antigen presentation, within which GILT functions to reduce disulfide bonds in antigens to enable their processing. PMID:17142755 directly demonstrated that thiol reductase activity of GILT is its essential function in MHC class II-restricted Ag processing using GILT-deficient cell lines reconstituted with wild-type and mutant GILT. The deep research confirms GILT is the principal endocytic thiol reductase governing disulfide reduction in antigen processing. Supporting Evidence: PMID:17142755 These studies demonstrate that the thiol reductase activity of GILT is its essential function in MHC class II-restricted Ag processing. Reactome:R-HSA-2213240 The lysosomal thiol reductase gamma-IFN-inducible lysosomal thiol reductase (GILT) has been shown to facilitate MHC class II-restricted antigen (Ag) processing by breaking disulphide bonds.
GO:0016667 oxidoreductase activity, acting on a sulfur group of donors	EXP PMID:10639150 Enzymatic reduction of disulfide bonds in lysosomes: charact...	ACCEPT	Summary: Direct experimental evidence from the original characterization of GILT's enzymatic activity demonstrating its thiol reductase function. Reason: PMID:10639150 provided the first comprehensive characterization of GILT as a lysosomal thiol reductase. The paper demonstrated catalytic activity both in vivo and in vitro, showing optimal activity at acidic pH and identifying the CXXC active site through mutagenesis. This is strong primary experimental evidence for the molecular function annotation. Supporting Evidence: PMID:10639150 We describe here a lysosomal thiol reductase optimally active at low pH and capable of catalyzing disulfide bond reduction both in vivo and in vitro.
GO:0016667 oxidoreductase activity, acting on a sulfur group of donors	EXP PMID:17142755 Functional requirements for the lysosomal thiol reductase GI...	ACCEPT	Summary: Follow-up experimental study confirming GILT's thiol reductase activity is essential for its function in antigen processing. Reason: PMID:17142755 extended the findings of PMID:10639150 by demonstrating the functional requirements for GILT in MHC class II antigen processing. The study showed that mutation of either active site cysteine (Cys46 or Cys49 in mouse, corresponding to Cys72/75 in human) abrogated both reductase activity and antigen processing function. This provides additional experimental support for the GO:0016667 annotation. Supporting Evidence: PMID:17142755 Mutation of either Cys(46) or Cys(49) abrogated MHC class II processing of a GILT-dependent HEL epitope.
GO:0043202 lysosomal lumen	TAS Reactome:R-HSA-1031716	ACCEPT	Summary: GILT is localized to the lysosomal lumen where it functions at acidic pH. This Reactome annotation provides more specific localization than "lysosome." Reason: GO:0043202 (lysosomal lumen) is more specific than GO:0005764 (lysosome) and accurately describes where GILT functions. As a soluble glycoprotein delivered via the mannose-6-phosphate pathway, the mature form of GILT resides in the lysosomal lumen where it reduces disulfide bonds in internalized antigens. Reactome pathway R-HSA-1031716 (Expression of IFNG-stimulated genes) includes GILT as an IFN-gamma inducible protein localized to this compartment. Supporting Evidence: PMID:10639150 The enzyme is a soluble glycoprotein that is synthesized as a precursor. After delivery into the endosomal/lysosomal system by the mannose 6-phosphate receptor, N- and C-terminal prosequences are removed.
GO:0043202 lysosomal lumen	TAS Reactome:R-HSA-2213240	ACCEPT	Summary: Duplicate Reactome annotation for lysosomal lumen localization from the pathway specifically describing GILT's function in disulfide reduction. Reason: Reactome pathway R-HSA-2213240 (Reduction of disulphide bonds in MHC II antigens) specifically describes GILT's function and localization. The pathway summary states The lysosomal thiol reductase GILT has been shown to facilitate MHC class II-restricted antigen processing by breaking disulphide bonds. GILT is constitutively expressed in APCs. The reduction of disulphide bonds by mature GILT is optimal at acidic pH. This confirms lysosomal lumen localization. Supporting Evidence: Reactome:R-HSA-2213240 The lysosomal thiol reductase gamma-IFN-inducible lysosomal thiol reductase (GILT) has been shown to facilitate MHC class II-restricted antigen (Ag) processing by breaking disulphide bonds. GILT is constitutively expressed in APCs. The reduction of disulphide bonds by mature GILT is optimal at acidic pH
GO:0042590 antigen processing and presentation of exogenous peptide antigen via MHC class I	ISS GO_REF:0000024	ACCEPT	Summary: GILT facilitates cross-presentation to MHC class I based on sequence similarity to mouse ortholog with demonstrated function. Reason: The ISS (Inferred from Sequence Similarity) annotation is based on manual curator judgment of sequence similarity to mouse GILT (UniProtKB:Q9ESY9), which has demonstrated function in cross-presentation. UniProt notes that GILT also facilitates MHC class I-restricted recognition of exogenous antigens containing disulfide bonds by CD8+ T-cells or crosspresentation (By similarity). This functional inference is reasonable given the high conservation between human and mouse GILT and the shared domain architecture.
GO:0005764 lysosome	IDA PMID:10639150 Enzymatic reduction of disulfide bonds in lysosomes: charact...	ACCEPT	Summary: Direct experimental demonstration of GILT lysosomal localization via immunofluorescence and mannose-6-phosphate trafficking studies. Reason: PMID:10639150 directly demonstrated lysosomal localization of GILT. The paper showed that GILT is delivered to lysosomes via the mannose-6-phosphate receptor pathway, a hallmark of lysosomal protein targeting. The precursor is processed to the mature form upon arrival in the endosomal/lysosomal system. This IDA evidence is the strongest experimental support for lysosomal localization. Supporting Evidence: PMID:10639150 After delivery into the endosomal/lysosomal system by the mannose 6-phosphate receptor, N- and C-terminal prosequences are removed.
GO:0005576 extracellular region	TAS PMID:3136170 Molecular and biochemical characterization of a novel gamma-...	KEEP AS NON CORE	Summary: Original characterization showed GILT (IP-30) can be secreted, forming extracellular disulfide-linked dimers. Reason: PMID:3136170 demonstrated that the 30-kDa precursor (IP-30) can be secreted and forms extracellular dimers. While this is a valid localization, the primary functional site of GILT is the lysosome. Secretion appears to be a secondary phenomenon, particularly in activated macrophages during inflammation. Supporting Evidence: PMID:3136170 a 30-kDa polypeptide (referred to as IP-30) is either secreted or converted intracellularly into a 25-kDa protein
GO:0005764 lysosome	TAS PMID:3136170 Molecular and biochemical characterization of a novel gamma-...	ACCEPT	Summary: Original characterization suggested vesicular/lysosomal localization of IP-30 based on immunofluorescence microscopy. Reason: PMID:3136170 provided early evidence for lysosomal localization of GILT, showing punctate fluorescence pattern in monocytes consistent with a vesicular subcellular location. While this was suggestive rather than definitive, it was later confirmed by PMID:10639150 which demonstrated mannose-6-phosphate receptor-mediated delivery to lysosomes. Supporting Evidence: PMID:3136170 Indirect immunofluorescence microscopy reveals a punctate fluorescence pattern in monocytes consistent with a vesicular subcellular location. These data are consistent with IP-30 being a novel IFN gamma-inducible protein which may be lysosomal in location.
GO:0015035 protein-disulfide reductase activity	IDA PMID:10639150 Enzymatic reduction of disulfide bonds in lysosomes: charact...	NEW	Summary: GO:0015035 (protein-disulfide reductase activity) is more specific than GO:0016671 because it specifies that the substrates are proteins. GILT specifically reduces disulfide bonds in endocytosed protein antigens to facilitate their unfolding and proteolytic processing. Reason: This term is a more precise annotation than GO:0016671 because GILT's established physiological substrates are proteins - endocytosed antigens that require disulfide bond reduction for processing. PMID:10639150 demonstrated that GILT catalyzes disulfide bond reduction in proteins both in vivo and in vitro. The study showed efficient denaturation and reduction of internalized proteins is required for proteolysis in the lysosome. The child terms of GO:0015035 specify cofactors (glutathione, NAD(P)H), but GILT uses free cysteine transported into the lysosome as its electron donor, so the parent term GO:0015035 is most appropriate. Supporting Evidence: PMID:10639150 We describe here a lysosomal thiol reductase optimally active at low pH and capable of catalyzing disulfide bond reduction both in vivo and in vitro. The active site, determined by mutagenesis, consists of a pair of cysteine residues separated by two amino acids, similar to other enzymes of the thioredoxin family. PMID:17142755 These studies demonstrate that the thiol reductase activity of GILT is its essential function in MHC class II-restricted Ag processing. file:human/IFI30/IFI30-deep-research-falcon.md GILT is a lysosomal thiol reductase that enzymatically reduces disulfide bonds of endocytosed proteins, facilitating antigen processing. Known GILT-dependent substrates include disulfide-rich model antigens (e.g., hen egg lysozyme) and melanocyte differentiation antigens such as tyrosinase/TRP1.