NDUFS4

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005739 mitochondrion	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for mitochondrial localization. NDUFS4 is a nuclear-encoded mitochondrial protein with an N-terminal transit peptide (residues 1-42) that targets it to the mitochondrion (UniProt O43181). The protein is confirmed as mitochondrial by immunopurification (PMID:12611891), structural studies (PMID:28844695), and high-confidence mitochondrial proteomics (PMID:34800366). The IBA annotation is phylogenetically informed and accurate. Reason: Core cellular component annotation. NDUFS4 is unambiguously a mitochondrial protein, confirmed by multiple experimental approaches. The IBA annotation is sound and consistent with all available evidence. Supporting Evidence: PMID:12611891 we describe an immunocapture procedure for isolating this multisubunit membrane-bound complex from human tissue PMID:28844695 Architecture of Human Mitochondrial Respiratory Megacomplex I(2)III(2)IV(2)
GO:0022904 respiratory electron transport chain	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for involvement in the respiratory electron transport chain. NDUFS4 is an accessory subunit of Complex I, the first enzyme of the respiratory chain. While NDUFS4 itself does not catalyze electron transfer, it is essential for assembly and stability of a functional Complex I that carries out NADH-to-ubiquinone electron transfer. Loss of NDUFS4 causes substantially reduced NADH:ubiquinone oxidoreductase activity (PMID:11181577, PMID:16478720) and ~50% reduction of intact Complex I abundance (Yin et al. 2024, EMBO J). Reason: Core biological process. NDUFS4 is essential for the function of Complex I within the respiratory electron transport chain. Although it is not a catalytic core subunit, its structural and regulatory role is indispensable for the pathway. The IBA annotation is phylogenetically well supported. Supporting Evidence: PMID:11181577 Fibroblast cultures from the patient exhibited severe reduction of the rotenone-sensitive NADH-->UQ oxidoreductase activity of complex I PMID:16478720 the NDUFS4 mutation prevented complete assembly of the complex and caused full suppression of the activity
GO:0032981 mitochondrial respiratory chain complex I assembly	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for involvement in Complex I assembly. Recent cryo-EM structural analyses of Ndufs4-/- mouse tissue (Yin et al. 2024, EMBO J) reveal that NDUFS4 is critical for the late-stage maturation of Complex I. Loss of NDUFS4 prevents the displacement of the assembly factor NDUFAF2 and results in failure to incorporate NDUFA12, yielding incomplete assembly intermediates. Multiple patient studies show that NDUFS4 mutations abolish normal Complex I assembly (PMID:11181577, PMID:11112787, PMID:15038602). Reason: Core biological process. This is one of the most important functions of NDUFS4. The protein is essential for the final maturation step of Complex I assembly. The IBA annotation is phylogenetically sound and strongly supported by experimental evidence from both human patient fibroblasts and mouse knockout models. Supporting Evidence: PMID:11181577 Two-dimensional electrophoresis showed the absence of detectable normally assembled complex I in the inner mitochondrial membrane. These findings show that the expression of the NDUFS4 gene is essential for the assembly of a functional complex I. PMID:15038602 All the NDUFS4 mutations resulted in impairment of the assembly of a functional complex file:human/NDUFS4/NDUFS4-deep-research-falcon.md knockout complexes lack NDUFA12 in all visualized classes and adopt distinct assembly states where either the assembly factor NDUFAF2 remains bound or NDUFS6 is incompletely associated
GO:0045271 respiratory chain complex I	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for NDUFS4 being part of respiratory chain Complex I. NDUFS4 is one of the 45 subunits of human Complex I, specifically an accessory subunit located within the iron-sulfur protein (IP) fragment at the interface of the N- and Q-modules (PMID:27626371, PMID:12611891, PMID:28844695). The IBA annotation is phylogenetically well supported and correct. Reason: Core cellular component. NDUFS4 is an integral subunit of Complex I, identified by mass spectrometry in immunopurified complex (PMID:12611891) and resolved in cryo-EM structures (PMID:28844695). The IBA annotation is accurate. Supporting Evidence: PMID:27626371 Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the mitochondrial respiratory chain and is composed of 45 subunits in humans PMID:12611891 we can resolve and identify the human homologues of 42 polypeptides detected so far in the more extensively studied beef heart complex I
GO:1902600 proton transmembrane transport	IEA GO_REF:0000108	ACCEPT	Summary: IEA annotation inferred from logical inference based on GO:0008137 (NADH dehydrogenase (ubiquinone) activity). Complex I couples electron transfer from NADH to ubiquinone with proton translocation across the inner mitochondrial membrane. While NDUFS4 is in the N-module (hydrophilic arm) rather than the proton-pumping membrane arm, the complex as a whole carries out proton transmembrane transport. As an accessory subunit essential for Complex I function, NDUFS4 contributes to this activity indirectly. Reason: The annotation is acceptable as a broader process annotation for a Complex I subunit. While NDUFS4 is not directly in the proton-pumping domain, the complex as a whole performs proton transmembrane transport, and NDUFS4 is essential for a functional complex. The IEA inference from the complex-level MF is reasonable.
GO:0005743 mitochondrial inner membrane	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation based on UniProtKB subcellular location mapping. NDUFS4 is localized to the mitochondrial inner membrane as a peripheral membrane protein on the matrix side (UniProt O43181, PMID:12611891). This is well supported by multiple experimental studies. Reason: Correct localization. NDUFS4 is a peripheral membrane protein on the matrix side of the mitochondrial inner membrane, confirmed by subcellular fractionation and structural studies. Supporting Evidence: PMID:12611891 we describe an immunocapture procedure for isolating this multisubunit membrane-bound complex from human tissue
GO:0022900 electron transport chain	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation from InterPro mapping (IPR006885). GO:0022900 (electron transport chain) is a parent term of GO:0022904 (respiratory electron transport chain). Given that the more specific IBA annotation to GO:0022904 is already present, this broader IEA annotation is redundant but not incorrect. Reason: Correct but broader than the IBA annotation to GO:0022904. As an IEA annotation it provides additional automated support. It is consistent with the known role of NDUFS4 as a Complex I subunit in the electron transport chain.
GO:0022904 respiratory electron transport chain	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation based on UniProtKB keyword mapping (KW-0679, Respiratory chain). This duplicates the IBA annotation to the same term. The IEA mapping is correct for NDUFS4 as a Complex I subunit. Reason: Correct annotation, consistent with the IBA annotation to the same term. Duplicate GO IDs with different evidence codes are acceptable.
GO:0045271 respiratory chain complex I	IEA GO_REF:0000117	ACCEPT	Summary: IEA annotation from ARBA machine learning models. NDUFS4 is a confirmed subunit of respiratory chain Complex I. This duplicates the IBA annotation to the same term but with a different evidence source. Reason: Correct annotation. NDUFS4 is an established subunit of Complex I. Duplicate with different evidence code is acceptable.
GO:0072593 reactive oxygen species metabolic process	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: IEA annotation from ARBA machine learning models for ROS metabolic process. Complex I is a major source of reactive oxygen species in mitochondria. However, NDUFS4 loss (which abolishes Complex I activity) actually prevented ROS production in one study (PMID:16478720), contrasting with the NDUFS1 mutant which showed increased ROS. The relationship between NDUFS4 and ROS is complex and context-dependent. The deep research report also notes that ROS phenotypes may be tissue/context dependent. Reason: While Complex I is a well-established source of ROS, the relationship between NDUFS4 specifically and ROS is indirect and context-dependent. NDUFS4 loss can either increase or decrease ROS depending on conditions (PMID:16478720). ROS metabolism is a secondary consequence of Complex I dysfunction, not a core function of NDUFS4. Consistent with the IMP annotation to the same term. Supporting Evidence: PMID:16478720 No ROS increase was observed in the NDUFS4 mutation
GO:0005739 mitochondrion	IDA GO_REF:0000052	ACCEPT	Summary: IDA annotation based on immunofluorescence data from the Human Protein Atlas. Mitochondrial localization is well established for NDUFS4 from multiple lines of evidence. Reason: Correct localization supported by immunofluorescence data. Consistent with all other evidence for mitochondrial localization of NDUFS4.
GO:0005743 mitochondrial inner membrane	IDA PMID:28844695 Architecture of Human Mitochondrial Respiratory Megacomplex ...	ACCEPT	Summary: IDA annotation from ComplexPortal based on cryo-EM structural data. Guo et al. (2017) determined the architecture of the human respiratory megacomplex I2III2IV2, which resolves all Complex I subunits including NDUFS4 within the inner membrane-associated complex. This structural data directly confirms NDUFS4 localization to the mitochondrial inner membrane. Reason: Strong structural evidence from cryo-EM. NDUFS4 is resolved as a peripheral subunit on the matrix side of the inner membrane within the intact Complex I structure. Supporting Evidence: PMID:28844695 The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole
GO:0009060 aerobic respiration	NAS PMID:30030361 Assembly of mammalian oxidative phosphorylation complexes I-...	ACCEPT	Summary: NAS annotation from ComplexPortal based on a review of OXPHOS complex assembly (Signes & Fernandez-Vizarra, 2018). NDUFS4 is an accessory subunit of Complex I, which is part of the oxidative phosphorylation system that carries out aerobic respiration. This is a broad but correct process annotation for a Complex I subunit. Reason: Correct broad biological process. Complex I is the first enzyme in the OXPHOS system which is central to aerobic respiration. NDUFS4 is essential for a functional Complex I. Supporting Evidence: PMID:30030361 The assembly of the five oxidative phosphorylation system (OXPHOS) complexes in the inner mitochondrial membrane is an intricate process
GO:0042776 proton motive force-driven mitochondrial ATP synthesis	NAS PMID:30030361 Assembly of mammalian oxidative phosphorylation complexes I-...	KEEP AS NON CORE	Summary: NAS annotation from ComplexPortal. Complex I contributes to the proton motive force by pumping protons across the inner membrane, which drives ATP synthase (Complex V). NDUFS4 is not directly involved in proton pumping or ATP synthesis but is essential for Complex I function. This annotation is somewhat indirect for an accessory subunit that resides in the hydrophilic arm rather than the proton-pumping membrane domain. Reason: While technically accurate that loss of NDUFS4 impairs proton motive force generation (because it collapses Complex I), this annotation is more of a downstream consequence than a direct function of NDUFS4. The primary role of NDUFS4 is in Complex I assembly and stability, not directly in ATP synthesis. Keeping as non-core reflects that this is an indirect contribution. Supporting Evidence: PMID:30030361 complexes I, III and IV interact with each other, forming the so-called respiratory supercomplexes or 'respirasomes'
GO:0005739 mitochondrion	HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an...	ACCEPT	Summary: HTP annotation from high-throughput mitochondrial proteomics (Morgenstern et al. 2021). NDUFS4 was identified as part of the high-confidence human mitochondrial proteome. This is consistent with all other evidence. Reason: Correct localization confirmed by quantitative proteomics. Consistent with all other evidence for NDUFS4 mitochondrial localization. Supporting Evidence: PMID:34800366 Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context
GO:0045271 respiratory chain complex I	IMP PMID:11112787 Human complex I defects can be resolved by monoclonal antibo...	ACCEPT	Summary: IMP annotation based on Triepels et al. (2001), who used monoclonal antibodies against Complex I subunits to analyze assembly patterns in patients with Complex I defects, including NDUFS4 mutant patients. The study demonstrated that NDUFS4 mutations cause distinct subunit assembly patterns, providing indirect evidence that NDUFS4 is part of Complex I (its loss disrupts the complex). Reason: Valid experimental evidence. The monoclonal antibody analysis and sucrose gradient studies in NDUFS4 mutant patient cells demonstrate that NDUFS4 is a component whose loss disrupts Complex I assembly, confirming its membership in the complex. Supporting Evidence: PMID:11112787 different mutations in the same gene are shown to give very similar subunit profiles
GO:0045271 respiratory chain complex I	IDA PMID:12611891 The subunit composition of the human NADH dehydrogenase obta...	ACCEPT	Summary: IDA annotation based on Murray et al. (2003), who used immunocapture followed by mass spectrometry to identify NDUFS4 as one of the subunits of immunopurified human Complex I. This is direct experimental evidence for NDUFS4 as a Complex I component. Reason: Strong direct evidence. NDUFS4 was identified by MALDI-TOF and LC-MS/MS in immunopurified human Complex I, directly demonstrating its presence as a subunit of the complex. Supporting Evidence: PMID:12611891 Using small amounts of immunoisolated protein, one-dimensional and two-dimensional gel electrophoresis, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) peptide mass finger printing (PMF), and nanoflow liquid chromatography mass spectrometry/mass spectrometry (LC-MS/MS), we can resolve and identify the human homologues of 42 polypeptides
GO:0045271 respiratory chain complex I	IMP PMID:16478720 Dysfunctions of cellular oxidative metabolism in patients wi...	ACCEPT	Summary: IMP annotation based on Iuso et al. (2006), who studied the effects of NDUFS4 mutations on Complex I in patient fibroblasts. The NDUFS4 G44A nonsense mutation prevented complete assembly and caused full suppression of Complex I activity, providing mutant phenotype evidence that NDUFS4 is an essential component of Complex I. Reason: Valid mutant phenotype evidence confirming NDUFS4 as an essential Complex I subunit. Loss of NDUFS4 abolishes Complex I assembly and activity. Supporting Evidence: PMID:16478720 the NDUFS4 mutation prevented complete assembly of the complex and caused full suppression of the activity
GO:0045271 respiratory chain complex I	IDA PMID:27626371 Accessory subunits are integral for assembly and function of...	ACCEPT	Summary: IDA annotation based on Stroud et al. (2016), who used gene editing to generate knockout cell lines for all Complex I accessory subunits and performed quantitative proteomics. NDUFS4 was shown to be one of 25 accessory subunits strictly required for assembly of a functional complex. This study provides both identification of NDUFS4 within the complex and functional evidence for its essentiality. Reason: Strong experimental evidence from a systematic gene-editing and proteomics study. NDUFS4 knockout cells showed loss of functional Complex I, confirming it as an essential accessory subunit. Supporting Evidence: PMID:27626371 We show that 25 subunits are strictly required for assembly of a functional complex and 1 subunit is essential for cell viability
GO:0005515 protein binding	IPI PMID:31206022 BAP31 regulates mitochondrial function via interaction with ...	MARK AS OVER ANNOTATED	Summary: IPI annotation for protein binding, based on Namba (2019) who showed that NDUFS4 interacts with BAP31 (BCAP31, UniProtKB:P51572) and TOMM40 via co-immunoprecipitation. BAP31 acts as an ER-mitochondria bridging factor that stimulates translocation of NDUFS4 from the cytosol to mitochondria through interaction with Tom40. However, "protein binding" (GO:0005515) is uninformative and does not capture the specific nature of these interactions. Reason: The generic "protein binding" term does not convey useful information about the biological context. The NDUFS4-BAP31-TOMM40 interaction relates to mitochondrial protein import and is better captured by more specific terms. Per project guidelines, generic protein binding annotations should be flagged as over-annotated. Supporting Evidence: PMID:31206022 BAP31 interacts with mitochondria-localized proteins, including Tom40, to stimulate the translocation of NDUFS4, the component of complex I from the cytosol to the mitochondria
GO:0005739 mitochondrion	IDA PMID:31206022 BAP31 regulates mitochondrial function via interaction with ...	ACCEPT	Summary: IDA annotation for mitochondrial localization based on Namba (2019). The study used subcellular fractionation and showed NDUFS4 localization in the mitochondria-associated ER membrane (MAM) and mitochondrial fractions. BAP31 knockout reduced NDUFS4 in the mitochondrial fraction, confirming its normal mitochondrial localization. Reason: Valid experimental evidence from subcellular fractionation confirming NDUFS4 mitochondrial localization. Consistent with all other evidence. Supporting Evidence: PMID:31206022 NDUFS4 and Tom40 were localized to the MAM and mitochondria
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-163217	ACCEPT	Summary: TAS annotation from Reactome pathway R-HSA-163217 (Complex I oxidises NADH to NAD+, reduces CoQ to CoQH2). NDUFS4 is annotated as part of Complex I which functions at the mitochondrial inner membrane. This is consistent with all structural and biochemical evidence. Reason: Correct localization supported by Reactome pathway annotation. NDUFS4 is a peripheral membrane protein on the matrix side of the inner mitochondrial membrane as part of Complex I.
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-6799179	ACCEPT	Summary: TAS annotation from Reactome pathway R-HSA-6799179 (Peripheral arm subunits bind the 815kDa complex to form a 980kDa complex). This Reactome entry describes the assembly step where peripheral arm subunits including NDUFS4 are incorporated into the growing Complex I at the inner membrane. Reason: Correct localization. The Reactome assembly pathway places NDUFS4 at the mitochondrial inner membrane during Complex I biogenesis.
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-6799196	ACCEPT	Summary: TAS annotation from Reactome pathway R-HSA-6799196 (The MCIA complex, NDUFAF2-7 all dissociate from the 980kDa complex, resulting in Complex I). This represents the final maturation step of Complex I assembly where assembly factors dissociate. NDUFS4 is critical for this step, as its incorporation helps displace NDUFAF2. Reason: Correct localization. Consistent with the role of NDUFS4 in the final maturation of Complex I at the mitochondrial inner membrane.
GO:0005743 mitochondrial inner membrane	TAS Reactome:R-HSA-6800870	ACCEPT	Summary: TAS annotation from Reactome pathway R-HSA-6800870 (NDUF subunits bind to form the FP subcomplex). This refers to early assembly of the flavoprotein subcomplex. NDUFS4 is part of the iron-sulfur protein fragment rather than the FP subcomplex, but the overall annotation of inner membrane localization is still correct. Reason: Correct localization. While NDUFS4 is in the IP fragment rather than the FP subcomplex, the annotation of mitochondrial inner membrane localization is accurate regardless.
GO:0072593 reactive oxygen species metabolic process	IMP PMID:16870178 cAMP controls oxygen metabolism in mammalian cells.	KEEP AS NON CORE	Summary: IMP annotation based on Piccoli et al. (2006). This study found that a missense genetic defect in the NDUFS4 subunit suppressed Complex I activity and prevented ROS production, while cAMP-dependent activation of Complex I was associated with reduced ROS accumulation. Notably, the NDUFS4 mutation decreased ROS rather than increasing it, in contrast to the NDUFS1 mutant. This shows NDUFS4 mutations alter ROS metabolism, but the direction of effect depends on context. Reason: While NDUFS4 mutations do affect ROS metabolism, this appears to be a secondary consequence of Complex I dysfunction rather than a direct function of NDUFS4. The relationship is complex since NDUFS4 loss can either increase or decrease ROS depending on the tissue and conditions. This is not a core function but a downstream phenotypic consequence. Supporting Evidence: PMID:16870178 A missense genetic defect in the NDUFS4 subunit, putative substrate of PKA, suppressed, on the other hand, the activity of the complex and prevented ROS production
GO:0032981 mitochondrial respiratory chain complex I assembly	IMP PMID:11112787 Human complex I defects can be resolved by monoclonal antibo...	ACCEPT	Summary: IMP annotation based on Triepels et al. (2001), who analyzed Complex I assembly patterns in NDUFS4 mutant patients using monoclonal antibodies against Complex I subunits. The NDUFS4 mutations caused distinct assembly defects, demonstrating that NDUFS4 is required for normal Complex I assembly. Reason: Valid experimental evidence showing that NDUFS4 mutations disrupt Complex I assembly, as revealed by altered subunit profiles. Complex I assembly is a core function of NDUFS4. Supporting Evidence: PMID:11112787 Western blotting with these antibodies, particularly when used in conjunction with sucrose gradient studies and enzymatic activity measurements, helps distinguish catalytic versus assembly defects
GO:0032981 mitochondrial respiratory chain complex I assembly	IMP PMID:15038602 Respiratory complex I in brain development and genetic disea...	ACCEPT	Summary: IMP annotation based on Papa et al. (2004), who studied Complex I expression, activity, and assembly during brain development and in children with inherited encephalopathies carrying NDUFS4 mutations. All NDUFS4 mutations studied resulted in impairment of the assembly of a functional complex. Reason: Core function confirmed by multiple NDUFS4 mutations all resulting in impaired Complex I assembly. This is consistent with the structural role of NDUFS4 in the late-stage maturation of Complex I. Supporting Evidence: PMID:15038602 All the NDUFS4 mutations resulted in impairment of the assembly of a functional complex
GO:0006120 mitochondrial electron transport, NADH to ubiquinone	NAS PMID:9463323 Demonstration of a new pathogenic mutation in human complex ...	ACCEPT	Summary: NAS annotation based on van den Heuvel et al. (1998), the original cloning and mutation report for NDUFS4. The paper describes NDUFS4 as encoding the 18 kDa subunit of mitochondrial respiratory chain Complex I, which carries out NADH to ubiquinone electron transport. While NDUFS4 itself does not catalyze this reaction, it is essential for the function of the complex that does. Reason: Correct biological process annotation. NDUFS4 is essential for Complex I function, and Complex I catalyzes NADH to ubiquinone electron transfer. NAS evidence code is appropriate for this literature-based inference. Supporting Evidence: PMID:9463323 We report the cDNA cloning, chromosomal localization, and a mutation in the human nuclear gene encoding the 18-kD (AQDQ) subunit of the mitochondrial respiratory chain complex I
GO:0007420 brain development	IMP PMID:14765537 Clinical heterogeneity in patients with mutations in the NDU...	MARK AS OVER ANNOTATED	Summary: IMP annotation based on Budde et al. (2003), who compared clinical presentation of NDUFS4 mutation patients. The paper describes marked clinical heterogeneity in patients with NDUFS4 mutations, with neurological presentations including Leigh syndrome. However, brain development impairment in these patients is a disease consequence of global Complex I deficiency, not a direct developmental function of NDUFS4. NDUFS4 is expressed ubiquitously (HPA shows low tissue specificity), and its role in brain development is secondary to its essential role in Complex I function in metabolically demanding tissues. Reason: Brain development impairment in NDUFS4 patients is a downstream consequence of Complex I deficiency in metabolically demanding neural tissue, not a direct developmental function of NDUFS4. The gene is ubiquitously expressed and has no brain-specific function. Annotating NDUFS4 to brain development conflates disease phenotype with gene function. Supporting Evidence: PMID:14765537 A comparison of the clinical presentation, disease course and results of laboratory and imaging studies of all patients so far published with a NDUFS4 mutation are presented. This reveals marked clinical heterogeneity, even in patients with the same genotype.
GO:0008137 NADH dehydrogenase (ubiquinone) activity	IMP PMID:15038602 Respiratory complex I in brain development and genetic disea...	ACCEPT	Summary: IMP annotation with contributes_to qualifier based on Papa et al. (2004). The study showed that NDUFS4 mutations impair Complex I assembly and thus NADH dehydrogenase activity. The contributes_to qualifier is appropriate because NDUFS4 is an accessory subunit that does not directly catalyze the reaction but contributes to the complex-level enzymatic activity through its structural and assembly role. Reason: The contributes_to qualifier is correctly applied for an accessory subunit. NDUFS4 does not directly catalyze NADH oxidation but is essential for the assembly and stability of the complex that does. This is consistent with GO annotation practices for multi-subunit enzyme complexes where accessory subunits use contributes_to. Supporting Evidence: PMID:15038602 All the NDUFS4 mutations resulted in impairment of the assembly of a functional complex
GO:0008137 NADH dehydrogenase (ubiquinone) activity	IMP PMID:16870178 cAMP controls oxygen metabolism in mammalian cells.	ACCEPT	Summary: IMP annotation with contributes_to qualifier based on Piccoli et al. (2006). The study showed that an NDUFS4 missense defect suppressed Complex I NADH-ubiquinone oxidoreductase activity. The contributes_to qualifier is appropriate for this accessory subunit. Reason: Correct annotation with appropriate contributes_to qualifier. NDUFS4 mutations suppress Complex I activity, confirming that NDUFS4 contributes to the complex-level enzymatic activity. Supporting Evidence: PMID:16870178 A missense genetic defect in the NDUFS4 subunit, putative substrate of PKA, suppressed, on the other hand, the activity of the complex
GO:0051591 response to cAMP	IMP PMID:11165261 Mutation in the NDUFS4 gene of complex I abolishes cAMP-depe...	ACCEPT	Summary: IMP annotation based on Papa et al. (2001), who showed that mutation in NDUFS4 abolishes cAMP-dependent phosphorylation of the protein and cAMP-dependent activation of Complex I. NDUFS4 contains a PKA phosphorylation site (Ser-173), and cAMP-dependent phosphorylation of this site activates Complex I. The NDUFS4 mutation abolished this cAMP-dependent response, providing evidence that NDUFS4 mediates the response of Complex I to cAMP signaling. Reason: Valid experimental evidence. NDUFS4 is a direct substrate of PKA, and its phosphorylation at Ser-173 mediates cAMP-dependent activation of Complex I. This is a genuine regulatory function of NDUFS4 as a signal-responsive subunit. Supporting Evidence: PMID:11165261 the homozygous 5 bp duplication in the cDNA of the NDUFS4 18 kDa subunit of complex I abolishes cAMP-dependent phosphorylation of this protein and activation of the complex. These findings show for the first time that human complex I is regulated via phosphorylation of the subunit encoded by the NDUFS4 gene.
GO:0051591 response to cAMP	IMP PMID:11181577 A nonsense mutation in the NDUFS4 gene encoding the 18 kDa (...	ACCEPT	Summary: IMP annotation based on Petruzzella et al. (2001), who showed that a nonsense mutation in NDUFS4 resulted in Complex I activity that was insensitive to cAMP stimulation. Since NDUFS4 is the PKA substrate through which cAMP activates Complex I, its loss abolishes this response. Reason: Valid experimental evidence confirming that NDUFS4 is required for the cAMP-dependent regulation of Complex I. The loss of NDUFS4 eliminated cAMP responsiveness of Complex I activity. Supporting Evidence: PMID:11181577 Fibroblast cultures from the patient exhibited severe reduction of the rotenone-sensitive NADH-->UQ oxidoreductase activity of complex I, which was insensitive to cAMP stimulation
GO:0006120 mitochondrial electron transport, NADH to ubiquinone	NAS PMID:9878551 cDNA of eight nuclear encoded subunits of NADH:ubiquinone ox...	ACCEPT	Summary: NAS annotation based on Loeffen et al. (1998), who completed the cDNA characterization of all nuclear-encoded Complex I subunits. The paper describes NDUFS4 in the context of NADH:ubiquinone oxidoreductase function but does not specifically study NDUFS4 function. The NAS code is appropriate. Reason: Correct biological process annotation. NDUFS4 is a subunit of NADH:ubiquinone oxidoreductase, which catalyzes mitochondrial electron transport from NADH to ubiquinone. NAS evidence code is appropriate for this literature-based characterization. Supporting Evidence: PMID:9878551 NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone
GO:0008137 NADH dehydrogenase (ubiquinone) activity	IMP PMID:16478720 Dysfunctions of cellular oxidative metabolism in patients wi...	ACCEPT	Summary: IMP annotation based on Iuso et al. (2006), showing that NDUFS4 mutation prevents complete Complex I assembly and fully suppresses Complex I activity. This supports NDUFS4 participation in the complex-level NADH dehydrogenase function. Reason: The GO term is supported by strong experimental evidence that NDUFS4 loss causes complete suppression of Complex I activity. As a supernumerary subunit, NDUFS4 supports the complex-level activity through assembly/stability rather than direct catalysis, consistent with other accepted GO:0008137 entries for this gene. Supporting Evidence: PMID:16478720 the NDUFS4 mutation prevented complete assembly of the complex and caused full suppression of the activity
GO:0001932 regulation of protein phosphorylation	IMP PMID:11165261 Mutation in the NDUFS4 gene of complex I abolishes cAMP-depe...	MARK AS OVER ANNOTATED	Summary: IMP annotation from MGI for regulation of protein phosphorylation, based on Papa et al. (2001). The GOA TSV shows the qualifier acts_upstream_of_or_within, suggesting this is an indirect involvement. The study showed that NDUFS4 mutation abolishes cAMP-dependent phosphorylation of the NDUFS4 protein itself and activation of Complex I. NDUFS4 is a phosphorylation substrate, not a kinase or phosphatase. The annotation seems to conflate being a substrate of phosphorylation with regulating phosphorylation. NDUFS4 does not regulate protein phosphorylation; rather, its own phosphorylation by PKA regulates Complex I activity. Reason: NDUFS4 is a substrate of PKA phosphorylation at Ser-173, not a regulator of protein phosphorylation. The annotation conflates being phosphorylated (a substrate) with regulating phosphorylation (a kinase/phosphatase/regulatory function). The cAMP/PKA-dependent phosphorylation of NDUFS4 is better captured by the response to cAMP annotations (GO:0051591). Supporting Evidence: PMID:11165261 the homozygous 5 bp duplication in the cDNA of the NDUFS4 18 kDa subunit of complex I abolishes cAMP-dependent phosphorylation of this protein and activation of the complex

Gene Description

Existing Annotations Review

Core Functions

References

Deep Research

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