car-1

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GO Term	Evidence	Action	Reason
GO:0000932 P-body	IBA GO_REF:0000033	ACCEPT	Summary: CAR-1 is a well-established P-body component. Multiple IDA annotations support P-body localization (PMID:16267265, PMID:18515547, PMID:24367695). CAR-1 colocalizes with DCAP-1, the mRNA decapping component, in cytoplasmic foci that are characteristic of P-bodies (PMID:16267265). Reason: IBA annotation is fully supported by experimental evidence. CAR-1 localizes with the mRNA decapping component DCAP-1 (PMID:16267265) and localizes to germline P bodies (PMID:18515547). P-body localization is central to CAR-1 function. Supporting Evidence: file:worm/car-1/car-1-deep-research-falcon.md CAR-1 localizes both to P granules (germ granules) and to DCAP-1-positive cytoplasmic foci interpreted as P-body-like structures.
GO:0003729 mRNA binding	IBA GO_REF:0000033	ACCEPT	Summary: CAR-1 contains an atypical Sm domain at its N-terminus that directly binds RNA. The Sm domain and RGG box both bind to poly(U)-sepharose beads in vitro (PMID:16247027). The Sm domain is essential for CAR-1 function but not localization. Reason: IBA annotation is well-supported. CAR-1 is a predicted RNA-binding protein with demonstrated RNA binding activity. The annotation is appropriately specific as CAR-1 functions in mRNA metabolism through P-body and P-granule complexes. Falcon deep research confirms direct poly(U) binding by the RGG region and an N-terminal Lsm domain consistent with the LSM14/Scd6/Rap55 family assignment. Supporting Evidence: file:worm/car-1/car-1-deep-research-falcon.md RGG region binds poly(U) in vitro, supporting direct RNA-binding capacity. file:worm/car-1/car-1-deep-research-falcon.md an N-terminal Lsm domain (family feature) and poly(U) binding by the RGG region
GO:0033962 P-body assembly	IBA GO_REF:0000033	ACCEPT	Summary: CAR-1 is a core P-body component, but evidence suggests CGH-1 controls CAR-1 localization and P-body/particle formation rather than CAR-1 driving assembly. In cgh-1 mutants, CAR-1 forms aberrant bar-like structures (PMID:16247027, PMID:24367695). Reason: IBA annotation is reasonable given CAR-1's conserved role as a P-body component. While CGH-1 appears more upstream in controlling particle assembly, CAR-1 is required for proper P-body function and its depletion affects RNP organization. Falcon deep research adds direct support for a scaffold contribution: in edc-3(0);edc-4(0) embryos lacking canonical decapping scaffolds, car-1 RNAi reduces DCAP-2 foci 2-4.5-fold. Supporting Evidence: file:worm/car-1/car-1-deep-research-falcon.md car-1 RNAi (64% knockdown) in this background reduces DCAP-2 foci 2–4.5-fold, supporting a scaffold role for CAR-1 in alternative condensate frameworks when canonical scaffolds are absent.
GO:0034063 stress granule assembly	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: While CAR-1 is a known component of RNP granules that share features with stress granules, direct evidence for CAR-1 involvement in stress granule assembly in C. elegans is limited. The annotation is based on phylogenetic inference from yeast Scd6 and other orthologs. Reason: This annotation is derived from phylogenetic inference. In C. elegans, stress granules and P-bodies colocalize and share components (PMID:24367695), but the primary characterized roles of CAR-1 are in P-body/P-granule function, cytokinesis, and apoptosis regulation rather than stress response. Falcon deep research likewise frames CAR-1 as a regulated condensate component whose condensation increases under stress rather than as a dedicated stress-granule assembly factor. Supporting Evidence: file:worm/car-1/car-1-deep-research-falcon.md multiple condensate types (P-bodies, germ granules, stress granules) can coexist and interact
GO:0003723 RNA binding	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation is consistent with experimental evidence. CAR-1 contains Sm domain and RGG box that bind RNA. The more specific mRNA binding (GO:0003729) annotation exists via IBA. Reason: IEA annotation is valid and supported by experimental evidence demonstrating CAR-1 RNA binding via its Sm domain and RGG box (PMID:16247027). The annotation is appropriately general as a parent term to mRNA binding.
GO:0005634 nucleus	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: UniProt annotation indicates nuclear localization based on PMID:18430416, which identified CAR-1 as a transcriptional regulator that binds the cdc-48.1 promoter. However, the predominant localization of CAR-1 in other studies is cytoplasmic (P-bodies and P-granules). Reason: Nuclear localization appears to be a minor or context-specific aspect of CAR-1 function. The primary and well-characterized localizations are to cytoplasmic P-bodies and P-granules. The transcriptional regulator function in PMID:18430416 is atypical compared to other CAR-1 studies.
GO:0005681 spliceosomal complex	IEA GO_REF:0000043	REMOVE	Summary: This annotation is based on UniProt keyword mapping. While CAR-1 contains an Sm domain related to spliceosomal Sm proteins, CAR-1 itself has an atypical Sm domain and functions in P-body/mRNA metabolism rather than splicing. Reason: This annotation is misleading. CAR-1 contains an atypical Sm domain that is distinct from canonical spliceosomal Sm domains (PMID:16247027). CAR-1 functions in mRNA metabolism and cytokinesis, not pre-mRNA splicing. The sequence divergence within the Sm domain is predicted to confer unique RNA binding properties to this protein family distinct from spliceosomal Sm proteins.
GO:0005737 cytoplasm	IEA GO_REF:0000117	ACCEPT	Summary: Cytoplasmic localization is well-supported by multiple experimental studies. CAR-1 localizes to cytoplasmic P-bodies and P-granules. Reason: IEA annotation is correct and redundant with multiple IDA annotations for cytoplasm localization (PMID:16221731, PMID:16267265). CAR-1 is a cytoplasmic protein that localizes to RNP granules.
GO:0006351 DNA-templated transcription	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: This annotation is based on UniProt keyword mapping from the transcription regulator function described in PMID:18430416. However, CAR-1's primary characterized function is post-transcriptional mRNA regulation. Reason: While PMID:18430416 provides evidence for CAR-1 involvement in transcriptional regulation of cdc-48.1, this appears to be a secondary or specialized function. The preponderance of evidence supports CAR-1's primary role in post-transcriptional regulation through P-body/P-granule function.
GO:0006397 mRNA processing	IEA GO_REF:0000043	ACCEPT	Summary: CAR-1 functions in mRNA metabolism through P-bodies, which are sites of mRNA storage and degradation. CAR-1 colocalizes with DCAP-1, the decapping enzyme. Reason: IEA annotation is appropriate. CAR-1 is involved in post-transcriptional mRNA regulation as a P-body component. It functions with CGH-1 to regulate maternally loaded mRNAs required for cytokinesis (PMID:16247027). Falcon deep research describes CAR-1 as acting with CGH-1/DDX6 and interfacing with the mRNA decapping machinery (DCAP-1/DCAP-2), with context-dependent roles in either repressing translation or routing mRNAs into decay. Supporting Evidence: file:worm/car-1/car-1-deep-research-falcon.md Acts with CGH-1/DDX6 and can interface with mRNA decapping machinery
GO:0008380 RNA splicing	IEA GO_REF:0000043	REMOVE	Summary: This annotation is based on UniProt keyword mapping, likely from the Sm domain. However, CAR-1 has an atypical Sm domain and functions in mRNA metabolism, not pre-mRNA splicing. Reason: This annotation is incorrect. CAR-1's atypical Sm domain is functionally distinct from canonical spliceosomal Sm proteins. CAR-1 functions in P-body-mediated mRNA regulation and cytokinesis, not RNA splicing. There is no experimental evidence supporting CAR-1 involvement in splicing.
GO:0035770 ribonucleoprotein granule	IDA PMID:25261697 Translational control of the oogenic program by components o...	ACCEPT	Summary: CAR-1 is a component of OMA ribonucleoprotein particles that regulate translation during oogenesis. CAR-1 was identified as an OMA-1-associated protein in affinity purification experiments. Reason: IDA annotation is well-supported. CAR-1 localizes to multiple types of RNP granules including P-bodies, P-granules, and OMA RNPs. This annotation captures the general RNP granule localization. Falcon deep research frames CAR-1 as a protein that partitions into cytoplasmic ribonucleoprotein condensates including germ granules and P-body-like foci. Supporting Evidence: PMID:25261697 Sep 26. Translational control of the oogenic program by components of OMA ribonucleoprotein particles in Caenorhabditis elegans. file:worm/car-1/car-1-deep-research-falcon.md CAR-1 localizes both to P granules (germ granules) and to DCAP-1-positive cytoplasmic foci interpreted as P-body-like structures.
GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding	IDA PMID:18430416 Involvement of HMG-12 and CAR-1 in the cdc-48.1 expression o...	UNDECIDED	Summary: PMID:18430416 identified CAR-1 as binding to Element B in the cdc-48.1 promoter using South-Western blotting from embryonic nuclear extracts. However, this is an unusual function for CAR-1 compared to its well-characterized cytoplasmic RNA metabolism functions. Reason: The annotation is based on South-Western blotting which identifies proteins that bind DNA, but this method may not distinguish direct from indirect binding. This finding has not been replicated and is inconsistent with CAR-1's primary characterization as a cytoplasmic RNA-binding protein. Further evidence would be needed to confirm this atypical function. Supporting Evidence: PMID:18430416 2008 Mar 13. Involvement of HMG-12 and CAR-1 in the cdc-48.1 expression of Caenorhabditis elegans.
GO:0010628 positive regulation of gene expression	IMP PMID:18430416 Involvement of HMG-12 and CAR-1 in the cdc-48.1 expression o...	KEEP AS NON CORE	Summary: car-1(RNAi) reduces cdc-48.1 expression, supporting a positive regulatory role. However, this may be indirect through mRNA stabilization rather than transcriptional activation. Reason: The annotation reflects a phenotypic observation. Given CAR-1's primary role in mRNA metabolism, the effect on gene expression may be at the post-transcriptional level (mRNA stability/translation) rather than transcriptional activation. The term is broad enough to encompass both possibilities. Supporting Evidence: PMID:18430416 2008 Mar 13. Involvement of HMG-12 and CAR-1 in the cdc-48.1 expression of Caenorhabditis elegans.
GO:0005783 endoplasmic reticulum	IDA PMID:16267265 CAR-1, a protein that localizes with the mRNA decapping comp...	KEEP AS NON CORE	Summary: PMID:16267265 reports CAR-1 affects ER organization, but the primary localization data in this paper focuses on P-bodies, P-granules, spindle, and pericentriolar material. ER localization may be indirect or context-specific. Reason: The paper describes organization of the endoplasmic reticulum is aberrant upon CAR-1 depletion, suggesting CAR-1 affects ER organization. However, ER localization is not a primary characterized site for CAR-1. The relationship may be functional rather than direct localization. Falcon deep research reinforces that CAR-1 is functionally coupled to the ER in embryos, with depletion disrupting ER reticulation and spindle/midzone-associated ER, consistent with an ER-linked mRNP/granule function rather than a constitutive ER residency. Supporting Evidence: PMID:16267265 Nov 2. CAR-1, a protein that localizes with the mRNA decapping component DCAP-1, is required for cytokinesis and ER organization in Caenorhabditis elegans embryos. file:worm/car-1/car-1-deep-research-falcon.md CAR-1 is also functionally coupled to the endoplasmic reticulum (ER) in embryos, where depletion disrupts ER reticulation and spindle/midzone-associated ER
GO:0072686 mitotic spindle	IDA PMID:16267265 CAR-1, a protein that localizes with the mRNA decapping comp...	ACCEPT	Summary: CAR-1 is required for proper anaphase spindle structure. CAR-1 depletion causes failure of interzonal microtubule bundle formation. The localization to spindle may be related to CAR-1's function in regulating mRNAs required for spindle assembly. Reason: IDA annotation is supported by functional evidence. CAR-1 depletion causes a specific defect in the microtubule cytoskeleton with loss of interzonal microtubule bundles (PMID:16247027). This suggests CAR-1 localizes to or functions at the spindle during cytokinesis. Supporting Evidence: PMID:16267265 Nov 2. CAR-1, a protein that localizes with the mRNA decapping component DCAP-1, is required for cytokinesis and ER organization in Caenorhabditis elegans embryos.
GO:1990023 mitotic spindle midzone	IDA PMID:16267265 CAR-1, a protein that localizes with the mRNA decapping comp...	ACCEPT	Summary: CAR-1 is required for spindle midzone formation. In car-1 depleted embryos, the spindle midzone fails to form, even though midzone components are present (PMID:16267265). Reason: IDA annotation is well-supported. CAR-1 depletion causes failure of interzonal microtubule bundle formation and loss of AIR-2 and ZEN-4 recruitment to the midzone (PMID:16247027). CAR-1 function is essential for midzone assembly. Supporting Evidence: PMID:16267265 Nov 2. CAR-1, a protein that localizes with the mRNA decapping component DCAP-1, is required for cytokinesis and ER organization in Caenorhabditis elegans embryos.
GO:0005515 protein binding	IPI PMID:25261697 Translational control of the oogenic program by components o...	REMOVE	Summary: CAR-1 interacts with OMA-1 in the context of OMA ribonucleoprotein particles. CAR-1 also forms complexes with CGH-1 and CEY-2 (PMID:16247027). Reason: Generic protein binding is uninformative here. The IPI records a protein-protein interaction (CAR-1 co-purified with OMA-1), but this OMA-1 interaction maps to no specific informative MF term. GO:0003729 (mRNA binding) is an RNA-binding molecular function unrelated to this protein-protein interaction and is already separately annotated (IBA), so it is not a valid replacement. CAR-1's RNP-complex context is already captured by GO:1990904 (ribonucleoprotein complex, IDA, PMID:16247027). Supporting Evidence: PMID:25261697 Sep 26. Translational control of the oogenic program by components of OMA ribonucleoprotein particles in Caenorhabditis elegans. PMID:16247027 A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis elegans. file:worm/car-1/car-1-deep-research-falcon.md Acts with CGH-1/DDX6 and can interface with mRNA decapping machinery
GO:0000932 P-body	IDA PMID:24367695 PAB-1, a Caenorhabditis elegans poly(A)-binding protein, reg...	ACCEPT	Summary: CAR-1 colocalizes with P-body components CGH-1 and PAB-1 in both P-granules and P-bodies in embryos and gonads (PMID:24367695). Reason: IDA annotation is well-supported by colocalization studies showing CAR-1 with P-body markers in multiple contexts. Supporting Evidence: PMID:24367695 eCollection 2013. PAB-1, a Caenorhabditis elegans poly(A)-binding protein, regulates mRNA metabolism in germline by interacting with CGH-1 and CAR-1.
GO:0043186 P granule	IDA PMID:24367695 PAB-1, a Caenorhabditis elegans poly(A)-binding protein, reg...	ACCEPT	Summary: CAR-1 localizes to P granules, the germline-specific RNP particles in C. elegans. P-granule localization is well-documented across multiple studies. Reason: IDA annotation is well-supported by multiple studies. CAR-1 localizes to P-granules (germ-line specific ribonucleoprotein particles) (PMID:16267265) and colocalizes with PGL-1, a P-granule marker. Supporting Evidence: PMID:24367695 eCollection 2013. PAB-1, a Caenorhabditis elegans poly(A)-binding protein, regulates mRNA metabolism in germline by interacting with CGH-1 and CAR-1.
GO:1990904 ribonucleoprotein complex	IDA PMID:16247027 A complex containing the Sm protein CAR-1 and the RNA helica...	ACCEPT	Summary: CAR-1 is part of a multiprotein RNP complex containing CGH-1 and CEY-2. The interaction with CGH-1 is RNA-dependent. Reason: IDA annotation is well-supported. CAR-1 is a component of a multiprotein complex that also contains the DEAD box RNA helicase, CGH-1, and a Y-box-containing protein, CEY-2 (PMID:16247027). Falcon deep research further describes CAR-1/CGH-1/IFET-1 repressive complexes that can repress translation and prevent decapping/decay in some developmental contexts. Supporting Evidence: PMID:16247027 A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis elegans. file:worm/car-1/car-1-deep-research-falcon.md CAR-1/CGH-1/IFET-1 complexes can repress translation and prevent decapping/decay
GO:0000932 P-body	IDA PMID:18515547 C. elegans La-related protein, LARP-1, localizes to germline...	ACCEPT	Summary: CAR-1 colocalizes with LARP-1 in germline P-bodies. This study provides additional evidence for CAR-1 P-body localization. Reason: IDA annotation is supported. LARP-1 colocalizes with P bodies and CAR-1 is established as a P-body component. Supporting Evidence: PMID:18515547 C. elegans La-related protein, LARP-1, localizes to germline P bodies and attenuates Ras-MAPK signaling during oogenesis.
GO:0000242 pericentriolar material	IDA PMID:16267265 CAR-1, a protein that localizes with the mRNA decapping comp...	ACCEPT	Summary: CAR-1 localizes to pericentriolar material as shown in PMID:16267265. This localization is consistent with CAR-1's role in spindle-related processes during cytokinesis. Reason: IDA annotation captures a specific localization relevant to CAR-1's function in cytokinesis and spindle organization. Supporting Evidence: PMID:16267265 Nov 2. CAR-1, a protein that localizes with the mRNA decapping component DCAP-1, is required for cytokinesis and ER organization in Caenorhabditis elegans embryos.
GO:0000932 P-body	IDA PMID:16267265 CAR-1, a protein that localizes with the mRNA decapping comp...	ACCEPT	Summary: Original characterization of CAR-1 P-body localization. CAR-1 colocalizes with DCAP-1, the mRNA decapping component, in cytoplasmic foci. Reason: IDA annotation from the foundational CAR-1 characterization paper. This study established CAR-1 as a P-body component. Supporting Evidence: PMID:16267265 Nov 2. CAR-1, a protein that localizes with the mRNA decapping component DCAP-1, is required for cytokinesis and ER organization in Caenorhabditis elegans embryos.
GO:0005737 cytoplasm	IDA PMID:16221731 A conserved RNA-protein complex component involved in physio...	ACCEPT	Summary: CAR-1 localizes to cytoplasmic particles in the gonad and early embryo. Reason: IDA annotation is well-supported. CAR-1 is primarily a cytoplasmic protein that localizes to various RNP granules. Supporting Evidence: PMID:16221731 A conserved RNA-protein complex component involved in physiological germline apoptosis regulation in C.
GO:0005737 cytoplasm	IDA PMID:16267265 CAR-1, a protein that localizes with the mRNA decapping comp...	ACCEPT	Summary: CAR-1 localizes to cytoplasmic foci and P-granules. Reason: IDA annotation is correct. CAR-1 is a cytoplasmic protein. Supporting Evidence: PMID:16267265 Nov 2. CAR-1, a protein that localizes with the mRNA decapping component DCAP-1, is required for cytokinesis and ER organization in Caenorhabditis elegans embryos.
GO:0043186 P granule	IDA PMID:16221731 A conserved RNA-protein complex component involved in physio...	ACCEPT	Summary: CAR-1 localizes to P granules and associates with CGH-1 in a conserved germline RNP complex. Reason: IDA annotation is well-supported. P-granule localization is a core aspect of CAR-1 function in the germline. Supporting Evidence: PMID:16221731 A conserved RNA-protein complex component involved in physiological germline apoptosis regulation in C.
GO:0043186 P granule	IDA PMID:16247027 A complex containing the Sm protein CAR-1 and the RNA helica...	ACCEPT	Summary: CAR-1 localizes to P-granules that concentrate in germline precursors. P-granule localization is confirmed by colocalization with PGL-1. Reason: IDA annotation is well-supported. CAR-1 localizes to RNA-containing P-granules that concentrate in the germline precursors (PMID:16247027). Supporting Evidence: PMID:16247027 A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis elegans.
GO:0043186 P granule	IDA PMID:16267265 CAR-1, a protein that localizes with the mRNA decapping comp...	ACCEPT	Summary: Original characterization showing CAR-1 localization to P-granules. Reason: IDA annotation from foundational CAR-1 paper. P-granule localization is central to CAR-1 germline function. Supporting Evidence: PMID:16267265 Nov 2. CAR-1, a protein that localizes with the mRNA decapping component DCAP-1, is required for cytokinesis and ER organization in Caenorhabditis elegans embryos.
GO:0000281 mitotic cytokinesis	IMP PMID:16247027 A complex containing the Sm protein CAR-1 and the RNA helica...	NEW	Summary: CAR-1 is essential for embryonic cytokinesis. car-1(RNAi) and car-1 mutant embryos fail to complete cytokinesis, with cleavage furrows regressing and spindle midzone failing to form. Reason: This is a core function of CAR-1 not explicitly annotated. CAR-1 was named for Cytokinesis, Apoptosis, RNA-associated reflecting its essential role in cytokinesis. Multiple studies demonstrate cytokinesis failure upon CAR-1 depletion. Falcon deep research confirms CAR-1 is required for late cytokinesis/scission, with depletion causing cleavage furrows to ingress then regress alongside disrupted membrane accumulation and spindle midzone organization. Supporting Evidence: PMID:16247027 A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis elegans. file:worm/car-1/car-1-deep-research-falcon.md CAR-1 is required for late cytokinesis/scission; depletion causes cleavage furrows to ingress then regress and disrupts membrane accumulation and spindle midzone organization
GO:0017148 negative regulation of translation	IMP PMID:18695046 Maternal mRNAs are regulated by diverse P body-related mRNP ...	NEW	Summary: CAR-1 functions in translational repression as part of P-body and OMA RNP complexes. CAR-1 is part of the IFET-1/CGH-1/CAR-1/PATR-1 repressive complex. Reason: This is a core molecular function of CAR-1, demonstrated by direct mutant/RNAi phenotype evidence. Noble et al. 2008 (PMID:18695046) show that loss of CAR-1 causes ectopic GLP-1 (Notch receptor) protein expression in oocytes while glp-1 mRNA levels remain unchanged, establishing that CAR-1 controls glp-1 translation rather than mRNA production or stability. This is consistent with CAR-1 acting in PUF-dependent translational repression and with its association with translational repressors in OMA RNPs (PMID:25261697). The original IBA annotation (GO_REF:0000033) is retained as a supporting reference. Supporting Evidence: PMID:18695046 ectopic GLP-1 protein expression in oocytes of both wild-type and fog-2(q71) arrested gonads PMID:18695046 glp-1 mRNA levels were similar in car-1(tm1753) mutant and wild-type animals, which supports CAR-1 control of glp-1 translation rather than mRNA production or stability file:worm/car-1/car-1-deep-research-falcon.md In the germline/oogenesis, CAR-1 promotes PUF-dependent repression of the Notch-like receptor mRNA glp-1, and car-1 depletion elevates GLP-1 protein while glp-1 mRNA levels remain similar, consistent with primary control at the translation level.
GO:0043066 negative regulation of apoptotic process	IMP PMID:16221731 A conserved RNA-protein complex component involved in physio...	NEW	Summary: CAR-1 regulates physiological germline apoptosis. car-1(RNAi) leads to increased germline cell death, indicating CAR-1 normally suppresses apoptosis. Reason: This is a core function of CAR-1 (the A in CAR-1 stands for Apoptosis). Depletion of CAR-1 increases physiological germline apoptosis, demonstrating a negative regulatory role. Supporting Evidence: PMID:16221731 A conserved RNA-protein complex component involved in physiological germline apoptosis regulation in C.