BUB3.1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0007094 mitotic spindle assembly checkpoint signaling	IBA GO_REF:0000033	ACCEPT	Summary: BUB3.1 is a core component of the spindle assembly checkpoint in plants. IBA annotation is supported by phylogenetic conservation and experimental evidence in Arabidopsis. BUB3.1 interacts with MAD2 and BUBR1, localizes to unattached kinetochores upon SAC activation, and shows cell cycle-regulated expression with G2/M peak [PMID:19710914]. Reason: Core function of BUB3 family proteins. Experimental evidence from Caillaud et al. (2009) demonstrates BUB3.1 localization to kinetochores following SAC activation and interaction with other MCC components. This represents a conserved function from yeast to plants. Supporting Evidence: PMID:19710914 the plant BUBR1, BUB3.1 and MAD2 partners identified in this study are all in place at the unattached kinetochores and may therefore fulfil the evolutionarily conserved functions of SAC proteins, delaying anaphase until all the chromosomes are attached to both poles of the spindle
GO:1990298 bub1-bub3 complex	IBA GO_REF:0000033	ACCEPT	Summary: BUB3.1 forms complexes with BUB1-related proteins in Arabidopsis. The BUB1/BUB3 complex is a conserved component of the SAC across eukaryotes. Experimental evidence supports BUB3.1 interactions with BUBR1/MAD3 family proteins [PMID:19710914, PMID:21687678]. Reason: Phylogenetically conserved complex. Y2H and BiFC experiments confirm BUB3.1 interactions with BUBR1 and other SAC components. The BUB1-BUB3 complex is essential for checkpoint signaling. Supporting Evidence: PMID:19710914 Coexpression of BUBR1:Cub:URA3 with either Nub:BUB3.1 and Nub:MAD2 conferred resistance to 5-FOA, indicating that BUBR1 interacted with both BUB3.1 and MAD2 PMID:21687678 Binding of AtCDC20.1 and AtCDC20.2 was detected to MAD2 and BUBR1/MAD3 and a weaker one to BUB3.1
GO:0000776 kinetochore	IBA GO_REF:0000033	ACCEPT	Summary: BUB3.1 localizes to kinetochores upon SAC activation. IBA annotation is consistent with experimental IDA evidence from PMID:19710914 showing kinetochore localization. Reason: Conserved localization supported by direct experimental evidence. BUB3.1-GFP localizes to unattached kinetochores in propyzamide-treated cells and to kinetochores in MG132-treated metaphase-arrested cells. Supporting Evidence: PMID:19710914 At a prometaphase-like stage, following treatment with the microtubule-destabilizing herbicide propyzamid, which prevents the formation of microtubule-kinetochore attachments, the MAD2 fusion protein was found to cluster strongly in bright spots on condensing chromosomes corresponding to unattached kinetochores (n = 20; Fig. 3). Similar localisation was observed for the BUB3.1 and BUBR1 fusion proteins (n = 20; Fig. 3).
GO:0005654 nucleoplasm	IBA GO_REF:0000033	ACCEPT	Summary: BUB3.1 shows nuclear localization during interphase. This is consistent with its role as a cell cycle checkpoint protein and is supported by experimental evidence. Reason: BUB3.1-GFP is detected in the nucleus during interphase, consistent with phylogenetic inference and direct experimental observation. Supporting Evidence: PMID:19710914 BUB3.1:GFP and MAD2:GFP were detected in both the nucleus and the cytoplasm
GO:0009524 phragmoplast	IBA GO_REF:0000033	ACCEPT	Summary: BUB3.1 localizes to the phragmoplast midline during cytokinesis. This plant-specific function is well-supported by experimental evidence. IBA annotation is appropriate as this function appears conserved across plant species. Reason: Plant-specific core function of BUB3.1. Multiple studies demonstrate phragmoplast midline localization and interaction with MAP65-3 for cytokinesis regulation. Supporting Evidence: PMID:19710914 Unexpectedly, BUB3.1 was also found in the phragmoplast midline during the final step of cell division in plants
GO:0043130 ubiquitin binding	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Ubiquitin binding is inferred for BUB3.1 based on phylogenetic analysis. While BUB3 proteins interact with the APC/C complex which is involved in ubiquitination, direct evidence for ubiquitin binding by BUB3.1 is limited. This may be inferred from the WD40 domain architecture and complex formation with ubiquitin ligase machinery. Reason: While BUB3 proteins are involved in SAC signaling that ultimately regulates APC/C-mediated ubiquitination, ubiquitin binding per se is not a core molecular function of BUB3.1. The primary functions are protein scaffolding and checkpoint signaling. This annotation may reflect the broader complex context rather than intrinsic BUB3.1 activity.
GO:0000776 kinetochore	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for kinetochore localization. This is consistent with the IBA and IDA annotations for the same term. Redundant with more specific evidence. Reason: Consistent with experimental evidence. IEA provides additional computational support for a well-established localization.
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation for nuclear localization based on UniProtKB subcellular location mapping. Consistent with experimental observations of nuclear/nucleoplasm localization. Reason: Supported by experimental evidence showing BUB3.1-GFP in the nucleus during interphase. This is a more general term than nucleoplasm (GO:0005654) but both are correct. Supporting Evidence: PMID:19710914 BUB3.1 and MAD2 proteins were localised to the nucleus and gave a weak cytoplasmic signal during interphase (n = 30; Fig. 5A).
GO:0005819 spindle	IEA GO_REF:0000044	ACCEPT	Summary: BUB3.1 associates with spindle structures during mitosis. This is consistent with experimental observations of spindle microtubule association. Reason: Experimental evidence shows BUB3.1 association with spindle microtubules in arrested metaphase cells. The term spindle is appropriate. Supporting Evidence: PMID:19710914 Three hours after MG132 treatment, the initially diffuse spindle BUBR1, BUB3.1 and MAD2:GFP staining accumulated progressively onto MT-like structures within the spindle
GO:0007059 chromosome segregation	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation from UniProtKB keyword mapping. BUB3.1 is involved in ensuring proper chromosome segregation through its role in the spindle assembly checkpoint. This is a correct but somewhat general annotation. Reason: BUB3 function in the SAC is essential for proper chromosome segregation. The checkpoint delays anaphase until chromosomes are properly attached, preventing mis-segregation. Supporting Evidence: PMID:19710914 In eukaryotes, the spindle assembly checkpoint (SAC) is a sophisticated surveillance mechanism that ensures the fidelity of chromosome segregation during mitosis
GO:0009524 phragmoplast	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation for phragmoplast localization. Redundant with IBA annotation but correctly assigned based on UniProtKB subcellular location vocabulary. Reason: Consistent with IBA and experimental evidence. Phragmoplast localization is a well-established feature of BUB3.1.
GO:0051301 cell division	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation from UniProtKB keyword mapping. BUB3.1 plays roles in both mitotic checkpoint and cytokinesis, making this a broadly appropriate term. Reason: General but accurate term. BUB3.1 functions in cell division through both SAC signaling and phragmoplast-mediated cytokinesis.
GO:0051321 meiotic cell cycle	IEA GO_REF:0000043	MODIFY	Summary: IEA annotation from UniProtKB keyword mapping. UniProt lists "Meiosis" as a keyword, likely derived from the observation that BUB3.1 disruption affects gametophyte development. However, the experimental evidence primarily demonstrates MITOTIC functions. There is no direct experimental evidence showing BUB3.1 functions specifically in meiosis as opposed to the mitotic divisions during gametophyte development. Reason: This appears to be an over-annotation. While BUB3.1 is essential for gametophyte development (PMID:18508582), the gametophyte defects could result from mitotic errors during the post-meiotic mitoses, not meiosis itself. The primary experimental evidence (PMID:19710914) focuses on mitotic cells. BUB3 proteins are general cell cycle checkpoint proteins - they function in any dividing cell. The annotation to "meiotic cell cycle" implies a meiosis-specific function that is not experimentally supported for BUB3.1. In Arabidopsis, BUB3.3 appears to be the paralog with specialized kinetochore checkpoint functions, while BUB3.1/BUB3.2 are specialized for cytokinesis. A more appropriate annotation would be the parent term "cell cycle" (GO:0007049) or "mitotic cell cycle" (GO:0000278). Proposed replacements: mitotic cell cycle Supporting Evidence: PMID:19710914 We conclude that plant BUBR1, BUB3.1 and MAD2 proteins may have the SAC protein functions conserved from yeast to humans
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: ISM annotation from AtSubP analysis predicting nuclear localization. Consistent with experimental evidence and other annotations. Reason: Computational prediction confirmed by experimental observation.
GO:0005515 protein binding	IPI PMID:19710914 Spindle assembly checkpoint protein dynamics reveal conserve...	MODIFY	Summary: IPI annotation based on demonstrated interactions with MAD2 and BUBR1 in Caillaud et al. (2009). While the interactions are real and well-documented, "protein binding" is a generic term that provides little functional information. Reason: "Protein binding" is too generic and uninformative. The specific binding partners are MAD2 and BUBR1/MAD3. A more informative molecular-function replacement is protein-macromolecule adaptor activity, reflecting BUB3.1's WD40 scaffold role in checkpoint assemblies. Proposed replacements: protein-macromolecule adaptor activity
GO:0005828 kinetochore microtubule	IDA PMID:19710914 Spindle assembly checkpoint protein dynamics reveal conserve...	ACCEPT	Summary: IDA annotation based on localization to kinetochore microtubules in Caillaud et al. (2009). In MG132-treated cells arrested in metaphase, BUB3.1 accumulated on MT-like structures and was confirmed to colocalize with spindle microtubules. Reason: Direct experimental evidence demonstrates BUB3.1 association with kinetochore microtubules during SAC activation. This is part of the core checkpoint function. Supporting Evidence: PMID:19710914 In cases of 'wait anaphase', plant SAC proteins were associated with both kinetochores and kinetochore microtubules
GO:0005876 spindle microtubule	IDA PMID:19710914 Spindle assembly checkpoint protein dynamics reveal conserve...	ACCEPT	Summary: IDA annotation based on localization studies in Caillaud et al. (2009). BUB3.1 associates with spindle microtubules during metaphase arrest. Reason: Well-supported by experimental evidence showing BUB3.1 accumulation on spindle MT-like structures in MG132-treated cells. Supporting Evidence: PMID:19710914 Progressively, much of the BUBR1, BUB3.1, MAD2:GFP-derived fluorescence took on a fibrillar appearance, probably as a result of association with the acentrosomal metaphase spindle apparatus
GO:0005515 protein binding	IPI PMID:21687678 Conserved CDC20 cell cycle functions are carried out by two ...	MODIFY	Summary: IPI annotation based on Y2H interaction with CDC20-1 and CDC20-2 in Kevei et al. (2011). While the interaction is documented, "protein binding" is too generic. Reason: Same issue as the other "protein binding" annotation - too generic. The interaction with CDC20 is functionally meaningful in the context of MCC formation and APC/C regulation. A scaffold/adaptor MF better captures the inferred role without using a cellular-component term as an MF replacement. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:21687678 Binding of AtCDC20.1 and AtCDC20.2 was detected to MAD2 and BUBR1/MAD3 and a weaker one to BUB3.1
GO:0005515 protein binding	IPI PMID:20706207 Targeted interactomics reveals a complex core cell cycle mac...	MODIFY	Summary: IPI annotation from Van Leene et al. (2010) targeted interactomics study. This high-throughput TAP-MS study identified BUB3.1 interactions in the context of cell cycle machinery. Reason: Generic "protein binding" annotation from a high-throughput study. While valid, this provides minimal functional insight. A scaffold/adaptor activity term is more informative for BUB3.1's documented cell-cycle interaction context. Proposed replacements: protein-macromolecule adaptor activity
GO:0000776 kinetochore	IDA PMID:19710914 Spindle assembly checkpoint protein dynamics reveal conserve...	ACCEPT	Summary: IDA annotation for kinetochore localization from Caillaud et al. (2009). This is direct experimental evidence showing BUB3.1-GFP at kinetochores following SAC activation. Reason: Strong experimental evidence. BUB3.1-GFP localizes to kinetochores in both propyzamide-treated cells (prometaphase arrest) and MG132-treated cells (metaphase arrest). Supporting Evidence: PMID:19710914 Similar localisation was observed for the BUB3.1 and BUBR1 fusion proteins (n = 20; Fig. 3). Thus, the plant BUBR1, BUB3.1 and MAD2 partners identified in this study are all in place at the unattached kinetochores
GO:0007094 mitotic spindle assembly checkpoint signaling	IDA PMID:19710914 Spindle assembly checkpoint protein dynamics reveal conserve...	ACCEPT	Summary: IDA annotation for mitotic SAC signaling based on Caillaud et al. (2009). BUB3.1 is part of the SAC machinery, interacting with MAD2 and BUBR1, and localizing appropriately during checkpoint activation. Reason: Core function of BUB3.1 with strong experimental support. The study demonstrates physical interactions between SAC components, appropriate localization dynamics, and cell cycle-regulated expression. Supporting Evidence: PMID:19710914 We conclude that plant BUBR1, BUB3.1 and MAD2 proteins may have the SAC protein functions conserved from yeast to humans
GO:0009524 phragmoplast	IDA PMID:19710914 Spindle assembly checkpoint protein dynamics reveal conserve...	ACCEPT	Summary: IDA annotation for phragmoplast localization from Caillaud et al. (2009). Time-lapse imaging showed BUB3.1 at the phragmoplast midline during cytokinesis. Reason: Plant-specific core function with strong experimental evidence. This is one of the key findings of the Caillaud et al. study - BUB3.1 has a dual role in SAC and cytokinesis. Supporting Evidence: PMID:19710914 BUB3.1 displayed an unexpected distribution during cytokinesis in late anaphase to telophase in plant cells. It first appeared in the centre of the forming cell plate, and was subsequently redistributed to the growing margins of the cell plate as the cell plate grew outwards
GO:0080008 Cul4-RING E3 ubiquitin ligase complex	ISS PMID:18223036 Characterization of Arabidopsis and rice DWD proteins and th...	UNDECIDED	Summary: ISS annotation suggesting BUB3.1 is part of a CUL4-RING E3 ubiquitin ligase complex, based on Lee et al. (2008). This paper identified DWD (DDB1-binding WD40) proteins as potential substrate receptors for CUL4-based E3 ligases. BUB3.1 contains WD40 repeats and may have a DWD motif. Reason: The Lee et al. (2008) paper is about DWD proteins as CUL4 substrate receptors. While BUB3.1 contains WD40 repeats, its primary known functions are in SAC and cytokinesis, not as a CUL4 substrate receptor. This annotation may be based on domain architecture rather than functional evidence. Need to verify whether BUB3.1 was specifically identified as a CUL4 complex component or if this is inference from domain structure. The connection between BUB3 and CUL4 is not clearly established in the core BUB3.1 literature.
GO:0030674 protein-macromolecule adaptor activity	IPI PMID:19710914 Spindle assembly checkpoint protein dynamics reveal conserve...	NEW	Summary: BUB3.1 functions as a WD40 scaffold/adaptor in Arabidopsis cell division complexes. It interacts with MAD2 and BUBR1/MAD3 in the spindle assembly checkpoint context and, in plants, with MAP65-3 during phragmoplast organization. Reason: This is a more informative molecular function than generic protein binding. The adaptor/scaffold interpretation is inferred from BUB3.1's WD40 scaffold architecture, conserved BUB3 family role, and multiple documented binary interactions with checkpoint/cytokinesis partners; PMID:19710914 alone shows interaction topology rather than an isolated obligate-bridge assay. This term therefore captures the supported macromolecular organizing role more accurately than unspecified protein binding. Supporting Evidence: PMID:19710914 Coexpression of BUBR1:Cub:URA3 with either Nub:BUB3.1 and Nub:MAD2 conferred resistance to 5-FOA, indicating that BUBR1 interacted with both BUB3.1 and MAD2 file:ARATH/BUB3.1/BUB3.1-deep-research-falcon.md BUB3.1 interacts with MAD2 and BUBR1/MAD3 family proteins and a plant-specific interaction with MAP65-3 links SAC to microtubule bundling.
GO:0080175 phragmoplast microtubule organization	IGI DOI:10.1038/s41477-018-0192-z	NEW	Summary: BUB3.1 and BUB3.2 have a plant-specific role in phragmoplast microtubule organization. BUB3.1 localizes to the phragmoplast midline, interacts with MAP65-3, and the bub3.1 bub3.2 double mutant shows defective phragmoplast expansion and cell plate assembly. Reason: Existing annotations capture phragmoplast localization, but the functional evidence is more specific than generic cytokinesis. Mutant, localization, and MAP65-3 interaction evidence support phragmoplast microtubule organization as the BUB3.1/BUB3.2-mediated process. Because the phenotype evidence is from the bub3.1 bub3.2 double mutant, IGI is more appropriate than IMP. Supporting Evidence: DOI:10.1038/s41477-018-0192-z BUB3.1 and BUB3.2 interact with MAP65-3 to promote phragmoplast microtubule reorganization file:ARATH/BUB3.1/BUB3.1-deep-research-falcon.md bub3;1 bub3;2 double mutants exhibit uncoordinated phragmoplast expansion, failed cell plate assembly, and hypersensitivity to caffeine, consistent with defective cytokinesis.

Gene Description

Existing Annotations Review

Core Functions

BUB3.1 functions as a component of the spindle assembly checkpoint (SAC), interacting with MAD2 and BUBR1/MAD3 to ensure proper chromosome segregation. It localizes to unattached kinetochores and spindle microtubules during SAC activation. This is a conserved function from yeast to plants.

BUB3.1 has a plant-specific function in phragmoplast-mediated cytokinesis. It localizes to the phragmoplast midline during cell plate formation and interacts with MAP65-3 to promote microtubule reorganization. This dual function distinguishes plant BUB3 proteins from their animal/yeast counterparts.

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