dimB

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005634 nucleus	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic inference that DimB acts in the nucleus is consistent with direct experimental evidence that DimB accumulates in the nucleus upon DIF-1 stimulation and binds target promoters there. This is a core location. Reason: Nuclear localization is directly demonstrated for DimB and is where its transcription factor activity is exerted; the IBA inference is fully corroborated. Supporting Evidence: PMID:16410410 In the absence of DIF-1, GFP was fairly uniformly distributed throughout the cells. However, after DIF-1 treatment, both DimA:GFP and DimB:GFP exhibited nuclear accumulation
GO:0010468 regulation of gene expression	IBA GO_REF:0000033	ACCEPT	Summary: DimB regulates expression of multiple developmental genes (activating ecmB, repressing pspA and others). This general parent term is correct but a more specific descendant (regulation of DNA-templated transcription) better captures its mechanism. Reason: The annotation is accurate as a broad statement of DimB's function as a transcriptional regulator; more specific transcription terms are also present. Supporting Evidence: PMID:22253818 In response to the signaling polyketide DIF-1 DimB directly activates transcription of the ecmB gene in pstB cells
GO:0043565 sequence-specific DNA binding	IBA GO_REF:0000033	ACCEPT	Summary: DimB was purified by affinity chromatography on ecmA promoter fragments and binds defined sites in the ecmA, ecmB and pspA promoters, directly demonstrating sequence-specific DNA binding. The IBA inference is well supported. Reason: Sequence-specific DNA binding is a core molecular function of DimB, confirmed by direct experimental evidence. Supporting Evidence: PMID:16396914 We have purified a novel bZIP transcription factor, DimB, by affinity chromatography on two spatially separated ecmA promoter fragments
GO:0003700 DNA-binding transcription factor activity	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO inference from the bZIP domain. DimB is experimentally a DNA-binding transcription factor that both activates and represses target genes, so this is a correct core molecular function. Reason: The bZIP domain-based inference matches the demonstrated function of DimB as a sequence-specific transcription factor regulating prestalk and prespore genes. Supporting Evidence: PMID:22253818 In response to the signaling polyketide DIF-1 DimB directly activates transcription of the ecmB gene in pstB cells
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: UniProt subcellular-location mapping to nucleus, corroborated by direct experimental evidence of DIF-1-induced nuclear accumulation. Reason: Nuclear localization is a core, experimentally established location for DimB. Supporting Evidence: PMID:16410410 In the absence of DIF-1, GFP was fairly uniformly distributed throughout the cells. However, after DIF-1 treatment, both DimA:GFP and DimB:GFP exhibited nuclear accumulation
GO:0006355 regulation of DNA-templated transcription	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO inference consistent with DimB's demonstrated role as a direct transcriptional activator and repressor of developmental genes. Reason: DimB directly regulates transcription of ecmB (activation) and pspA (repression); this term accurately captures the process. Supporting Evidence: PMID:22253818 In response to the signaling polyketide DIF-1 DimB directly activates transcription of the ecmB gene in pstB cells
GO:0010629 negative regulation of gene expression	IMP PMID:20300194 BTG interacts with retinoblastoma to control cell fate in Di...	ACCEPT	Summary: In dimB-null cells the ALC-marker gene btg is over-induced during development, indicating that DimB normally represses btg as part of the DIF signalling response. Supports negative regulation of gene expression. Reason: Direct genetic evidence (mutant phenotype) shows DimB negatively regulates btg expression during development. Supporting Evidence: PMID:20300194 btg is overinduced in the DIF unresponsive mutants
GO:0043069 negative regulation of programmed cell death	IMP PMID:16410410 bZIP transcription factor interactions regulate DIF response...	KEEP AS NON CORE	Summary: In an 8-Br-cAMP monolayer assay, DIF-1-treated dimB-null cells undergo non-vacuolar cell death (NVCD) that is normally suppressed by DimB, which instead directs vacuolised stalk-cell formation. This is a genuine but downstream developmental consequence rather than a core molecular function. Reason: DimB is required to repress NVCD in the stalk differentiation pathway, so the annotation is supported, but it reflects a cell-fate outcome of DimB's transcriptional activity rather than its direct function. Supporting Evidence: PMID:16410410 NVCD is repressed by DimB
GO:1903014 cellular response to differentiation-inducing factor 1	HDA PMID:25518940 The Dictyostelium prestalk inducer differentiation-inducing ...	ACCEPT	Summary: DimB is a direct effector of DIF-1 that accumulates in the nucleus and is phosphorylated in response to DIF-1. This term accurately captures DimB's role in the cellular response to the DIF-1 morphogen. Reason: DimB nuclear accumulation and phosphorylation are direct, rapid responses to DIF-1, placing DimB centrally in the cellular DIF-1 response. Supporting Evidence: PMID:25518940 DimB accumulates in the nuclei of cells induced with DIF-1 and is phosphorylated
GO:0031153 slug development involved in sorocarp development	IMP PMID:16396914 The Dictyostelium bZIP transcription factor DimB regulates p...	KEEP AS NON CORE	Summary: dimB-null development proceeds normally to the finger stage, then produces extremely long, thin fingers/slugs, implicating DimB in normal slug morphogenesis. This is a downstream developmental phenotype. Reason: The mutant slug phenotype supports a role in slug development, but this is an organismal-level consequence of DimB's transcriptional activity rather than its core molecular function. Supporting Evidence: PMID:16396914 DimB is not essential for normal expression of the ecmA gene, instead it spatially limits its expression
GO:0005634 nucleus	IDA PMID:16396914 The Dictyostelium bZIP transcription factor DimB regulates p...	ACCEPT	Summary: Direct evidence that DimB rapidly accumulates in the nucleus upon DIF-1 exposure and associates with the ecmA promoter there. Core active location. Reason: Nuclear localization where DimB exerts its transcription factor activity is directly demonstrated. Supporting Evidence: PMID:16396914 DimB rapidly accumulates in the nucleus when cells are exposed to DIF-1
GO:0005634 nucleus	IDA PMID:16410410 bZIP transcription factor interactions regulate DIF response...	ACCEPT	Summary: Direct GFP-localization evidence shows DimB accumulates in the nucleus after DIF-1 treatment. Core active location. Reason: Independent direct evidence confirms nuclear localization as the site of DimB action. Supporting Evidence: PMID:16410410 In the absence of DIF-1, GFP was fairly uniformly distributed throughout the cells. However, after DIF-1 treatment, both DimA:GFP and DimB:GFP exhibited nuclear accumulation
GO:0005634 nucleus	IDA PMID:21458438 DIF-1 regulates Dictyostelium basal disc differentiation by ...	ACCEPT	Summary: DimB is specifically nuclear enriched in pstB cells during normal development, where it activates basal-disc gene expression. Core active location. Reason: Direct evidence places active DimB in the nucleus of the responding cells. Supporting Evidence: PMID:21458438 DimB is specifically nuclear enriched in the pstB cells
GO:0005737 cytoplasm	IDA PMID:16396914 The Dictyostelium bZIP transcription factor DimB regulates p...	KEEP AS NON CORE	Summary: In the absence of DIF-1, DimB is distributed through the cytoplasm and only translocates to the nucleus upon DIF-1 stimulation. Cytoplasmic localization reflects the inactive/resting state rather than the functional compartment. Reason: The cytoplasmic pool is the pre-stimulation reservoir; DimB's functional compartment is the nucleus. The localization is real but not the core site of action. Supporting Evidence: PMID:16410410 In the absence of DIF-1, GFP was fairly uniformly distributed throughout the cells. However, after DIF-1 treatment, both DimA:GFP and DimB:GFP exhibited nuclear accumulation
GO:0031287 positive regulation of sorocarp stalk cell differentiation	IMP PMID:16396914 The Dictyostelium bZIP transcription factor DimB regulates p...	KEEP AS NON CORE	Summary: DimB promotes prestalk/basal-disc differentiation, and dimB-null cells fail to make stalk cells in response to DIF-1. This is a genuine developmental role, but a downstream outcome of DimB's transcriptional activity. Reason: Supported by mutant phenotype (loss of DIF-1-induced stalk differentiation), but represents an organismal cell-differentiation outcome rather than DimB's core molecular function. Supporting Evidence: PMID:21458438 leading to nuclear localization of DimB and direct activation of cell type-specific gene expression
GO:0043565 sequence-specific DNA binding	IDA PMID:16396914 The Dictyostelium bZIP transcription factor DimB regulates p...	ACCEPT	Summary: DimB was purified by affinity chromatography on ecmA promoter fragments, directly demonstrating sequence-specific DNA binding. Core molecular function. Reason: Direct biochemical evidence for sequence-specific promoter binding. Supporting Evidence: PMID:16396914 We have purified a novel bZIP transcription factor, DimB, by affinity chromatography on two spatially separated ecmA promoter fragments
GO:0045184 establishment of protein localization	IMP PMID:16410410 bZIP transcription factor interactions regulate DIF response...	KEEP AS NON CORE	Summary: DimB is required for DIF-1-induced nuclear accumulation of its partner DimA; in dimB-null cells DimA fails to accumulate in the nucleus. The annotation captures this regulatory effect but with a very general term. Reason: Supported by direct genetic evidence that DimB controls DimA nuclear localization, but this is a specialized downstream effect and the term is broad; not a core function. Supporting Evidence: PMID:16410410 nuclear accumulation of DimA in response to DIF-1 is dependent on DimB
GO:0005737 cytoplasm	IDA PMID:16410410 bZIP transcription factor interactions regulate DIF response...	KEEP AS NON CORE	Summary: Consistent with the other cytoplasm annotation, DimB:GFP is uniformly distributed (including cytoplasm) before DIF-1 and translocates to the nucleus after stimulation. Reason: Cytoplasmic localization is the resting-state distribution; the functional compartment is the nucleus. Supporting Evidence: PMID:16410410 In the absence of DIF-1, GFP was fairly uniformly distributed throughout the cells. However, after DIF-1 treatment, both DimA:GFP and DimB:GFP exhibited nuclear accumulation
GO:0005515 protein binding	IPI PMID:16410410 bZIP transcription factor interactions regulate DIF response...	MODIFY	Summary: This IPI annotation records the physical interaction of DimB with the bZIP factor DimA (UniProtKB:Q54XG7). Bare protein binding is uninformative; the interaction is bZIP heterodimerization, better captured by protein heterodimerization activity. Reason: Pull-down assays show DimB forms heterodimeric complexes with DimA in vitro. Replacing the generic term with protein heterodimerization activity conveys the mechanistic nature (bZIP leucine-zipper dimerization) of the interaction. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:16410410 Pull-down assays with purified proteins showed that DimA and DimB can form homodimeric and heterodimeric complexes in vitro PMID:16410410 a second bZIP transcription factor (DimB) that can directly interact with DimA in vitro
GO:0000976 transcription cis-regulatory region binding	IDA PMID:21458438 DIF-1 regulates Dictyostelium basal disc differentiation by ...	ACCEPT	Summary: ChIP analysis directly shows DimB binding to the ecmB cis-regulatory region (promoter) in DIF-1-induced cells. Core molecular function. Reason: Direct in vivo evidence of DimB binding a defined promoter cis-regulatory region. Supporting Evidence: PMID:21458438 ChIP analysis shows that DimB binds to the ecmB promoter in DIF-induced cells
GO:0000976 transcription cis-regulatory region binding	IDA PMID:22253818 Transcriptional repression by a bZIP protein regulates Dicty...	ACCEPT	Summary: ChIP analysis shows DIF-1-induced binding of DimB to the pspA promoter, confirming cis-regulatory region binding at a prespore-gene promoter. Core molecular function. Reason: Independent direct in vivo evidence of DimB binding a promoter cis-regulatory region. Supporting Evidence: PMID:22253818 Thus DIF induces binding of DimB to the pspA promoter
GO:0010628 positive regulation of gene expression	IMP PMID:21458438 DIF-1 regulates Dictyostelium basal disc differentiation by ...	ACCEPT	Summary: DimB directly activates ecmB transcription in pstB cells; in dimB-null cells ecmB is not DIF-inducible. Supports positive regulation of gene expression. Reason: Direct activation of ecmB, supported by ChIP and mutant analysis, makes this a well-supported functional annotation. Supporting Evidence: PMID:22253818 In response to the signaling polyketide DIF-1 DimB directly activates transcription of the ecmB gene in pstB cells
GO:0010629 negative regulation of gene expression	IMP PMID:20080085 A new Dictyostelium prestalk cell sub-type.	ACCEPT	Summary: Genome-wide microarray analysis of dimB-null cells identified genes that become DIF-inducible only when DimB is absent, i.e. genes normally under negative control by DimB. Supports negative regulation of gene expression. Reason: Direct genetic (mutant) evidence that DimB represses a set of DIF-1 target genes. Supporting Evidence: PMID:20080085 these genes fall under negative control by the same two transcription factors
GO:0010629 negative regulation of gene expression	IMP PMID:22253818 Transcriptional repression by a bZIP protein regulates Dicty...	ACCEPT	Summary: DimB directly represses the prespore gene pspA; DIF-1-dependent repression of pspA is abrogated in a dimB-null strain, and DimB binds the pspA promoter. Core repressive activity. Reason: Direct in vivo binding plus mutant analysis establish DimB as a direct repressor of pspA. Supporting Evidence: PMID:22253818 DIF-1 represses pspA gene expression in a suspension cell assay but this repression is abrogated in a dimB null strain
GO:0042802 identical protein binding	IPI PMID:16410410 bZIP transcription factor interactions regulate DIF response...	ACCEPT	Summary: Pull-down assays show DimB can form homodimeric complexes (self- interaction; UniProtKB:Q54ER9), consistent with bZIP homodimerization. This is informative (unlike bare protein binding) and supported. Reason: Direct in vitro evidence of DimB homodimerization; retained as an informative interaction annotation reflecting bZIP dimerization behavior. Supporting Evidence: PMID:16410410 Pull-down assays with purified proteins showed that DimA and DimB can form homodimeric and heterodimeric complexes in vitro
GO:0030587 sorocarp development	IEP PMID:25887420 Leaps and lulls in the developmental transcriptome of Dictyo...	KEEP AS NON CORE	Summary: An IEP annotation based on dimB's developmentally regulated expression trajectory in a genome-wide transcriptome study. Expression-based inference of a broad developmental role. Reason: The developmental-transcriptome correlation is consistent with a role in sorocarp development, but this very general term rests on expression pattern rather than direct functional evidence and is not a core function. Supporting Evidence: PMID:25887420 dimB and dstC continued on a more graded trajectory

Gene Description

Existing Annotations Review

Core Functions

DimB binds defined cis-regulatory (promoter) regions of its target genes in a sequence-specific, DIF-1-induced manner, as shown by affinity purification on the ecmA promoter and ChIP at the ecmB and pspA promoters.

References

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