cotB

id: P15269
gene_symbol: cotB
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:44689
  label: Dictyostelium discoideum
description: Spore coat protein SP70 (also called Beejin) is a developmentally
  regulated, secreted glycoprotein of the social amoeba Dictyostelium discoideum.
  It is synthesized specifically in prespore cells during multicellular
  development, where it is packaged into prespore vesicles as part of a
  preassembled multiprotein glycoprotein complex (the PsB complex). Late in
  culmination this complex is secreted and deposited into the spore coat, the
  cellulose-and-glycoprotein extracellular matrix that surrounds the mature
  dormant spore. SP70 carries an N-terminal signal peptide, a Dictyostelium
  spore-coat (DSCP-N) domain and multiple follistatin-like cysteine-rich
  repeats, and is post-translationally modified by N-linked glycosylation,
  fucosylation and phosphorylation. Together with the other major coat proteins
  SP96 (CotC) and SP60 (CotA) it contributes to the structural integrity and
  permeability barrier of the spore coat; loss of these proteins leaves spores
  viable but more porous. Because its expression is tightly restricted to
  prespore cells, cotB is widely used as a molecular marker of the prespore
  cell type.
existing_annotations:
- term:
    id: GO:0030435
    label: sporulation resulting in formation of a cellular spore
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: Electronic (ARBA) annotation placing SP70 in sporulation. SP70 is a
      prespore-specific spore coat glycoprotein deposited into the spore coat
      during sporulation, so involvement in spore formation is correct. This is
      redundant with the experimental IMP/IGI annotations to the same term.
    action: ACCEPT
    reason: SP70/cotB is a prespore-restricted structural component of the spore
      coat, and its synthesis and deposition are part of the sporulation
      program. The electronic inference is consistent with the direct
      experimental evidence for a role in spore formation.
    supported_by:
    - reference_id: PMID:7813801
      supporting_text: lacking the major spore coat proteins, SP96, SP70, or SP60
- term:
    id: GO:0031160
    label: spore wall
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: located_in
  review:
    summary: Electronic annotation locating SP70 in the spore wall (spore coat).
      SP70 is secreted from prespore vesicles and incorporated into the spore
      coat extracellular matrix, so this localization is correct and is
      supported by direct experimental evidence.
    action: ACCEPT
    reason: SP70 is a component of the assembled spore coat. Both the electronic
      inference and experimental data place the protein in this extracellular
      structure.
    supported_by:
    - reference_id: PMID:8662961
      supporting_text: the complex is synchronously secreted from the prespore
        vesicles and incorporated into the spore coat
- term:
    id: GO:0031160
    label: spore wall
  evidence_type: IDA
  original_reference_id: PMID:499661
  qualifier: is_active_in
  review:
    summary: Direct assay localizing SP70 to the spore coat. The cited paper
      (Orlowski & Loomis 1979) is an early biochemical characterization of the
      Dictyostelium spore coat proteins; the cached record is abstract-only, but
      the localization of SP70 to the spore coat is independently and robustly
      supported by later work on the secreted PsB glycoprotein complex.
    action: ACCEPT
    reason: SP70 is an established structural constituent of the spore coat, the
      cellulose-and-glycoprotein extracellular matrix surrounding the spore.
      This is core to the protein's function and is corroborated by direct
      evidence that the coat glycoprotein complex is secreted and incorporated
      into the coat.
    supported_by:
    - reference_id: PMID:8662961
      supporting_text: the complex is synchronously secreted from the prespore
        vesicles and incorporated into the spore coat
- term:
    id: GO:0003677
    label: DNA binding
  evidence_type: IDA
  original_reference_id: PMID:7713325
  qualifier: enables
  review:
    summary: This annotation assigns DNA binding to the SP70 gene product, but
      the cited paper describes DNA binding by a distinct trans-acting factor
      that recognizes CA-rich elements upstream of the cotB gene, not by the
      SP70 protein itself. SP70 is a secreted, signal-peptide-bearing spore coat
      glycoprotein with follistatin-like repeats and has no nuclear
      localization or DNA-binding architecture; DNA binding is biologically
      implausible for it.
    action: REMOVE
    reason: The DNA-binding activity in Hopper et al. 1995 belongs to a separate
      regulatory (CA-box-binding) protein that controls transcription of the cot
      genes, whereas cotB/SP70 is the structural spore coat glycoprotein being
      regulated. Attributing DNA binding to the SP70 product is a
      misassignment; the protein's secreted, glycosylated, extracellular nature
      is incompatible with a DNA-binding molecular function.
    supported_by:
    - reference_id: PMID:7713325
      supporting_text: the binding activity that recognizes the CA-rich
        sequences upstream of the cotB gene
    - reference_id: PMID:7713325
      supporting_text: modulating the activity of a DNA binding protein
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:8662961
  qualifier: enables
  review:
    summary: Interaction-based annotation reflecting SP70's participation in the
      PsB multiprotein glycoprotein complex. Bare 'protein binding' is
      uninformative; the biologically meaningful content (membership in the
      preassembled spore coat glycoprotein complex) is better captured by the
      glycoprotein complex annotation.
    action: KEEP_AS_NON_CORE
    reason: SP70 does engage in protein-protein interactions as a subunit of the
      PsB complex, but GO:0005515 is too general to convey function. The
      informative aspect is retained via the glycoprotein complex (GO:0090665)
      annotation, so this term is kept only as non-core.
    supported_by:
    - reference_id: PMID:8662961
      supporting_text: some of these spore coat glycoproteins exist as a
        preassembled multiprotein complex
- term:
    id: GO:0030435
    label: sporulation resulting in formation of a cellular spore
  evidence_type: IMP
  original_reference_id: PMID:7813801
  qualifier: involved_in
  review:
    summary: Mutational (knockout) evidence for SP70's role in spore formation.
      Fosnaugh et al. compared spores of strains lacking SP96, SP70 and/or SP60
      and showed altered spore coat properties, supporting a role in
      sporulation.
    action: ACCEPT
    reason: Direct knockout analysis of the major spore coat proteins including
      SP70 establishes their contribution to the spore-formation program. This
      is a core biological process for the protein.
    supported_by:
    - reference_id: PMID:7813801
      supporting_text: lacking the major spore coat proteins, SP96, SP70, or SP60
- term:
    id: GO:0030435
    label: sporulation resulting in formation of a cellular spore
  evidence_type: IGI
  original_reference_id: PMID:7813801
  qualifier: involved_in
  review:
    summary: Genetic-interaction evidence from single, double and triple
      knockouts of the major spore coat proteins, supporting an overlapping,
      partially redundant role of SP70 with SP96 and SP60 in spore formation.
    action: ACCEPT
    reason: The combinatorial knockout analysis demonstrates that SP70 acts
      together with the other major coat proteins in building a functional
      spore, supporting involvement in sporulation.
    supported_by:
    - reference_id: PMID:7813801
      supporting_text: The intensity of staining with fluorescently labeled
        ricinA increased as the spore coat proteins were incrementally lost
- term:
    id: GO:0042244
    label: spore wall assembly
  evidence_type: IMP
  original_reference_id: PMID:7813801
  qualifier: involved_in
  review:
    summary: Knockout analysis shows that loss of the major coat proteins
      including SP70 makes spores more porous, indicating a contribution to the
      structure and permeability barrier of the assembled spore coat, even
      though the coat still forms in their absence.
    action: ACCEPT
    reason: SP70 contributes to the structural completeness of the spore coat;
      its loss increases porosity and exposes underlying polysaccharide. This
      places it in spore wall assembly as a structural constituent, which is a
      core function.
    supported_by:
    - reference_id: PMID:7813801
      supporting_text: the spores are more porous which might make them at risk
        to predators before germination
- term:
    id: GO:0090665
    label: glycoprotein complex
  evidence_type: IDA
  original_reference_id: PMID:8662961
  qualifier: part_of
  review:
    summary: SP70 is part of the preassembled PsB spore coat glycoprotein
      complex that is stored in prespore vesicles and later secreted and
      incorporated into the spore coat. This complex membership is a core
      structural feature of the protein.
    action: ACCEPT
    reason: The spore coat glycoproteins, including SP70, exist as a preassembled
      multiprotein glycoprotein complex, directly supporting the glycoprotein
      complex annotation.
    supported_by:
    - reference_id: PMID:8662961
      supporting_text: some of these spore coat glycoproteins exist as a
        preassembled multiprotein complex
    - reference_id: PMID:8662961
      supporting_text: This unique extracellular matrix is composed of cellulose
        and glycoproteins
- term:
    id: GO:0030248
    label: cellulose binding
  evidence_type: IMP
  original_reference_id: PMID:8662961
  qualifier: contributes_to
  review:
    summary: The assembled PsB glycoprotein complex has specific in vitro
      cellulose binding activity that requires all protein subunits to be
      assembled. As a subunit, SP70 contributes to this complex-level activity
      rather than binding cellulose independently, consistent with the
      contributes_to qualifier.
    action: ACCEPT
    reason: Analysis of subunit-deletion mutants showed that the PsB complex must
      be fully assembled for cellulose binding, so individual subunits including
      SP70 contribute to the activity. The contributes_to qualifier correctly
      captures this complex-dependent molecular function.
    supported_by:
    - reference_id: PMID:8662961
      supporting_text: the PsB complex has a specific in vitro cellulose binding
        activity
    - reference_id: PMID:8662961
      supporting_text: the protein subunits must be assembled for cellulose
        binding activity
- term:
    id: GO:0031153
    label: slug development involved in sorocarp development
  evidence_type: IEP
  original_reference_id: PMID:25887420
  qualifier: acts_upstream_of_or_within
  review:
    summary: This annotation derives from expression profiling in which cotB is
      used as a marker of prespore-cell differentiation during the slug stage.
      Expression timing as a cell-type marker indicates when and where the gene
      is transcribed, not that SP70 functionally drives slug development. SP70's
      demonstrated role is structural, in the spore coat.
    action: MARK_AS_OVER_ANNOTATED
    reason: cotB is a prespore marker whose developmental expression profile was
      measured, but there is no evidence that the SP70 protein participates
      causally in slug development. An IEP inference from a marker gene's
      expression pattern overstates a functional role; the gene's core function
      lies in spore coat structure, not in the morphogenesis of the slug.
    supported_by:
    - reference_id: PMID:25887420
      supporting_text: The genes cotB and ecmB are often used to mark the
        differentiation of prespore and prestalk cell-types, respectively
references:
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: PMID:25887420
  title: Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.
  findings:
  - statement: cotB is used as a canonical marker of prespore cell-type
      differentiation in Dictyostelium development.
    supporting_text: The genes cotB and ecmB are often used to mark the
      differentiation of prespore and prestalk cell-types, respectively
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Full text confirms cotB is used purely as a prespore
      cell-type marker in a transcriptome time-course; supports the marker
      framing but not a causal role in slug development.
- id: PMID:499661
  title: 'Plasma membrane proteins of Dictyostelium: the spore coat proteins.'
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: UNVERIFIED
    review_notes: Cached record is abstract-only (no abstract body available),
      so the specific spore-coat localization assay could not be quoted
      verbatim; localization is corroborated by later PsB-complex work.
- id: PMID:7713325
  title: Protein kinase A is a positive regulator of spore coat gene transcription
    in Dictyostelium.
  findings:
  - statement: cotB encodes a major spore coat protein whose transcription is
      controlled by PKA acting via a CA-rich-element DNA-binding factor.
    supporting_text: The cotA, cotB, and cotC genes encode the major spore coat
      proteins of Dictyostelium
  reference_review:
    relevance: MEDIUM
    correctness: MISCITED
    review_notes: Paper is correctly identified but does not support DNA binding
      by the SP70 product; the DNA-binding activity it describes is a separate
      trans-acting factor regulating cotB transcription.
- id: PMID:7813801
  title: Structural roles of the spore coat proteins in Dictyostelium discoideum.
  findings:
  - statement: Knockouts of the major spore coat proteins (including SP70) yield
      viable but more porous spores, indicating a structural role in the coat.
    supporting_text: the spores are more porous which might make them at risk to
      predators before germination
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Directly assays SP70 (SP70/SP96/SP60) knockouts; establishes
      the structural, permeability-barrier role of the coat proteins.
- id: PMID:8662961
  title: PsB multiprotein complex of Dictyostelium discoideum. Demonstration of cellulose
    binding activity and order of protein subunit assembly.
  findings:
  - statement: The spore coat glycoproteins form a preassembled multiprotein
      complex (PsB) stored in prespore vesicles and later secreted into the coat.
    supporting_text: the complex is synchronously secreted from the prespore
      vesicles and incorporated into the spore coat
  - statement: The assembled PsB complex has specific cellulose binding activity
      that requires all subunits to be assembled.
    supporting_text: the protein subunits must be assembled for cellulose
      binding activity
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Establishes PsB glycoprotein complex membership and
      complex-dependent cellulose binding underlying several cotB annotations.
core_functions:
- description: SP70 is a secreted structural glycoprotein subunit of the
    preassembled PsB spore coat glycoprotein complex. Stored in prespore vesicles
    and secreted during sporulation, it is incorporated into the spore coat,
    where it acts as a structural constituent that contributes to the coat's
    cellulose-anchored architecture and permeability barrier. As a complex
    subunit it contributes to, but does not independently enable, the complex's
    cellulose binding activity.
  molecular_function:
    id: GO:0005198
    label: structural molecule activity
  contributes_to_molecular_function:
    id: GO:0030248
    label: cellulose binding
  directly_involved_in:
  - id: GO:0042244
    label: spore wall assembly
  - id: GO:0030435
    label: sporulation resulting in formation of a cellular spore
  locations:
  - id: GO:0031160
    label: spore wall
  in_complex:
    id: GO:0090665
    label: glycoprotein complex
  supported_by:
  - reference_id: PMID:8662961
    supporting_text: This unique extracellular matrix is composed of cellulose
      and glycoproteins
  - reference_id: PMID:8662961
    supporting_text: the protein subunits must be assembled for cellulose
      binding activity
  - reference_id: PMID:7813801
    supporting_text: lacking the major spore coat proteins, SP96, SP70, or SP60