ecmB

id: P11976
gene_symbol: ecmB
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:44689
  label: Dictyostelium discoideum
description: ecmB (prestalk protein; also called extracellular matrix protein ST310
  or pDd56) is a Cys-rich, tandem-repeat secreted glycoprotein of Dictyostelium
  discoideum that is a structural component of the stalk tube, the extracellular
  matrix that encases the cellular stalk of the mature fruiting body (sorocarp). The
  protein carries an N-terminal signal peptide and a long array of imperfect
  cysteine-rich 24-residue repeats, and is secreted into the extracellular space
  and deposited in the stalk-tube matrix. Its synthesis is a hallmark of prestalk
  and stalk-cell differentiation. Expression is induced by the stalk-inducing
  morphogen DIF-1 and is up-regulated sharply during the culmination stage of
  multicellular development, which is why ecmB (like ecmA) is widely used as a
  molecular marker of the prestalk/stalk cell lineage.
existing_annotations:
- term:
    id: GO:0031012
    label: extracellular matrix
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: Phylogenetic inference that ecmB is active in the extracellular matrix
      is consistent with its curated biology as a secreted stalk-tube matrix
      protein and with the UniProt subcellular location (secreted, extracellular
      matrix). This is a core aspect of the protein's role.
    action: ACCEPT
    reason: ecmB is a secreted structural protein deposited in the stalk-tube
      extracellular matrix. The IBA localization is congruent with the curated
      function and with the gene's identity as one of the prestalk/stalk
      extracellular-matrix (ecm) genes.
    supported_by:
    - reference_id: PMID:25887420
      supporting_text: Expression of the prestalk genes ecmA, ecmB and ecmF
- term:
    id: GO:0099120
    label: socially cooperative development
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: ecmB participates in Dictyostelium multicellular (social) development,
      contributing the stalk-tube matrix during fruiting-body formation. The term
      is correct but very high-level; the more specific culmination term better
      captures the developmental stage at which ecmB acts.
    action: KEEP_AS_NON_CORE
    reason: Socially cooperative development is a broad parent process. ecmB is
      indeed involved in Dictyostelium sorocarp development as a prestalk/stalk
      marker, but its specific contribution is better represented by culmination
      involved in sorocarp development, so this general term is retained as
      non-core context.
    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
- term:
    id: GO:0009642
    label: response to light intensity
  evidence_type: HEP
  original_reference_id: PMID:41057014
  qualifier: acts_upstream_of_or_within
  review:
    summary: This is a high-throughput expression-pattern (HEP) annotation derived
      from a transcriptomic/metabolomic study of light-mediated development. ecmB
      is not discussed by name in the accessible text of that study; the annotation
      reflects differential expression under light rather than a demonstrated
      mechanistic role of ecmB in sensing or responding to light. As a downstream
      structural matrix protein, ecmB is unlikely to act upstream of or within a
      light-response pathway.
    action: MARK_AS_OVER_ANNOTATED
    reason: HEP evidence captures that ecmB transcript levels change with light
      exposure, but light-driven expression of a structural stalk-tube protein does
      not establish that ecmB acts upstream of or within the response to light
      intensity. The differential expression is most parsimoniously explained by
      light acceleration of the developmental program that induces prestalk genes
      generally, so annotating ecmB to response to light intensity overstates its
      role.
- term:
    id: GO:0031154
    label: culmination involved in sorocarp development
  evidence_type: IEP
  original_reference_id: PMID:25887420
  qualifier: acts_upstream_of_or_within
  review:
    summary: ecmB is a canonical prestalk/stalk marker whose transcripts are
      up-regulated sharply during the late (culmination) phase of development, when
      the stalk tube is built. The IEP annotation to culmination involved in
      sorocarp development is well supported by the developmental expression
      profiling and reflects a core process for this gene.
    action: ACCEPT
    reason: The transcriptome time-course shows ecmB (with ecmA and ecmF) rising
      dramatically during late development/culmination and serving as a prestalk
      cell-type marker. This matches the gene's role in building the stalk-tube
      matrix during culmination of the fruiting body.
    supported_by:
    - reference_id: PMID:25887420
      supporting_text: Expression of the prestalk genes ecmA, ecmB and ecmF
    - 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
- term:
    id: GO:0005198
    label: structural molecule activity
  evidence_type: TAS
  original_reference_id: PMID:8016318
  qualifier: enables
  review:
    summary: ecmB acts as a structural molecule, forming part of the stalk-tube
      matrix that encases stalk cells. The TAS annotation captures the core
      molecular function of this secreted, repeat-rich extracellular-matrix protein.
    action: ACCEPT
    reason: ecmB is a curated structural component of the stalk tube (UniProt
      FUNCTION), and the developmental transcriptome study classifies the prestalk
      ecm genes among structural genes. Structural molecule activity is the best
      available molecular-function description for this matrix protein.
    supported_by:
    - reference_id: PMID:25887420
      supporting_text: Structural prestalk transcripts accumulated to levels an
        order of magnitude less than those of the surveyed prespore genes
    - reference_id: PMID:25887420
      supporting_text: genes whose products contribute to structural composition
- term:
    id: GO:0030198
    label: extracellular matrix organization
  evidence_type: TAS
  original_reference_id: PMID:8016318
  qualifier: acts_upstream_of_or_within
  review:
    summary: As a structural component secreted into and assembled within the
      stalk-tube matrix, ecmB contributes to organization of the extracellular
      matrix of the stalk. This TAS annotation is consistent with its curated role
      in stalk-tube formation.
    action: ACCEPT
    reason: ecmB is deposited in and helps build the stalk-tube extracellular
      matrix during stalk morphogenesis, so participation in extracellular matrix
      organization is appropriate and complements the structural molecule activity
      annotation.
    supported_by:
    - reference_id: PMID:25887420
      supporting_text: Expression of the prestalk genes ecmA, ecmB and ecmF
- term:
    id: GO:0031012
    label: extracellular matrix
  evidence_type: TAS
  original_reference_id: PMID:8016318
  qualifier: located_in
  review:
    summary: ecmB is located in the extracellular matrix (the stalk tube). This TAS
      localization matches the curated UniProt subcellular location (secreted,
      extracellular matrix) and the IBA localization annotation, and is a core
      feature of the protein.
    action: ACCEPT
    reason: The stalk-tube matrix is an extracellular matrix, and ecmB is a secreted
      structural component of it. Localization to the extracellular matrix is
      well established for this prestalk ecm-family protein.
    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:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: PMID:25887420
  title: Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.
  findings:
  - statement: ecmB is a widely used molecular marker of prestalk cell-type
      differentiation (paired with cotB as a prespore marker).
    supporting_text: The genes cotB and ecmB are often used to mark the
      differentiation of prespore and prestalk cell-types, respectively
  - statement: ecmB is a prestalk gene whose expression, detectable from ~12 h, is
      up-regulated dramatically during late development/culmination (16-18 h).
    supporting_text: Expression of the prestalk genes ecmA, ecmB and ecmF
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: PMC full text directly names ecmB as a prestalk marker and
      documents its late-developmental (culmination-stage) up-regulation, supporting
      the culmination and structural-prestalk annotations.
- id: PMID:41057014
  title: Transcriptomic and metabolomic insights into light-mediated unicellular-to-multicellular
    transition in Dictyostelium discoideum.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Light-development transcriptomic/metabolomic study; ecmB is not
      discussed by name in the accessible text. Supports only a HEP expression-based
      annotation, which is judged an over-annotation for a downstream structural
      protein.
- id: PMID:8016318
  title: Prestalk cell-differentiation and movement during the morphogenesis of Dictyostelium
    discoideum.
  findings: []
  full_text_unavailable: true
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Review of prestalk-cell differentiation and morphogenesis used as
      the traceable source (TAS) for ecmB structural, extracellular-matrix, and
      matrix-organization annotations. Only the abstract is cached (full text
      unavailable), so no verbatim ecmB quote is available from this reference.
core_functions:
- description: Structural extracellular-matrix protein that is secreted by prestalk
    and stalk cells and assembled into the stalk-tube matrix encasing the cellular
    stalk of the fruiting body. Acts as a structural molecule contributing to
    organization of the stalk-tube extracellular matrix during culmination.
  molecular_function:
    id: GO:0005198
    label: structural molecule activity
  locations:
  - id: GO:0031012
    label: extracellular matrix
  directly_involved_in:
  - id: GO:0031154
    label: culmination involved in sorocarp development
  supported_by:
  - reference_id: PMID:25887420
    supporting_text: Structural prestalk transcripts accumulated to levels an order
      of magnitude less than those of the surveyed prespore genes
  - reference_id: PMID:25887420
    supporting_text: Expression of the prestalk genes ecmA, ecmB and ecmF