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.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0031012 extracellular matrix | IBA GO_REF:0000033 | ACCEPT | 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. 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. Supporting Evidence: PMID:25887420 Expression of the prestalk genes ecmA, ecmB and ecmF |
| GO:0099120 socially cooperative development | IBA GO_REF:0000033 | KEEP AS NON CORE | 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. 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. Supporting Evidence: PMID:25887420 The genes cotB and ecmB are often used to mark the differentiation of prespore and prestalk cell-types, respectively |
| GO:0009642 response to light intensity | HEP PMID:41057014 Transcriptomic and metabolomic insights into light-mediated ... | MARK AS OVER ANNOTATED | 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. 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. |
| GO:0031154 culmination involved in sorocarp development | IEP PMID:25887420 Leaps and lulls in the developmental transcriptome of Dictyo... | ACCEPT | 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. 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. Supporting Evidence: PMID:25887420 Expression of the prestalk genes ecmA, ecmB and ecmF PMID:25887420 The genes cotB and ecmB are often used to mark the differentiation of prespore and prestalk cell-types, respectively |
| GO:0005198 structural molecule activity | TAS PMID:8016318 Prestalk cell-differentiation and movement during the morpho... | ACCEPT | 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. 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. Supporting Evidence: PMID:25887420 Structural prestalk transcripts accumulated to levels an order of magnitude less than those of the surveyed prespore genes PMID:25887420 genes whose products contribute to structural composition |
| GO:0030198 extracellular matrix organization | TAS PMID:8016318 Prestalk cell-differentiation and movement during the morpho... | ACCEPT | 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. 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. Supporting Evidence: PMID:25887420 Expression of the prestalk genes ecmA, ecmB and ecmF |
| GO:0031012 extracellular matrix | TAS PMID:8016318 Prestalk cell-differentiation and movement during the morpho... | ACCEPT | 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. 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. Supporting Evidence: PMID:25887420 The genes cotB and ecmB are often used to mark the differentiation of prespore and prestalk cell-types, respectively |
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