TraitMech

TraitMech › PHYSIOLOGY

macropinocytosis

traitmech:000634 · CLASS · PROPOSED

A physiological phenotype in which a microbial organism internalizes bulk extracellular fluid by closing actin-driven plasma-membrane ruffles into large intracellular vesicles.

Trait evidence (2)

  • DOI:10.1242/jcs.213736
    Macropinocytosis is a conserved endocytic process used by Dictyostelium amoebae for feeding on liquid medium.

    PMID:29440238, PMC5897714. Scientific ABSTRACT quote. Introduction supports the ruffle-closure definition. Relevant uptake Results, Methods, Discussion and actual Figure 2 were read at https://pmc.ncbi.nlm.nih.gov/articles/PMC5897714/. Figure 2E reports P=0.057 for DdB formation-rate upregulation; do not call this significant. Diameter measurements use a transgenic reporter, unlike the dextran formation assay. Other figures and supplements were not visually audited.

  • DOI:10.7554/eLife.04940
    These cells can also internalise bulk fluid without the guidance of a particle using a closely related process, macropinocytosis

    PMID:25815683, PMC4374526. Contiguous Introduction quote, not the scientific Abstract or eLife digest. Relevant Results, confocal Methods, Discussion, Table 2 and actual Figure 3 were read at https://pmc.ncbi.nlm.nih.gov/articles/PMC4374526/. Figure 3C measures formation events; Figure 3B single sections cannot quantify cumulative uptake. Other figures and movies were not visually audited.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1242/jcs.213736

Parent traits (1)

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Dictyostelium discoideum NCBITaxon:44689 DOI:10.7554/eLife.04940 Wild-type parental DdB cells freshly harvested from bacterial growth, observed by dextran imaging in Figure 3C; not Ax2, AX4, NF1 knockouts or reporter transformants. Table 2 links DdB to DdB(Wel). Strain genealogy at https://link.springer.com/article/10.1186/gb-2008-9-4-r75 identifies a laboratory-selected NC4 clone with copy-number differences, not an unchanged original wild isolate. NCBI EFetch verified the name and species rank on 2026-10-06; this ID does not identify the strain.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Keep bulk-fluid uptake distinct from neighboring uptake traits.

CURATION TODO RESOLVED macropinocytosis-scope-and-hierarchy · raised by codex · 2026-10-06

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

Retain phenotype METPO:1000059 pending a closer endocytic capability hierarchy. This is uptake by a microbe, not microbial induction of uptake by a host cell. Phagocytosis traitmech:000627 is particle engulfment, phagotrophy traitmech:000628 requires nutritional assimilation, and trogocytosis traitmech:000633 removes portions of living cells. These are neither equivalents nor disjoint organismal capabilities. Generic pinocytosis is broader; its existing phagocytosis discussion mention is not an exact unresolved macropinocytosis node. Membrane ruffling without closure, solute transport alone and uptake into small endocytic vesicles are insufficient. No fixed diameter cutoff, enhanced uptake rate, axenic growth or nutrition is required. No unverified synonym or process-level ontology xref is asserted.

Resolution: Added pinocytosis traitmech:000635 as the direct broader phenotype. The existing ruffle-mediated bulk-fluid definition entails vesicular fluid uptake; its definition, evidence and DdB example are unchanged. This resolves the temporary phenotype-parent gap, not the separate native-mechanism discussion or any ontology equivalence. Preserve the historical v510 phenotype axiom and add METPO:1058700 SubClassOf METPO:1058800 on upstream adoption.

Separate native capability from mutant and reporter mechanisms.

KNOWLEDGE GAP OPEN macropinocytosis-native-mechanism · raised by codex · 2026-10-06

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

The papers share a research group and organism; they are not independent taxon replication. NF1 loss enhances uptake but is not required for the phenotype. Do not equate a drug response, localization or sequence similarity with a universal causal dependency. Protein accessions, native functional scope and remaining figures require review before adding protein examples or a causal graph.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added macropinocytosis with two DOI-backed source snippets and a parental DdB-qualified example. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1058700 in v510. Distinguished native uptake from axenic mutants, reporter measurements and universal mechanisms.

  2. · REFINE_PINOCYTOSIS_PARENT · codex

    Refined the direct parent to pinocytosis traitmech:000635 and resolved the temporary hierarchy discussion by definition-based inference. Preserved identity, definition, evidence, canonical example, mechanism gap, earlier history and the true broader historical proposal axiom.