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eukaryotic flagellar axoneme internalization

traitmech:000734 · CLASS · PROPOSED

A physiological phenotype in which a microbial eukaryote internalizes the intact axoneme of its own cilium or flagellum into its cell body.

Trait evidence (2)

  • DOI:10.1002/cm.21637
    axonemes remain intact during internalization

    Venard et al. 2020, PMID:33103844, PMCID:PMC7944584, Results 2.2, TEM interpretation paragraph following Figure 2. Contiguous span checked in direct PMC HTML; native NOT_IN_ABSTRACT retained. Live phase microscopy, fixed immunofluorescence and TEM concern Rhizoclosmatium globosum JEL800 and Spizellomyces punctatus DAOM BR117. Internalized cross-sections retain 9+2 architecture without a surrounding ciliary membrane; fixed TEM is not continuous same-cell tracking. Figure 1's 23 and 32 cells are selected retraction events, not biological-culture counts. Methods time zero is plating, whereas Figure 2's TEM caption says post-retraction; retain that timing discrepancy. Table 1 labels length/diameter with rate units unlike Table 2; no numerical conversion or rate is asserted here. Main text and all five actual main figures were inspected. The main PDF and actual supplemental PDFs/videos remain unread. Subsequent degradation is a separate phase, not a requirement for this internalization phenotype.

  • DOI:10.1083/jcb.201701074
    Bd zoospores retracting their flagella by coiling the entire axoneme into the cell body

    Fritz-Laylin et al. 2017, PMID:28473602, PMCID:PMC5461030.1, Discussion JATS s11, printed page 1681, PDF page 9. Direct normalized JATS and typeset passage checked; native NOT_IN_ABSTRACT retained. Bd denotes Batrachochytrium dendrobatidis, source strain JEL423, with synchronized zoospores observed under the described confinement preparation. Results s10, Discussion s11 and Methods s20 were read, along with selected PDF pages. Video 5 was inspected through 16 sampled frames and one enlarged frame, not continuous playback or every-frame analysis. File metadata reports 10.1 seconds at nominal 10 fps, burned-in labels span 0-20 seconds, and the caption states 0.1-second acquisition with 20-fps playback. These are not silently reconciled; no retraction rate or replicate count is inferred. The paper's WASP/SCAR pseudopod experiments do not establish an axoneme-internalization mechanism.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1002/cm.21637

Parent traits (1)

kg-microbe context

Matched 1 kg-microbe node via parent_proxy.

  • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Discussions and Knowledge Gaps (4)

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

Review intact withdrawal separately from later axonemal disassembly.

CURATION TODO OPEN eukaryotic-axoneme-internalization-scope · raised by codex · 2026-10-15

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 defining endpoint is internalization of the cell's own intact eukaryotic axoneme. Static internal localization, uptake of another cell's material, external coiling, failed assembly, motor arrest, passive breakage or shedding alone do not establish it. Venard et al. 2020 place internalization within a broader cilium-disassembly program while distinguishing subsequent degradation. The operational resorption record traitmech:000733 requires shortening through axonemal disassembly, not intact withdrawal alone. Later degradation can occur after internalization; no organism-level disjointness or permanently intact internal axoneme is asserted. Autotomy traitmech:000731 and bacterial polar flagellar ejection traitmech:000732 have different endpoints; bacterial periplasmic flagella and type IV pili are different structures. Phenotype METPO:1000059 is a definition-based parent inference, without a locomotion requirement.

Evidence

  • DOI:10.1091/mbc.E24-12-0577 SUPPORT
    Centrioles separated from the degrading axoneme and remained parallel
    Supports the later-degradation and centriole-remodeling distinction, not an additional definition citation, a universal centriole fate or a same-cell kinetic measurement.

Review microbial-eukaryote scope and the proposed phenotype parent.

CURATION TODO OPEN eukaryotic-axoneme-internalization-metpo · raised by codex · 2026-10-15

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.

No active exact term was identified in the inspected pinned/current METPO release, editor and templates. Deprecated METPO:0000089 and METPO:000090 carry OMO:0001000; METPO:1000381 carries IAO:0000226. Their active replacement METPO:1000704 denotes locomotory flagellar possession, not internalization. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for those or deprecated flagellum METPO:1000123 with OMO:0001000. Historical identifiers are not exact xrefs and are not reactivated. https://github.com/berkeleybop/metpo/issues/521 leaves reason-code interpretation unresolved. Upstream's bacterial/archaeal focus requires maintainer review of microbial-eukaryote inclusion. Proposal v610 reserves METPO:1068700 in 1068700-1068799, not a released identifier or human-approved mapping. The ontology pin is unchanged.

Keep observable internalization separate from universal molecular mechanisms.

KNOWLEDGE GAP OPEN eukaryotic-axoneme-internalization-mechanism · raised by codex · 2026-10-15

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.

Do not require a universal reeling, lash-around, membrane-loss, cortical tethering, actin-dependent, dynein-dependent or proteolytic mechanism. The 2020 latrunculin live-movie analysis selected complete retractions and excluded cells retaining cilia; its conditional results cannot establish all-cell retraction probabilities. Do not transfer 2017 pseudopod perturbations or 2025 transcript/orthology patterns to this phenotype. A gene, domain, motif or profile alone does not establish intact axoneme internalization. A protein-resolved graph requires taxon-paired, authority-checked accessions and edge-specific evidence. No universal rate, cell-cycle stage, complete degradation, protein recycling, exact synonym or equivalent external mapping is asserted.

Resolve canonical strain provenance while preserving source-access limits.

KNOWLEDGE GAP OPEN eukaryotic-axoneme-internalization-provenance · raised by codex · 2026-10-15

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 named laboratory strains remain qualified life-stage observations, not authority-verified canonical taxa or proof of natural provenance. Two distinct supporting publications are not a claim of independent-lab replication. The 2025 follow-up shares authors with earlier work and is scope context, not a third definition citation. Qualified MED/Crossref identities and available notice fields were checked, not comprehensive correction/retraction clearance. The linked 2017 Comment/Editorial, DOI:10.1080/15384101.2017.1360655, PMID:28820330, PMC5628642, has no returned abstract and its content remains unread; it is not counted evidence. Publisher/PMC access failures remain failures. The 2020 supplement endpoint returned an API error with HTTP 200, not a ZIP; no actual supplement contents are inferred. No raw-data reanalysis, paid research or human scientific sign-off is implied.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added the microbial-eukaryote intact-axoneme internalization phenotype with two primary DOI sources and checked 5/14-word full-text snippets. Kept a nine-word 2025 later-degradation excerpt in a scope discussion, not definition evidence. All three retain native NOT_IN_ABSTRACT. Reserved 000734, v610 and 1068700-1068799 after ignored/hidden current-file, retained-history, complete-range and open/draft PR checks. Preserved source-access and assay limitations; no obsolete identifier, canonical taxon, exact mapping or universal protein mechanism is inferred. The timestamp is the observed allocation decision, not source acquisition.

  2. · CORRECT_EVIDENCE_LOCATOR · codex

    Corrected the 2025 expansion-factor locator from Methods/S3B to Results S6, MTOC remodeling from mitosis to ciliogenesis, first paragraph, citing Supplemental Figure S3A-B. Cached JATS S6/S15 and actual Figure S3 were reread for issue #1950. Preserved values, discrepancy, definition, source roles, snippets and previous history.

Recorded curation sessions

  • · codex
    • CREATE — Add eukaryotic flagellar axoneme internalization

      Added one PROPOSED microbial-eukaryote intact-axoneme internalization phenotype with two primary DOI sources and directly checked 5/14-word full-text snippets. Kept a nine-word 2025 later-degradation excerpt in a scope discussion, not definition evidence. All three preserve native NOT_IN_ABSTRACT outcomes. Reserved 000734, v610 and 1068700-1068799 after ignored/hidden current files, retained history, complete ranges and open/draft PR checks. The phenotype parent is a definition-based inference. Preserved assay, video-sampling, source-access and strain limits; no obsolete identifier, canonical taxon, exact mapping, independent-laboratory replication or universal molecular mechanism is inferred. The per-record timestamp records the observed post-guard allocation decision, not source acquisition.

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  • · codex
    • EDIT — Correct the expansion-factor source locator

      Corrected discussions[0].evidence[0].notes and the guarded writer: the 2025 value 5.5 +/- 0.2 is in Results S6, MTOC remodeling from mitosis to ciliogenesis, first paragraph, citing Supplemental Figure S3A-B, not Methods/S3B. Cached JATS S6 and S15 and actual Figure S3 were reread. Preserved the 4.5 versus 5.5 discrepancy, biological definition, supporting sources, excerpts, native verdicts, proposal and prior research/history/review observations. This supplements history/records/eukaryotic_flagellar_axoneme_internalization/2026-10-15T201607Z-codex-b269cd.yaml. Issue #1950 tracks the locator correction and successor review.

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