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bacterial flagellar filament internalization

traitmech:000735 · CLASS · PROPOSED

A physiological phenotype in which a bacterium withdraws an assembled portion of its own flagellar filament from outside its cell body into its cell-body periplasm.

Trait evidence (2)

  • DOI:10.1038/s41564-023-01401-2
    most or all of the filament was internalized to the periplasm

    Kaplan et al. 2023, PMID:37349588, PMC11061892.1, Results S3, Attachment of B. bacteriovorus to prey, paragraph beginning In cells with larger portions. Direct manuscript JATS match; native NOT_IN_ABSTRACT retained. Source strain HD100 and frozen cryo-ET stages support partial through nearly complete withdrawal into the predator's own periplasm, not the prey's. Methods S8-S12 qualify minicell enrichment and possible physiology effects; the images contain no same-cell temporal information. Main Figure 3 and supplement PDF pages 1, 22-35, 66-67 were visually inspected. S20-S21 distinguish external and internal filament portions; S22 is a schematic, not a tracked trajectory. Table S2's 8/4/30 early/intermediate/late absorbed-flagellum observations are not culture replicates or a prevalence denominator. Publisher Figure 3's main scale bar is 100 nm, versus 50 nm in the manuscript caption; no dimension or rate is inferred. Main PDF, other actual main figures, unselected supplemental images and movies remain unread. Later breakage or degradation is not required by the definition.

  • DOI:10.1063/pt.nkma.bqid
    B. bacteriovorus retracts its extracellular hook and filament into its own periplasmic space

    Kaplan 2024, Physics Today, Figure 5 caption; contiguous span checked in directly retrieved publisher HTML. Disassembly processes and reference 16 were read, and actual Figure 5 was inspected. This is a distinct author-perspective publication describing the same 2023 experiment, not independent experimental replication. The colored segmentation is not another experiment. Native UNRESOLVED means no usable abstract was returned, not that the DOI is invalid; Crossref identity and direct publisher wording were checked separately. Presumed digestion and the hypothesized evolutionary connection to spirochaete endoflagella are not defining requirements or established consequences.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1038/s41564-023-01401-2

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 the withdrawal endpoint without making universal entry-time claims.

CURATION TODO OPEN bacterial-flagellar-internalization-scope · raised by codex · 2026-10-16

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.

Cell-body periplasm distinguishes withdrawal from an external flagellar sheath lumen, static endoflagella, abnormal assembly, import of free flagellin, uptake of another cell's material and predator entry into the prey's periplasm. Partial withdrawal counts; permanent intactness and complete withdrawal are not required. Bacterial polar ejection traitmech:000732 releases structures externally; eukaryotic axoneme internalization traitmech:000734 involves a different apparatus. These distinctions do not imply disjoint organisms. Earlier 109J observations of externally retained filaments constrain universal early-entry claims but neither demonstrate own-periplasmic withdrawal nor establish its absence. Different strains and preparations are not pooled into one time series.

Evidence

  • DOI:10.1111/j.1365-2958.2006.05081.x NO EVIDENCE
    In our experiments unshed flagella were seen early during the establishment of an infection.
    Comparison context, not positive support for internalization or a third supporting definition citation. External retention alone does not measure subsequent or partial internalization.

Review the proposed phenotype parent and unresolved ontology equivalence.

CURATION TODO OPEN bacterial-flagellar-internalization-metpo · raised by codex · 2026-10-16

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.

Phenotype METPO:1000059, below quality METPO:1000188, is a broader definition-based parent inference, not an assertion of locomotion. No active exact withdrawal term was identified in the inspected pinned and current METPO release/templates. Axially filamented METPO:1000705 describes static periplasmic location under motile; flagellated METPO:1000704 describes locomotory possession. Neither is equivalent to withdrawal. Deprecated METPO:0000089 and METPO:000090 carry OMO:0001000; METPO:1000381 carries IAO:0000226. Their replacement is METPO:1000704. Deprecated flagellum METPO:1000123 carries OMO:0001000 with no observed replacement or consider annotation. These historical identifiers are not revived or asserted as exact xrefs. The ontology pin is unchanged; no upstream acceptance or human sign-off is implied.

Separate observed internalization from universal molecular mechanisms.

KNOWLEDGE GAP OPEN bacterial-flagellar-internalization-mechanism · raised by codex · 2026-10-16

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.

Motor displacement and P/L-ring separation are structural observations, not universal requirements. Sheath/outer-membrane zippering and lipid effects are hypotheses. A missing motor can reflect the cryo-ET missing wedge; vesicles may reflect sample preparation. No universal force, protease, complete digestion, recycling, rate or order of events is asserted. A sequence feature or flagellin expression alone does not establish this phenotype. A protein-resolved causal graph requires edge-specific evidence and authority-checked, taxon-paired accessions; mechanism curation is deferred, not claimed absent.

Preserve transient-state, source-version and replication limits.

KNOWLEDGE GAP OPEN bacterial-flagellar-internalization-provenance · raised by codex · 2026-10-16

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.

HD100 is a qualified experimental observation, not an unqualified archetypal taxon assertion. Canonical examples remain omitted pending strain-provenance and representative-state review. The 2024 perspective and 2023 study satisfy two distinct supporting citations, not two independent experiments; supplements are part of the same study. Crossref and qualified MED identities and returned notice fields were checked, not comprehensive correction/retraction clearance. The 2023 linked post-publication review remains unread; unsuccessful publisher/PubMed access does not prove that no notice exists. Source scale-bar and preparation discrepancies are retained rather than silently harmonized. No raw-data reanalysis, exact synonym, equivalent external mapping, paid research or human scientific approval is implied.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added own-flagellar-filament withdrawal into the bacterial cell-body periplasm with two supporting DOI citations and checked 11/13-word full-text snippets. The author perspective concerns the same primary experiment, not independent replication. Kept the 14-word 2006 retained-flagella excerpt as comparison context, not definition evidence. Native NOT_IN_ABSTRACT/UNRESOLVED/NOT_IN_ABSTRACT outcomes are preserved. Reserved 000735, v611 and 1068800-1068899 after ignored/hidden current-file, retained-history, complete-range and open/draft PR checks. Preserved partial-withdrawal, frozen-stage, source-version and preparation limits. No obsolete ID, canonical taxon, exact mapping or universal protein mechanism is inferred. Timestamp records observed allocation, not acquisition.

Recorded curation sessions

  • · codex
    • CREATE — Add bacterial flagellar filament internalization

      Added one PROPOSED own-flagellar-filament withdrawal phenotype with primary DOI:10.1038/s41564-023-01401-2 and author-perspective DOI:10.1063/pt.nkma.bqid. Checked 11/13-word full-text excerpts; the perspective describes the same experiment, not independent replication. Kept DOI:10.1111/j.1365-2958.2006.05081.x and its 14-word excerpt as comparison context with NO_EVIDENCE, not a definition citation. Preserved native NOT_IN_ABSTRACT/UNRESOLVED/NOT_IN_ABSTRACT. Reserved traitmech:000735, v611 and full block 1068800-1068899 after ignored/hidden current-file, retained-history, complete-range and open/draft PR checks plus fresh state guard. Preserved partial-withdrawal, frozen-stage, scale-bar and preparation limits. No canonical taxon, exact synonym/xref or universal molecular graph is asserted. Per-record timestamp is the observed allocation decision, not source acquisition.

    Read this curation session