axially filamented

Deep research

Generated by just research-trait; source: research/traits/morphology/axially_filamented-deep-research-falcon.md

# Curation report: axially filamented

## Executive summary

**Trait:** axially filamented  
**Identifier:** **METPO:1000705**  
**Category:** morphology; class; reviewed  
**Parent:** METPO:1000702  
**Synonym:** axial filament

The trait should denote a bacterium possessing one or more **flagellar filaments confined to the periplasm**, rather than flagella projecting beyond the outer membrane. In spirochetes these structures are usually called **periplasmic flagella (PFs), endoflagella, or axial filaments**. They arise from motors at one or both poles and run along the protoplasmic cylinder beneath the outer membrane. Their rotation deforms or rotates the cell body, producing rolling or undulatory propulsion; in several taxa they also mechanically determine cell shape. The defining feature is therefore **filament topology/localization**, not motility alone and not merely a spiral cell shape. Nakamura states that spirochetal flagella are “hidden within the periplasmic space,” whereas external flagella directly interact with the surrounding fluid (published 4 April 2020; DOI [10.3390/biom10040550](https://doi.org/10.3390/biom10040550)). (nakamura2020spirocheteflagellaand pages 1-3)

The most defensible TraitMech causal chain is:

**FlaB-containing filament assembly + sheath/coiling proteins → periplasmic flagellar filament → hook/motor coupling → proton-driven stator–rotor torque → PF rotation → cell-body deformation/rolling/undulation → spirochetal motility**, with a parallel structural branch from **PF integrity → taxon-specific cell morphology**. Virulence and tissue dissemination are biologically important downstream consequences, but should remain taxon- and assay-qualified rather than defining the morphology trait. (nakamura2020spirocheteflagellaand pages 3-5, nakamura2020spirocheteflagellaand pages 9-11, chang2019structuralinsightsinto pages 10-12)

## 1. Trait scope and boundaries

### Included phenotype

A positive instance should have:

1. A bona fide bacterial flagellar filament.
2. Localization within the space bounded by the inner and outer membranes.
3. Connection through a hook to a basal motor embedded in the cytoplasmic membrane/peptidoglycan region.
4. No normal extension of the filament beyond the cell envelope.

The filament may be polar, bipolar, overlapping, or non-overlapping. *Borrelia burgdorferi* has approximately **14–22 PFs** that overlap near midcell; *Brachyspira hyodysenteriae* has **16–18**, also overlapping; *Leptospira interrogans* has **two short, non-overlapping PFs**. These are variants of the same topological trait, not separate trait states. (nakamura2020spirocheteflagellaand pages 1-3)

### Boundary cases and nearby traits

- **External polar or amphitrichous flagella:** exclude. *Campylobacter jejuni*, for example, bears external polar flagella; its motor findings can inform general flagellar mechanics but do not establish axial/periplasmic filamentation. (ribardo2024viscositydependentdeterminantsof pages 1-2)
- **Motility:** not equivalent. A cell can possess structurally defective PFs and be weakly motile or nonmotile. Conversely, nonflagellar gliding or twitching does not imply this trait.
- **Spiral or wavy morphology:** not sufficient. PFs straighten the whole body when lost in *B. burgdorferi*, but in *Leptospira* PF depletion principally changes the bent ends while the protoplasmic-cylinder helix is thought to involve MreB. Thus, “helical cell” must not be used as a proxy. (nakamura2020spirocheteflagellaand pages 3-5)
- **Flagellar sheath:** not universal in composition. FlaA/Fcp-dependent core–sheath organization is particularly developed in *Brachyspira* and *Leptospira*; *B. burgdorferi* has a different organization, with FlaB forming the filament and FlaA concentrated near its base. (nakamura2020spirocheteflagellaand pages 3-5)
- **Cytoplasmic axial structures or nonflagellar filaments:** exclude unless continuity with a flagellar motor, hook, and periplasmic filament is demonstrated.
- **Assay inference:** spiral motion in viscous medium, soft-agar migration, or gene presence alone is insufficient to assign the morphology trait without localization evidence.

## 2. Candidate graph nodes

### Trait and anatomical/localization nodes

- **axially filamented:** METPO:1000705
- **periplasmic flagellum / endoflagellum / axial filament:** label-only pending exact ontology alignment
- **periplasmic space:** GO:0042597
- **bacterial-type flagellum:** GO:0009288
- **bacterial-type flagellum hook:** GO:0009424
- **bacterial-type flagellum basal body:** GO:0009425
- **cell outer membrane:** GO:0009279
- **plasma membrane:** GO:0005886
- **peptidoglycan-based cell wall:** GO:0009274
- **protoplasmic cylinder:** label-only
- **flagellar core filament; flagellar sheath; P-collar/periplasmic collar; C-ring/rotor; stator complex:** retain as label-only if an exact ontology term cannot be verified.

### Genes and proteins

- **FlaB/FlaB1/FlaB2/FlaB3:** core flagellins; paralog requirements are taxon-specific.
- **FlaA/FlaA1/FlaA2:** sheath-associated or basal filament proteins; function differs among genera.
- **FcpA, FcpB:** *Leptospira*-specific sheath/coiling proteins.
- **FlgE:** hook protein; *Treponema denticola* FlgE has self-catalytic intersubunit crosslinks that stabilize the hook. (nakamura2020spirocheteflagellaand pages 3-5)

Showing the first 60 of 217 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.