flagellated

Deep research

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

# Curation report: **flagellated**

## 1. Trait record and recommended scope

- **Trait label:** flagellated
- **Trait identifier:** **METPO:1000704**
- **Category / kind:** MORPHOLOGY / CLASS
- **Parent:** METPO:1000702
- **Reviewed definition supplied:** “A motile in which an organism possesses flagella for locomotion.”

For TraitMech, the operational phenotype should be **possession of at least one morphologically detectable locomotory flagellar appendage**, rather than active movement itself. A bacterial flagellum comprises a basal-body motor, hook, and helical filament; the filament is assembled from thousands of FliC/flagellin subunits and capped by FliD. The hook transmits motor torque to the filament, which acts as a propeller. (nedeljkovic2021bacterialflagellarfilament pages 1-2, minamino2023structureassemblyand pages 22-23)

### Scope boundaries

1. **Flagellated is not equivalent to motile.** A cell may possess an assembled but paralyzed flagellum because its stator, switch, ion motive force, or another motor component is defective. Conversely, surface translocation can be mediated by type-IV pili, surfactants, gliding systems, or growth and therefore does not establish flagellation. In *Pseudomonas aeruginosa*, PA4367 overexpression restored swarming in a Δ*fliA* background without restoring flagella by TEM and did not restore swimming, directly separating a surface-motility assay from flagellar morphology. (lo2016regulationofmotility pages 11-14)
2. **Swimming or soft-agar expansion is functional evidence, not sufficient morphological evidence.** The strongest phenotype annotation should use electron microscopy, flagellin-specific fluorescence, sheared-filament protein analysis, or another direct appendage assay. Motility assays should be represented as downstream observations.
3. **Swarming is compound and assay-specific.** It can require flagella but also surfactants, cell differentiation, surface hydration, and pili. It should not be used as a universal synonym for flagellation. (lo2016regulationofmotility pages 11-14)
4. **Archaella require a separate mechanistic branch.** Archaeal archaella are analogous locomotory appendages but are evolutionarily and mechanistically distinct from bacterial flagella: archaella assemble from the base and use ATP, whereas bacterial flagella assemble distally and use ion motive force for rotation. Whether METPO:1000704 intentionally includes archaella should be settled by ontology policy before adding archaeal mechanisms.
5. **Eukaryotic cilia/flagella are out of scope** for a bacterial flagellar graph. They are microtubule/dynein machines rather than homologues of bacterial flagella.
6. **Periplasmic flagella are included morphologically** if the intended taxonomic scope covers spirochetes, but they need a taxon-specific structural branch rather than assumptions copied from external flagella.

The supplied definition is therefore slightly circular (“A motile…”) and conflates structure with function. A curation-oriented wording would be: **“A microbial cell morphology in which the organism possesses one or more flagellar locomotory appendages.”** Add “whether or not actively rotating under the assay conditions” if METPO permits an editorial note.

## 2. Current mechanistic model

The best-supported bacterial causal chain is:

**flagellar transcriptional program → hook–basal-body assembly → assembly checkpoint and late-gene expression → flagellin export/polymerization → capped filament → ion-driven stator torque → hook-mediated torque transmission → filament rotation and propulsion.**

In the canonical *Salmonella/E. coli* hierarchy, FlhD/FlhC activates class-II genes needed for hook–basal-body construction. FlgM inhibits FliA/σ28 until hook–basal-body completion permits FlgM export; liberated FliA then drives class-III genes including *fliC*. This checkpoint couples morphological development to gene expression. (chilcott2000couplingofflagellar pages 7-8, chilcott2000couplingofflagellar pages 1-1, nedeljkovic2021bacterialflagellarfilament pages 9-10)

The flagellar type-III secretion system contains the membrane export gate FliP/Q/R–FlhA/B and cytoplasmic FliH/I/J complex. It transports structural subunits through the growing organelle. Recent synthesis describes FlhA docking of chaperone–substrate complexes—FlgN–FlgK/L, FliS–FliC, and FliT–FliD—and a FliK/FlhB-dependent switch from hook-type to filament-type export. The export gate can exploit electrochemical energy, with FlhA conducting H⁺ and Na⁺ under studied conditions. (minamino2023structureassemblyand pages 22-23)

FliC polymerization creates the helical filament, while FliD caps its distal end and supports elongation. Presence of the filament is the most direct molecular realization of the target morphology. (nedeljkovic2021bacterialflagellarfilament pages 1-2, nedeljkovic2021bacterialflagellarfilament pages 27-28)

For function, MotAB-family stators convert transmembrane ion flow into torque; many motors are H⁺-driven, whereas PomAB systems in taxa such as marine *Vibrio* are commonly Na⁺-driven. The hook acts as a universal joint, and the filament converts rotation into thrust. These are downstream causes of **flagellar motility**, but stator activity is not required for the narrow structural state “flagellated.” (nedeljkovic2021bacterialflagellarfilament pages 1-2, wu2024torquespeedrelationshipof pages 17-19, minamino2023structureassemblyand pages 22-23)

Chemotaxis regulates behavior rather than appendage presence. CheY-P binds the C-ring protein FliM and biases directional switching. Likewise, c-di-GMP-bound YcgR can alter motor direction and speed through a “backstop brake.” These edges belong downstream of the morphology node unless a taxon-specific pathway also regulates flagellar biogenesis. (mckee2013thesecondmessenger pages 10-11, nedeljkovic2021bacterialflagellarfilament pages 27-28)

## 3. Candidate nodes

### A. Trait and observed structures

- **flagellated:** `METPO:1000704`
- flagellar filament — candidate GO cellular-component grounding; verify the current GO release before YAML insertion
- bacterial-type flagellum — candidate GO cellular-component grounding; verify
- basal body; MS ring; C ring; rod; hook; hook–filament junction; filament cap
- polar flagellation, peritrichous flagellation, lateral flagellation, periplasmic flagellation — label-only phenotype candidates unless an approved morphology ontology term is found

### B. Transcriptional and assembly regulators

- FlhD/FlhC master regulator complex, preferably represented as **FlhD₄C₂** where supported
- FliA / σ28
- FlgM anti-σ28 factor
- FliK hook-length control/export-switch protein
- FlhB substrate-specificity switch component
- FleQ and alternative polar-flagellum regulators — **taxon-specific**, not substitutes for universal FlhDC

### C. Export and assembly machinery

Showing the first 60 of 236 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.