FliK is the flagellar hook-length control protein that acts as a molecular ruler and terminator to control the length of the flagellar hook during assembly. FliK is intermittently exported through the flagellar type III secretion system (fT3SS) during hook assembly, and its C-terminal domain contacts the cytoplasmic domain of FlhB (FlhBC) to trigger the substrate-specificity switch from rod/hook-type substrates (e.g., FlgE) to filament-type substrates (e.g., FliC, FlgK, FlgL, FlgM). Loss of FliK causes a polyhook phenotype where hooks overgrow because the switch fails to occur. In B. subtilis, both FliK and the hook are approximately 25% longer than their Salmonella counterparts, indicating species-specific calibration of the length-control mechanism. FliK belongs to the FliK family characterized by an N-terminal export/assembly-interacting region, a flexible linker, and a C-terminal FlhB-binding domain.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009424 bacterial-type flagellum hook | IEA GO_REF:0000002 | MODIFY | Summary: This cellular component annotation indicates FliK is located in the flagellar hook. FliK is an export substrate of the flagellar type III secretion system (fT3SS) and is intermittently secreted through the basal body during hook assembly. However, FliK is not a structural component of the hook itself - the hook is composed of FlgE subunits. FliK transiently passes through the hook structure during secretion to sense hook length, but its primary localization is cytoplasmic until it is exported. The annotation is misleading as it suggests FliK is a stable component of the hook structure. Reason: FliK is not a structural component of the flagellar hook - the hook is built from FlgE protein. FliK is a cytoplasmic protein that is intermittently exported through the fT3SS during hook assembly to control hook length. While FliK transiently passes through the hook region during secretion, it does not permanently reside there. A more accurate CC annotation would be cytoplasm or the flagellar secretion apparatus. The InterPro domain annotation (IPR001635) correctly identifies FliK as a hook-length control protein, but the mapping to the hook CC term is inappropriate. Proposed replacements: cytoplasm bacterial-type flagellum secretion apparatus Supporting Evidence: PMID:22730131 We used the fluorescently labeled hook to demonstrate that FlgE is the hook structural protein and that FliK regulated hook length. file:BACSU/fliK/fliK-deep-research-falcon.md FliK is a cytosolic protein that is exported through the basal-body fT3SS during hook assembly; its export is reduced once hooks complete, consistent with a role as a periodic sensor/signal. |
| GO:0044780 bacterial-type flagellum assembly | IEA GO_REF:0000002 | ACCEPT | Summary: This biological process annotation indicates FliK is involved in bacterial flagellum assembly. This is accurate - FliK is essential for proper flagellum assembly as it controls the length of the hook and triggers the substrate-specificity switch that enables filament assembly to proceed. Without FliK, hooks overgrow (polyhook phenotype) and the switch to filament-type export fails, preventing completion of functional flagella. Reason: FliK is a core regulator of flagellum assembly. It controls hook length and triggers the critical switch from rod/hook substrate export to filament substrate export. Loss of FliK results in polyhook formation and failure to assemble functional flagella. This annotation accurately captures FliK's essential role in the flagellar assembly process. Supporting Evidence: PMID:22730131 We used the fluorescently labeled hook to demonstrate that FlgE is the hook structural protein and that FliK regulated hook length. file:BACSU/fliK/fliK-deep-research-falcon.md FliK is the dedicated flagellar hook-length control protein that times the transition from rod/hook-type export to filament-type export by the flagellar type III secretion system (fT3SS). Loss of FliK causes a polyhook phenotype because the export apparatus fails to switch substrates. |
| GO:0044781 bacterial-type flagellum organization | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: This biological process annotation indicates FliK is involved in bacterial flagellum organization, which encompasses assembly, arrangement, and disassembly. This is a parent term of GO:0044780 (bacterial-type flagellum assembly) and is therefore broader and less informative than the more specific assembly term that is also annotated to FliK. The annotation is not incorrect but redundant given the more specific annotation. Reason: While technically correct (FliK does participate in flagellum organization via its role in assembly), this term is broader and less informative than the more specific GO:0044780 (bacterial-type flagellum assembly) which is also annotated to FliK. The annotation is redundant but not incorrect. Keeping as non-core since the more specific assembly term better captures FliK's function. Supporting Evidence: PMID:22730131 We used the fluorescently labeled hook to demonstrate that FlgE is the hook structural protein and that FliK regulated hook length. |
| GO:0044780 bacterial-type flagellum assembly | IMP PMID:25313396 FlgM is secreted by the flagellar export apparatus in Bacill... | ACCEPT | Summary: This IMP (Inferred from Mutant Phenotype) annotation indicates FliK is involved in bacterial flagellum assembly based on evidence from PMID:25313396 (Calvo & Kearns 2015). This paper demonstrates that FliK is part of the minimal subset of flagellar proteins required for FlgM secretion, placing FliK functionally in the export apparatus pathway. The paper explicitly describes FliK as "the substrate specificity switch regulator," confirming its role in the assembly process through triggering the substrate switch. Reason: The IMP annotation is well-supported by the cited reference. PMID:25313396 demonstrates that FliK is required for FlgM secretion and explicitly names it as "the substrate specificity switch regulator FliK." This directly supports FliK's role in flagellum assembly - without FliK, the switch from hook to filament substrate export fails, preventing proper flagellum assembly. Supporting Evidence: PMID:25313396 FlgM secretion is strongly enhanced by, but does not strictly require, hook-basal body completion and instead demands a minimal subset of flagellar proteins that includes the FliF/FliG basal body proteins, the flagellar type III export apparatus components FliO, FliP, FliQ, FliR, FlhA, and FlhB, and the substrate specificity switch regulator FliK. |
| GO:0071978 bacterial-type flagellum-dependent swarming motility | IMP PMID:25313396 FlgM is secreted by the flagellar export apparatus in Bacill... | KEEP AS NON CORE | Summary: This IMP annotation indicates FliK is involved in bacterial swarming motility based on PMID:25313396. While FliK is essential for functional flagella (through its role in hook length control and substrate switching), and functional flagella are required for swarming motility, this annotation may represent an indirect/downstream effect rather than a direct role in swarming. FliK's primary function is in flagellum assembly (hook length control), not in the motility process itself. The paper's focus is on FlgM secretion and flagellar assembly, not specifically on swarming motility assays. Reason: FliK is indirectly required for swarming motility because it is essential for proper flagellum assembly. Without FliK, hooks overgrow and flagella are non-functional, which would impair swarming. However, FliK does not directly participate in the motility mechanism itself - its core function is hook length control and triggering the substrate-specificity switch. This annotation captures a downstream phenotypic effect rather than FliK's primary molecular function. The assembly annotation (GO:0044780) more directly reflects FliK's biological role. Supporting Evidence: PMID:25313396 FlgM secretion is strongly enhanced by, but does not strictly require, hook-basal body completion and instead demands a minimal subset of flagellar proteins that includes the FliF/FliG basal body proteins, the flagellar type III export apparatus components FliO, FliP, FliQ, FliR, FlhA, and FlhB, and the substrate specificity switch regulator FliK. file:BACSU/fliK/fliK-deep-research-falcon.md FliK is the dedicated flagellar hook-length control protein that times the transition from rod/hook-type export to filament-type export by the flagellar type III secretion system (fT3SS). Loss of FliK causes a polyhook phenotype because the export apparatus fails to switch substrates. |
| GO:0071978 bacterial-type flagellum-dependent swarming motility | IMP PMID:22730131 Molecular characterization of the flagellar hook in Bacillus... | KEEP AS NON CORE | Summary: This IMP annotation indicates FliK is involved in bacterial swarming motility based on PMID:22730131 (Courtney et al. 2012). This paper directly demonstrates in B. subtilis that "FliK regulated hook length" and shows that mutants affecting hook assembly result in reduced motility. However, like the other swarming annotation, this represents an indirect effect - FliK's primary function is hook length control, and the motility defect is a downstream consequence of faulty flagellum assembly. Reason: While PMID:22730131 directly demonstrates FliK's role in B. subtilis flagellum biology, its core finding is that "FliK regulated hook length." The swarming motility defect in fliK mutants is an indirect consequence of improper hook assembly rather than a direct role in the swarming process. The annotation is not incorrect but reflects a downstream phenotype rather than FliK's primary molecular function. Retaining as non-core because the experimental evidence does support the connection, even if indirect. Supporting Evidence: PMID:22730131 We used the fluorescently labeled hook to demonstrate that FlgE is the hook structural protein and that FliK regulated hook length. PMID:22730131 All mutants defective in hook completion resulted in homogeneously reduced sigma(D)-dependent gene expression due to the action of the anti-sigma factor FlgM. |
| GO:0005515 protein binding | NAS | NEW | Summary: Added to align core_functions with existing annotations. Reason: Core function term not present in existing_annotations. |
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Download this section (compressed HTML)Q: What is the precise mechanism by which FliK senses hook length in B. subtilis? Is it through physical spanning of the export channel (molecular ruler model) or through export frequency and stochastic interactions (molecular clock model)? Understanding this in B. subtilis, where hook and FliK are approximately 25% longer than Salmonella, could illuminate species-specific calibration of the length control system.
Q: Does FliK interact with FlgD (hook cap) in B. subtilis as it does in Salmonella? What is the role of FlhO and FlhP (B. subtilis-specific proteins) in the FliK-mediated switching mechanism? B. subtilis has unique hook assembly factors not found in Gram-negative bacteria, and understanding how these interact with the conserved FliK-FlhB switching mechanism could reveal Gram-positive-specific adaptations.
Experiment: Measure hook length distributions in B. subtilis fliK deletion, overexpression, and truncation mutants using cryo-EM or fluorescent labeling to quantify the length control function. Expected outcomes: fliK deletion should produce polyhooks (elongated hooks), overexpression should produce shorter hooks, and C-terminal truncations should disrupt switching without affecting secretion.
Experiment: Co-immunoprecipitation or bacterial two-hybrid to test FliK-FlhB interaction in B. subtilis, and test whether FlhO/FlhP affect this interaction. Expected outcome: Should detect FliK-FlhB interaction dependent on the FliK C-terminal domain, and may reveal whether FlhO/FlhP modulate the switch timing.
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