FliM (PP_4358) is the flagellar motor switch protein of the C ring of the polar flagella of Pseudomonas putida KT2440. It has an N-terminal region carrying the conserved CheY-P-binding motif, a middle FliM domain and a C-terminal FliN-like (SpoA) domain, and belongs to the FliM family (PIRSF002888, TIGR01397). By homology with the E. coli and Salmonella motors, FliM forms 1:3 complexes with FliN that bind the FliG ring through one-to-one FliG-FliM contacts, building the wall of the cytoplasmic C ring that hangs from the MS ring at the base of the basal body. FliM is the primary docking site for the phosphorylated response regulator CheY-P; CheY-P binding remodels FliM-FliM and FliM-FliN contacts and is relayed through FliG to the stator interface, switching the direction of motor rotation. In KT2440 this switching underlies the run-reverse-turn swimming pattern by which chemotactic signals control polar flagellar motility.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003774 cytoskeletal motor activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the FliM family signature. The GO definition of cytoskeletal motor activity covers generation of torque for rotation of a flagellum, but in the flagellar motor torque is generated at the stator-rotor interface between MotA and the C-terminal torque helix of FliG, not by FliM. Reason: The essence (FliM is a component of the flagellar motor) is sound, but the activity FliM itself contributes is structural and regulatory: it forms the C ring wall with FliN and FliG and binds CheY-P to switch rotation direction. Torque is generated by stator units (MotA/MotB, or MotC/MotD in P. putida) acting on the FliG torque helix. The row is therefore re-typed to the subunit's own activity, structural molecule activity (GO:0005198), which is also the complex-level activity assigned to the C ring switch module. This is a lateral correction, not a refinement. The starting motor term includes electrochemical rotation; the replacement is chosen to describe this subunit’s demonstrated structural switch role, not because flagellar motors fall outside GO0003774. Proposed replacements: structural molecule activity Supporting Evidence: PMID:31452860 Each stator unit is composed of two transmembrane proteins, MotA and MotB, and acts as a transmembrane proton channel to couple the proton flow through the channel with torque generation PMID:31452860 side-by-side associations between FliMM domains are responsible for the formation of the C ring wall file:PSEPK/fliM/fliM-uniprot.txt DR InterPro; IPR001689; Flag_FliM. |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | MODIFY | Summary: UniProt subcellular-location mapping (PIRNR002888): FliM is a peripheral inner-membrane protein, attached via the C ring to the cytoplasmic face of the membrane-embedded MS ring. Reason: Correct but general. fliM has no transmembrane segment and is held on the cytoplasmic face of the inner membrane through the C ring and MS ring, so the supported membrane location is GO:0009898 cytoplasmic side of plasma membrane, as for FliG and the soluble chemotaxis proteins at receptor arrays. The informative structural location, the C ring, is given on the MODIFY rows below. Proposed replacements: cytoplasmic side of plasma membrane Supporting Evidence: file:PSEPK/fliM/fliM-uniprot.txt SUBCELLULAR LOCATION: Cell inner membrane {ECO:0000256|PIRNR:PIRNR002888}; Peripheral membrane protein {ECO:0000256|PIRNR:PIRNR002888}. PMID:31452860 The C ring consisting of a cylindrical wall and inner lobes is formed by FliG, FliM and FliN on the cytoplasmic face of the MS ring |
| GO:0009288 bacterial-type flagellum | IEA GO_REF:0000104 | MODIFY | Summary: Correct but general. FliM is a component of the flagellar C ring, a substructure of the basal body. Reason: FliM is located in the flagellum specifically as a C ring subunit. GO bacterial-type flagellum basal body, C ring (GO:0009433) is a part_of descendant of bacterial-type flagellum and is defined as the cytoplasmic rotor ring containing the three switch proteins; it is supported by FliM-family membership and by structural work on the FliG/FliM/FliN C ring in E. coli and Salmonella. Proposed replacements: bacterial-type flagellum basal body, C ring Supporting Evidence: PMID:31452860 The C ring is composed of FliG, FliM and FliN. file:PSEPK/fliM/fliM-uniprot.txt FUNCTION: FliM is one of three proteins (FliG, FliN, FliM) that forms the rotor-mounted switch complex (C ring), located at the base of the basal body. |
| GO:0009425 bacterial-type flagellum basal body | IEA GO_REF:0000120 | MODIFY | Summary: Correct but general. Within the basal body, FliM is a component of the cytoplasmic C ring. Reason: GO:0009433 bacterial-type flagellum basal body, C ring is a part_of descendant of the basal body and is the specific substructure that contains FliM, so the row is refined to it. Proposed replacements: bacterial-type flagellum basal body, C ring Supporting Evidence: PMID:31452860 FliM and FliN together form the FliM1/FliN3 complex consisting of one copy of FliM and three copies of FliN [17], and the FliM1/FliN3 complex binds to the FliG ring structure through a one-to-one interaction between FliG and FliM to form the continuous C ring wall file:PSEPK/fliM/fliM-uniprot.txt FUNCTION: FliM is one of three proteins (FliG, FliN, FliM) that forms the rotor-mounted switch complex (C ring), located at the base of the basal body. |
| GO:0050918 positive chemotaxis | IEA GO_REF:0000118 | MODIFY | Summary: TreeGrafter transfer from the PANTHER FliM node. FliM does part of the work of chemotaxis, as the switch component that receives CheY-P and changes the direction of motor rotation, but nothing restricts this to movement toward attractants. Reason: Overly specific. The switch responds to CheY-P irrespective of whether the stimulus is an attractant or a repellent, so the same FliM activity serves positive and negative chemotaxis. The appropriate term is the parent, chemotaxis (GO:0006935), which is also the term used for FliN and for the other relay proteins of this pathway. Proposed replacements: chemotaxis Supporting Evidence: PMID:31452860 FliMN contains a well conserved LSQXEIDALL sequence, which is responsible for the interaction with CheY-P [33]. PMID:31452860 The binding of CheY-P to FliM and FliN affects subunit-subunit interactions between FliMM domains and between FliMC and FliN in the C ring to induce a 180° rotation of FliGCC relative to MotAC, thereby allowing the motor to rotate in CW direction [34]. file:PSEPK/fliM/fliM-uniprot.txt This complex interacts with the CheY and CheZ chemotaxis proteins, in addition to contacting components of the motor that determine the direction of flagellar rotation. |
| GO:0071973 bacterial-type flagellum-dependent cell motility | IEA GO_REF:0000002 | ACCEPT | Summary: FliM is an essential rotor/switch component of the flagellar motor and does part of the work of flagellum-dependent motility. Reason: As a structural subunit of the C ring rotor and the CheY-P-responsive switch, FliM participates directly in flagellar rotation and its direction. KT2440 swims with polar flagella in a run-reverse-turn pattern that depends on switching of motor direction. No KT2440 fliM mutant phenotype is in the cached literature, so the term is kept at the general motility level rather than refined to swimming. Supporting Evidence: file:PSEPK/fliM/fliM-uniprot.txt FUNCTION: FliM is one of three proteins (FliG, FliN, FliM) that forms the rotor-mounted switch complex (C ring), located at the base of the basal body. PMID:23728820 our results suggest a new "run-reverse-turn" paradigm for polar-flagellated Pseudomonas motility |
| GO:0071978 bacterial-type flagellum-dependent swarming motility | IEA GO_REF:0000118 | MARK AS OVER ANNOTATED | Summary: FliM supports flagellar motility, but the transferred swarming-specific claim is not established in KT2440. Reason: This electronic transfer does not distinguish flagellum-dependent surface swarming from swimming through semisolid agar or other surface spreading. The KT2440 stator study explicitly makes that distinction. Retain general flagellar motility; do not infer swarming from necessity for an intact flagellum. This does not reject swarming experiments in other strains or conditions. Supporting Evidence: PMID:36409076 However, P. putida does not swarm in a flagella-dependent manner (16) and is lophotrichously flagellated, having multiple flagella at one cell pole (17). |
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Download this section (compressed HTML)Q: In the lophotrichous KT2440 cell, do all polar motors share a common CheY-P sensitivity, and how does FliM-CheY-P binding coordinate reversal of the flagellar bundle into the wrapped mode?
Experiment: Construct an in-frame fliM deletion and CheY-P-binding-motif point mutants, then measure swimming, tethered-cell rotation bias and wrapped-mode frequency, and test polar FliM-fluorescent-protein foci for exchange in response to attractant addition.
Hypothesis: FliM is required for flagellar rotation and direction switching in KT2440.
Type: genetics and single-cell motility imaging
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