PFRC (also called PFR1, PFR-C/PFR-D) is the 73 kDa major structural protein of the paraflagellar rod (PFR) of Trypanosoma brucei, encoded by tandemly repeated, nearly identical genes. The PFR is a large, paracrystalline, extra-axonemal lattice that runs alongside the 9+2 axoneme inside the single flagellum of kinetoplastids, euglenoids and dinoflagellates. PFRC and the closely related but distinct 69 kDa protein PFRA (PFR2) are the two most abundant PFR components and are thought to co-polymerise into the coiled-coil-rich filaments of the rod. Both are restricted to the flagellum and are added mainly at the distal tip of the growing flagellum, where they form a stable cytoskeletal structure with low turnover. PFRC and PFRA are essential and non-redundant for PFR assembly; without PFRA, PFRC enters the flagellum but accumulates unassembled at the tip. Through its structural role in the PFR, PFRC supports flagellar motility, and the PFR also serves as a platform for calmodulin and for signalling and metabolic enzymes. A predicted calmodulin-binding segment is present, and the PFR complex binds calmodulin, but direct calmodulin binding by PFRC itself is not firmly established.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005516 calmodulin binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO transfer from the Flagellar_rod domain (IPR007824). UniProt marks a predicted (ECO:0000255) calmodulin-binding region at residues 317-337. Calmodulin is a resident PFR protein required for PFR assembly, and purified PFR protein preparations bind calmodulin-Sepharose in a calcium-dependent manner, but that experiment does not separate PFR1 (PFRC) from PFR2 or from co-purifying PAR proteins, so direct binding by PFRC specifically is not demonstrated in sources available to this review. Reason: Nothing positive is known about calmodulin binding by PFRC itself. The IEA is an InterPro2GO transfer off IPR007824, a structural Flagellar_rod domain shared by both major PFR subunits and by other PFR proteins, so it carries no protein-specific information, and the UniProt region is an ECO:0000255 sequence-analysis prediction. The only biochemistry is a calmodulin-Sepharose experiment run on a bulk purified PFR protein pool, which does not resolve PFR1 (PFRC) from PFR2 and which the authors themselves say may be explained by co-purifying PAR1/PAR4 homologues; the PFR interaction map likewise reports only "direct or indirect" complex-level interactions. Marked as over-annotated rather than removed, because a candidate calmodulin-binding segment exists and calmodulin is a resident, assembly-critical PFR protein, so the claim is plausible at the complex level; it is an over-annotation as a statement about PFRC. Supporting Evidence: file:TRYBB/PFRC/PFRC-uniprot.txt /note="Calmodulin-binding" PMID:19879876 This suggests that there are two pools of PFR proteins that are differentiated by their ability to bind calmodulin, although the presence in the preparations of proteins of similar molecular weight such as PAR1 and PAR4 homologues may also explain these results. PMID:19888464 There is also evidence for either direct or indirect interactions between the major PFR components and calmodulin [13], strengthening the hypothesis for a major role for calcium in PFR function. PMID:23787017 calmodulin (CaM) is found within the paraflagellar rod (PFR) |
| GO:0005856 cytoskeleton | IEA GO_REF:0000044 | MODIFY | Summary: UniProt SubCell mapping (Cytoplasm, cytoskeleton). PFRC is a major component of the paraflagellar rod, an extra-axonemal lattice inside the flagellum often described as cytoskeletal, but the generic term does not capture the actual location. Reason: The precise, well-established location is the paraflagellar rod (GO:0097740), the kinetoplastid-specific extra-axonemal lattice of which PFRC is one of the two major structural components. GO:0097740 is the standard cellular component used for T. brucei PFR proteins (over 170 TREU927 gene products in QuickGO). GO classifies GO:0097740 as a supramolecular complex, not under cytoskeleton, so this is a lateral correction to the correct structure rather than a refinement to a descendant term, consistent with the partner subunit PFRA. Proposed replacements: paraflagellar rod Supporting Evidence: PMID:10954429 The PFR is composed of 2 major proteins, PFRA and PFRC. PMID:10954429 resulting in a stable cytoskeletal structure with low turn-over. PMID:7961827 Their gene product, PFR-C, is closely related to, but clearly distinct from, the 69 kDa species PFR-A. This finding indicates that the PFR fibers of the flagellum might represent heteropolymers formed by PFR-A and PFR-C, akin to the situation seen in microtubules or intermediate filaments. |
| GO:0031514 motile cilium | IEA GO_REF:0000120 | MODIFY | Summary: PFRC is restricted to the motile flagellum of T. brucei, where it is a major constituent of the paraflagellar rod. Reason: Correct but general. GO:0097740 paraflagellar rod is a part_of descendant of motile cilium (the QuickGO ancestors of GO:0097740 include GO:0097729 9+2 motile cilium and GO:0031514 motile cilium), and it names the exact structure of which PFRC is one of the two major components. The PFR occurs only in kinetoplastids and euglenids, so the specific term is appropriate for a trypanosome protein. This matches the treatment of the identical GOA row in the partner subunit PFRA; the same replacement is proposed for the cytoskeleton row. Proposed replacements: paraflagellar rod Supporting Evidence: PMID:10567544 PFRA and PFRC are abundant, and their localization is restricted to the flagellum. PMID:10954429 The PFR is composed of 2 major proteins, PFRA and PFRC. |
| GO:0005198 structural molecule activity | IMP PMID:34257277 Structure of the trypanosome paraflagellar rod and insights ... | NEW | Summary: PFRC (PFR1) is one of the two major structural proteins of the paraflagellar rod lattice and is essential and non-redundant with PFRA (PFR2) for building it. Reason: No molecular-function annotation describes what PFRC actually does. It contributes structure to the PFR lattice, probably by co-polymerising with PFRA into coiled-coil filaments. GO:0005200 structural constituent of cytoskeleton was not used because the paraflagellar rod (GO:0097740) is classified in GO only as a supramolecular complex, not under cytoskeleton. The broader GO:0005198 is therefore the most accurate existing term, matching the treatment of the partner subunit PFRA. Supporting Evidence: PMID:34257277 despite sharing high-percentage amino acid identity, PFR1 and PFR2 are essential and non-redundant components of the PFR. PMID:34257277 suggesting that multiple subunits of PFR1 and PFR2 molecules could contribute to each arm of the wire. PMID:7961827 PFR fibers of the flagellum might represent heteropolymers formed by PFR-A and PFR-C, akin to the situation seen in microtubules or intermediate filaments. |
| GO:0060285 cilium-dependent cell motility | IMP PMID:12798502 Efficiency and specificity of RNA interference generated by ... | NEW | Summary: PFRC is described as a flagellar protein required for cell motility. The PFR it builds is required for flagellar beating; ablation of the PFR (classically by PFRA RNAi) paralyses procyclic T. brucei while the axoneme remains intact. Reason: Participation test - PFRC does part of the work of flagellar motility because it builds the PFR, an extra-axonemal structure on which the flagellar beat depends (the structural-contribution case), mirroring the partner subunit PFRA. The direct evidence for PFRC is weaker than for PFRA. Durand-Dubief et al. used PFRC dsRNA and describe both genes as required for cell motility, but the cached abstract reports only the PFRA phenotype. PFR1 and PFR2 are, however, each essential and non-redundant for PFR assembly, and PFR loss causes paralysis. Bloodstream-form lethality and cytokinesis defects follow from loss of motility, so no further process terms are proposed. Supporting Evidence: PMID:12798502 PFRA and PFRC genes, which code for flagellar proteins required for cell motility. PMID:10954429 PFR construction was affected, resulting in cell paralysis. PMID:34257277 despite sharing high-percentage amino acid identity, PFR1 and PFR2 are essential and non-redundant components of the PFR. |
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Download this section (compressed HTML)Q: Should structural subunits such as PFR1/PFR2 be annotated to GO:0120268 paraflagellar rod assembly, given that each is required for PFR construction and is incorporated at the flagellar tip (and PFRC fails to assemble without PFRA), or are they what is assembled rather than agents of assembly, so that a structural-molecule annotation is sufficient?
Q: Does PFRC bind calmodulin directly, through the predicted 317-337 segment, and is any such binding Ca2+-dependent and relevant to PFR assembly or flagellar beat regulation?
Q: Do PFRC and PFRA form an obligate heterodimer or heteropolymer, and which densities of the PFR distal-zone lattice (scissors, wires) do they occupy?
Q: Are PFRC/PFRA required for viability of bloodstream-form T. brucei in the same way as for motility of procyclic cells?
Experiment: Express recombinant PFRC (wild type and a 317-337 deletion) and measure calmodulin binding by Ca2+-dependent pull-down or ITC, then test the deletion for PFR incorporation and motility in a PFRC RNAi rescue background.
Hypothesis: PFRC carries a functional Ca2+-dependent calmodulin-binding site that contributes to PFR assembly or motility regulation.
Experiment: Use in situ tagging with small epitopes and cryo-ET subtomogram averaging, or crosslinking mass spectrometry of isolated PFRs, to map PFRC and PFRA positions in the distal-zone lattice.
Hypothesis: PFRC and PFRA co-assemble into the coiled-coil wires connecting the scissors stack network planes.
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