PFRA (P22225) notes — Trypanosoma brucei brucei 69 kDa paraflagellar rod protein (PFR2)

Automated deep research was unavailable for this gene (Falcon authentication and the
OpenAI key both failed in this environment). These notes are a manual literature review
based on the UniProt record, PubMed-verified primary papers and reviews cached in
publications/, and ontology lookups (OLS / local GO sqlite).

Identity and naming

• UniProt P22225 (PFR1_TRYBB, "69 kDa paraflagellar rod protein", AltName PFR-A/PFR-B), 600 aa,
  encoded by two tandem genes with identical ORFs, PFRA and PFRB
  [file:TRYBB/PFRA/PFRA-uniprot.txt "Coded by two tandemly repeated genes with identical ORF:"].
• Naming caution: in T. brucei literature this protein (PFRA) corresponds to PFR2 of the
  consolidated nomenclature (69 kDa band); the 73 kDa protein is PFRC = PFR1. Confirmed by
  the RNAi literature: the snl-2 line targets PFRA PMID:10954429, and Portman et al. call snl2 a PFR2 knockdown
  PMID:19888464.
  The UniProt mnemonic PFR1_TRYBB is therefore confusing; anchor to the 69 kDa protein.
• The original cloning paper proposed that one 600-aa protein produced both the 73 and 69 kDa
  bands by conformational difference PMID:2793936. This was overturned:
  PMID:19879876
  and PFR1 and PFR2 are distinct paralogs from a duplication predating the
  Euglenida/Kinetoplastida split PMID:19879876.

Structure / localisation

• Highly helical, coiled-coil-rich PMID:2793936;
  PMID:34257277.
• The PFR is a trilaminar lattice alongside the axoneme inside the flagellum
  PMID:19879876.
• Cryo-ET (Zhang et al. 2021) suggests PFR1/PFR2 coiled coils form the "wires" of the distal
  zone lattice PMID:34257277.
• GO has a specific CC term: GO:0097740 paraflagellar rod (part_of GO:0097729 9+2 motile cilium,
  thus part_of GO:0031514 motile cilium; NOT a descendant of GO:0005856 cytoskeleton in GO).

Function (loss of function)

• PFRA RNAi (snl-1 / snl-2) in procyclic T. brucei: PFR construction fails, cells paralysed
  PMID:10954429.
• PFR is assembled distally and is a stable cytoskeletal structure
  PMID:10954429.
• Non-redundant with PFR1 PMID:34257277.
• snl4 (PFR2 RNAi) PMID:19888464
  and PMID:19888464.
• Bloodstream form: PFR2 ablation is lethal (cytokinesis failure), in vitro and in mice
  PMID:19879876.
  This is likely an indirect consequence of motility loss — not a direct cytokinesis role.
• PFR2 is also required for incorporation of other PFR components (e.g. PAR1)
  PMID:19879876.
• Bastin et al. 1998 Nature letter (PMID:9468133) — "Paraflagellar rod is vital for
  trypanosome motility"; abstract-only cache has no text, used only as background.

Calmodulin

• IEA calmodulin binding comes from InterPro IPR007824 (Flagellar_rod, Pfam PF05149). UniProt
  marks a predicted CaM-binding region 335-355 (ECO:0000255, sequence analysis only).
• Ridgley et al. 2000 (PMID:10960180; abstract not available in cache) — as summarised by
  Portman & Gull 2010: PMID:19879876
  with caveats PMID:19879876
  and specificity PMID:19879876.
• CaM itself is required for PFR assembly PMID:23787017. Direct CaM binding by PFR2
  (vs PFR1, or co-purifying PAR proteins) is not resolved at the single-protein level.
  -> Calmodulin binding plausible but non-core; keep as non-core.

Decisions

• GO:0005516 calmodulin binding (IEA InterPro): KEEP_AS_NON_CORE.
• GO:0005856 cytoskeleton (IEA SubCell): MODIFY -> GO:0097740 paraflagellar rod.
• GO:0031514 motile cilium (IEA): MODIFY -> GO:0097740 paraflagellar rod (part_of descendant).
• NEW: GO:0005198 structural molecule activity (core MF; structural constituent of PFR lattice).
  Not GO:0005200 structural constituent of cytoskeleton because that term occurs_in
  GO:0005856 cytoskeleton, and the PFR is not classified under cytoskeleton in GO.
• NEW: GO:0060285 cilium-dependent cell motility (PFR2 supplies the structure on which
  motility depends; RNAi paralysis). Did not add GO:0120268 paraflagellar rod assembly — as a
  structural subunit the assembly phenotype is the expected necessity phenotype; left as
  a suggested question.
• No animal/plant-only terms, no host-process terms, no RNA-editing/trypanothione issues here.

Deliberately short supporting_text (do not "complete")

Two quotes in this review stop before the end of their source sentence on
purpose. Leave them as they are:

• PMID:34257277 ...major structural components of the PFR are two proteins, PFR1 and PFR2 — the source continues PFR259,60. where 59,60 are
  superscript reference markers flattened into the text. Completing the
  sentence invents a protein called PFR259. The next sentence of the same
  paragraph (quoted at the GO:0060285 row) states the claim cleanly. This one
  was expanded and reverted twice.
• PMID:19888464 EM analysis shows that the PFR structure is greatly reduced
  — the cached paragraph runs straight into a DOI and a figure caption. Expanded
  once and reverted; the later DOI guard refused it, so it was not expanded again.