ROP18 (Toxoplasma gondii ME49, TGME49_205250, A0A125YQL1) — curation notes

Note on provenance of these notes: automated deep research was not available in this
environment (Falcon authentication failed; OpenAI key invalid). No *-deep-research-*.md
file was generated. What follows is a manual literature review done by reading the
UniProt record, the cached publications in publications/, and primary papers fetched with
ai-gene-review fetch-pmid. Every assertion below carries an inline citation with a
verbatim quote from a cached source.

1. Sequence record and what it does/doesn't say

• UniProt A0A125YQL1 is a TrEMBL entry for the ME49 (type II) allele, annotated only by
  homology: PE 3: Inferred from homology, DE RecName: Full=Serine/threonine-protein,
  EC=2.7.11.1, protein kinase domain 252–531, ATP-binding residue 281, active-site
  (proton acceptor) residue 409 [file:TOXGM/ROP18/ROP18-uniprot.txt "SIMILARITY: Belongs to the protein kinase superfamily. Ser/Thr protein"].
• The record carries a Phobius-predicted transmembrane helix at 21–40
  [file:TOXGM/ROP18/ROP18-uniprot.txt "Membrane {ECO:0000256|SAM:Phobius}"]. This is the
  N-terminal signal peptide/pro-region of a rhoptry protein, not a bona fide membrane anchor;
  the literature on the ROP2 family explicitly rules out the transmembrane interpretation of
  the conserved hydrophobic stretch PMID:17305424.
• PANTHER places the protein in PTHR44167 ("OVARIAN-SPECIFIC SERINE/THREONINE-PROTEIN KINASE
  LOK-RELATED"), i.e. an animal STE20/LOK-like family. This is the source of the TreeGrafter
  IEAs for nucleus and mitotic DNA damage checkpoint signaling, which are metazoan
  functions with no counterpart in a secreted apicomplexan rhoptry kinase (see §5).

2. ROP18 is a rhoptry kinase secreted onto the parasitophorous vacuole membrane

• ROP18 belongs to the ROP2 family of rhoptry bulb proteins and relocalises to the PVM during
  invasion PMID:17305424.
• The protein is a genuinely active kinase discharged at the host–parasite interface
  PMID:17305424.
• Overexpression increases intravacuolar replication, and this depends on catalytic activity
  PMID:17305424.
• After secretion the protein is tethered to the cytosolic face of the PVM
  PMID:22906355,
  via an arginine-rich amphipathic helical region upstream of the kinase domain
  PMID:22906355.
• PVM targeting is functionally required: targeting mutants retain intrinsic kinase activity
  but cannot phosphorylate host substrates or confer virulence
  PMID:22906355.

3. Virulence factor identified by genetic mapping

• ROP18 was positionally cloned as a type I acute-virulence QTL and is secreted into the host
  cell during invasion; the phenotype requires kinase activity
  PMID:17170305,
  PMID:17170305.
• The companion mapping study framed ROP kinases generally as key virulence factors
  PMID:17170306.

4. Molecular mechanism: phosphorylation of host IFN-inducible GTPases (IRGs)

• ROP18 binds and phosphorylates host immunity-related GTPases, blocking the IRG-dependent
  clearance machinery
  PMID:21147463.
• The reaction is a direct, catalysis-dependent phospho-transfer; kinase-dead protein traps the
  substrate
  PMID:21147463,
  PMID:21147463.
• The modified residues are threonines in switch region I of the GTPase domain
  PMID:21203588,
  PMID:21203588
  — i.e. Thr102 and Thr108 PMID:22906355.
  This matters for GO: the RHEA-derived IEA asserts serine kinase activity, whereas the
  direct experimental substrate chemistry is threonine phosphorylation; the correct term is
  the dual protein serine/threonine kinase activity.
• ROP18 acts as part of a complex with the pseudokinase ROP5 and the dense granule protein GRA7
  PMID:26247512,
  and ROP5 allele identity gates ROP18 function
  PMID:22761577.
• Substrate scope among IRGs is narrower than first thought
  PMID:26247512.

5. A second host target: ER-bound ATF6β

• A yeast two-hybrid screen with the N-terminal extension identified host ATF6β
  PMID:21670204,
  and the kinase activity is required for its destruction
  PMID:21670204,
  PMID:21670204.
  Direct phosphorylation of ATF6β by ROP18 is not demonstrated in that paper (the effect is
  attributed to binding plus kinase-dependent proteasomal degradation), so no substrate-specific
  MF term is warranted for this interaction.

6. Strain / host context relevant to the ME49 entry being reviewed

• The entry under review is the type II ME49 allele. Type II ROP18 is expressed and is an
  active, functional allele
  PMID:22761577,
  PMID:22761577.
  The reduced acute virulence of type II strains comes from the ROP5 allele context, not from
  loss of ROP18 function
  PMID:22761577.
  So the IRG-evasion function is appropriate to annotate to the ME49 protein, while the extreme
  acute-virulence phenotype is a type I property.
• The IRG arm of the mechanism is mouse-specific; humans lack the expanded IRG family
  PMID:22761577.
  GO process terms should therefore be the generic symbiont/host terms, not anything implying a
  universal host range.

7. Curation calls arising from the above

• GO:0004674 protein serine/threonine kinase activity — core; experimentally supported
  (autophosphorylation, Irga6/Irgb6 phosphorylation, kinase-dead controls).
• GO:0106310 protein serine kinase activity (RHEA IEA) — the characterized chemistry is
  threonine phosphorylation in Irga6 switch I, so the serine-only child is the wrong level;
  MODIFY to GO:0004674.
• GO:0005524 ATP binding — accept (kinase with annotated ATP-binding residue).
• GO:0000166, GO:0004672, GO:0016301, GO:0016740 — true but entailed by GO:0004674
  / GO:0005524: TOO_GENERAL.
• GO:0005634 nucleus (TreeGrafter, PTHR44167) — wrong compartment. ROP18 is a rhoptry protein
  secreted onto the cytosolic face of the PVM; the term comes from metazoan LOK/STK20-family
  grafting. REMOVE.
• GO:0044773 mitotic DNA damage checkpoint signaling (TreeGrafter) — a metazoan checkpoint
  function with no support in any ROP18 study; the protein is an exported effector, not a
  nuclear checkpoint kinase. REMOVE.
• Missing from GOA and proposed as NEW: GO:0020008 rhoptry,
  GO:0020005 symbiont-containing vacuole membrane (the GO term used for the T. gondii PVM;
  cf. MAF1b1 A0A140H546 annotated IDA to GO:0020005 in QuickGO),
  GO:0052170 symbiont-mediated suppression of host innate immune response.