yorkie (PTSG_06057) encodes the Yorkie/YAP/TAZ homolog of the colonial choanoflagellate Salpingoeca rosetta, a 714-residue protein with two WW domains (residues 189-222 and 244-277) embedded in long disordered, low-complexity regions. In animals Yorkie/YAP is a transcriptional coactivator: it binds Scalloped/TEAD transcription factors through an N-terminal TEAD-binding domain, its WW domains bind PPxY motifs of partner proteins, and phosphorylation by Warts/LATS on HXRXXS motifs keeps it in the cytoplasm. The S. rosetta protein carries four HXRXXS motifs, one of them N-terminal to the WW domains as in YAP, but its predicted TEAD-binding region is poorly conserved, and whether it binds a TEAD protein or acts as a coactivator is unknown. yorkie knockout cells proliferate at the wild-type rate and form rosettes of normal size, whereas Warts and Yorkie both influence expression of extracellular matrix genes, including couscous.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: TreeGrafter transfer from PANTHER node PTN002569196. TreeGrafter places F2UDK1 in PTHR10316:SF68 (family "MEMBRANE ASSOCIATED GUANYLATE KINASE-RELATED"), and the node is an ecdysozoan speciation node whose members are Drosophila CG42788, Anopheles AGAP003128 and a Pristionchus gene (PANTHER 19 tree), not the YAP1 family (PTHR17616) of human YAP1 and Drosophila Yorkie. Our own analysis finds that F2UDK1 matches YAP1, Yorkie and Capsaspora coYki better than the S. rosetta protein that PANTHER does place in PTHR17616 (F2U5K0, PTSG_03848). The localization of S. rosetta Yorkie has not been examined. Reason: The propagation route is wrong: the term reaches a choanoflagellate Yorkie homolog from a node of insect and nematode MAGI-related proteins. The term itself is plausible on independent grounds, since Yorkie/YAP proteins shuttle between cytoplasm and nucleus and are held in the cytoplasm when phosphorylated by Warts/LATS, and F2UDK1 carries four HXRXXS motifs. Kept as a non-core, unverified location, and the nucleus should be tested alongside it. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN002569196 · Ecdysozoa node, PTHR10316:SF68 SUPPORTS SOURCE BUT NOT TARGET Node of insect and nematode MAGI-related WW/PDZ proteins; F2UDK1 is a Yorkie/YAP homolog misgrafted into this family. The term happens to be plausible for a Yorkie homolog anyway. Supporting Evidence: file:SALRS/yorkie/yorkie-uniprot.txt PANTHER; PTHR10316:SF68; AGAP003128-PA; 1. file:SALRS/yorkie/yorkie-bioinformatics/RESULTS.md F2UDK1 is the better match to all three Yorkie/YAP proteins. PMID:38729842 srYki has 4 putative Warts phosphorylation sites |
| GO:0007165 signal transduction | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: TreeGrafter transfer from the same misplaced ecdysozoan node (PTN002569196) in the MAGI-related family. As a Yorkie homolog, F2UDK1 is expected to be the transcriptional effector of hippo signaling. In S. rosetta, Warts and Yorkie both regulate extracellular matrix genes [PMID:41037400], but yorkie knockout has no effect on proliferation or rosette size [DOI:10.1101/2024.07.13.603360], and no experiment shows Yorkie responding to Warts. Reason: The term is broad, and is plausible for a Yorkie homolog through its own family. A shared set of extracellular-matrix target genes for Warts and Yorkie fits a Warts-to-Yorkie pathway, but the phenotypes do not follow the animal pattern (warts loss enlarges rosettes, yet yorkie loss has no size effect), so no specific S. rosetta signal or downstream process can be named. Kept as non-core because it rests on a wrong-family propagation and on family-level inference, not on S. rosetta data. Hippo signaling is not proposed as NEW for the same reason, and because the predicted TEAD-binding region needed for the canonical output is not conserved. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN002569196 · Ecdysozoa node, PTHR10316:SF68 SUPPORTS SOURCE BUT NOT TARGET Wrong family for a Yorkie homolog; the generic signalling term survives only because it is also plausible for Yorkie/YAP. Supporting Evidence: PMID:41037400 RNA sequencing revealed that Warts and Yorkie regulated several extracellular matrix genes involved in multicellularity (including couscous) DOI:10.1101/2024.07.13.603360 Growth curves indicated that yorkiepac1 KO cells proliferated at a similar rate to the wild type DOI:10.1101/2024.07.13.603360 The size of hippopac1 and yorkiepac1 rosettes did not significantly differ from wild type (11.6 ± 1.7 cells and 9.8 ± 3.1 cells |
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Download this section (compressed HTML)Q: Does S. rosetta Yorkie bind the S. rosetta Scalloped/TEAD homolog despite the poorly conserved TEAD-binding region, and does it activate transcription in a reporter assay?
Q: Is S. rosetta Yorkie phosphorylated by Warts on its four HXRXXS motifs, and does Warts loss shift it to the nucleus?
Q: Do Warts and Yorkie regulate the shared extracellular matrix genes (e.g. couscous) in opposite directions, as the canonical pathway predicts?
Q: Is F2UDK1 the Yorkie ortholog, given that PANTHER places it with MAGI-related proteins and puts another S. rosetta WW protein (F2U5K0, PTSG_03848) in the YAP1 family? A phylogeny of holozoan YAP/Yorkie and WW-domain proteins would settle it.
Q: Why does yorkie knockout not affect rosette size or proliferation? Is there redundancy with another WW-domain coactivator?
Experiment: Express fluorescently tagged wild-type and four-site S-to-A Yorkie in wild-type and warts knockout cells and score its nuclear-to-cytoplasmic ratio.
Hypothesis: S. rosetta Yorkie is a Warts-regulated nucleocytoplasmic protein.
Type: localization / imaging
Experiment: Co-immunoprecipitation or yeast two-hybrid of Yorkie with the S. rosetta Scalloped/TEAD homolog, with AlphaFold-Multimer modelling to locate any divergent interface.
Hypothesis: S. rosetta Yorkie binds the S. rosetta TEAD homolog.
Type: protein interaction assay
Experiment: Construct warts yorkie double knockouts and count cells per rosette and imaging of the ECM core.
Hypothesis: The enlarged rosettes of warts mutants require Yorkie.
Type: genetic epistasis
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