coYki (Capsaspora owczarzaki Yorkie/YAP/TAZ ortholog) - curation notes

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Identity

UniProt A0A0D2WY30 (TrEMBL, unreviewed, 610 aa), "WW domain-containing protein";
ORF name CAOG_007866 (UniProt) = CAOG_07866 (older Broad locus format used in
the key resources table of PMID:35659869: "GenBankCAOG_07866").
Gene named coYki in Phillips et al. 2022/2024; "Co-Yki"/"CoYki" in
Sebé-Pedrós et al. 2012.
InterPro: two WW domains (278-310, 340-373 in the UniProt model), IPR051583 YAP1
family; PANTHER PTHR17616:SF8 "TRANSCRIPTIONAL COACTIVATOR YORKIE".
Single Yorkie/YAP/TAZ ortholog in the genome PMID:38517944.

Sequence-numbering caveat (my own observation, not from a paper)

Phillips & Pan 2024 describe residue F123 of coYki as aligning with human YAP1 F95
(TEAD-binding). In the UniProt model A0A0D2WY30 the YAP1 motif LPDSFFKPP
(YAP1 S94/F95/F96) corresponds to LPASFFRSP at residues 54-62 (F58/F59), and there
is no Phe at position 123. HXRXXS motifs in the UniProt model sit at 20, 82, 114
and 235 (four motifs, matching the "four HXRXXS motifs" of the papers). So either the
published coYki cDNA (5'/3' RACE-checked in PMID:22832104) has a longer N-terminus
than the UniProt gene model, or the papers use a different numbering. Not resolved;
raised as a suggested question.

Domain architecture and predicted function

Conserved WW domains, phosphoregulatory sites and N-terminal TEAD-binding domain
PMID:35659869.
PMID:22832104.

Heterologous activity in Drosophila (PMID:22832104) - demonstrated, but not in Capsaspora

Co-Yki alone, overexpressed in the fly eye, does not cause overgrowth (small rough
eye) PMID:22832104.
Co-Yki + Co-Sd (Capsaspora Scalloped/TEAD) together give massive overgrowth
PMID:22832104.
Target genes Diap1 and Ex induced PMID:22832104.
Physical interaction (co-IP, epitope-tagged, S2R+ cells) and HRE-luciferase
activation PMID:22832104; PMID:22832104.
Co-Hpo phosphorylates/inhibits Co-Yki in S2R+ PMID:22832104; PMID:22832104.
Note the "growth-regulatory activity" is a property shown in Drosophila tissue, not
in Capsaspora, where coYki does not control proliferation (below).

In Capsaspora (PMID:35659869, PMID:38517944) - demonstrated

Knockout (coYki -/-, TBD replaced on both alleles by homologous recombination)

PMID:35659869.
No proliferation phenotype PMID:35659869; EdU in
aggregates also unchanged.
Aggregates flatter, less circular, same size PMID:35659869.
Increased cell-substrate adhesion, normal cell-cell adhesion PMID:35659869 (the full sentence contains an
en dash; see paper).
Ectopic actin-depleted blebs, rescued by coYki transgene
PMID:35659869; PMID:35659869.
Blebbistatin suppresses blebbing and rescues aggregate shape PMID:35659869.
RNA-seq: 1205 DE genes (397 down, 808 up in mutant); actin-binding genes enriched
among up-regulated; no proliferation/cell-cycle enrichment PMID:35659869;
PMID:35659869. Authors flag possible transcription-independent
action PMID:35659869.
Two integrin-beta genes upregulated in mutant PMID:35659869.

Localization

mScarlet-coYki (transient, WT cells) is cytoplasm-enriched; 4SA mutant uniform or
nuclear PMID:35659869; PMID:35659869.
In coHpo-/- and coWts-/- cells, mScarlet-coYki nuclear >= cytoplasmic
PMID:38517944;
PMID:38517944.
Density regulation of coYki localization was NOT examined in these papers (I found no
experiment varying cell density and scoring coYki localization).

Hyperactive coYki (PMID:38517944)

coYki 4SA stable transgene phenocopies coHpo/coWts loss (increased aggregate cell
packing, elongated adherent cells) PMID:38517944.
Requires the TEAD-binding residue: PMID:38517944;
PMID:38517944
107-gene "core Hippo pathway" DE set shared by coYki, coHpo, coWts mutants; enriched
in membrane proteins and laminin G domain proteins.
No direct coYki-coSd interaction or ChIP has been done in Capsaspora itself.

Annotation decisions (summary)

Term	Action	Reason
GO:0003713 transcription coactivator activity	ACCEPT	Co-Sd/Co-Yki activates HRE reporter and Diap1/Ex (heterologous); F123A abolishes 4SA phenotypes in Capsaspora
GO:0005634 nucleus	ACCEPT	nuclear in kinase mutants and 4SA; regulated nuclear entry
GO:0005737 cytoplasm	ACCEPT	predominantly cytoplasmic in WT cells (sequestration)
GO:0035329 hippo signaling	ACCEPT	coHpo/coWts regulate coYki localization in Capsaspora; coYki is the effector named in the GO definition; YAP1 and yki carry the term
GO:0045944 positive regulation of transcription by RNA polymerase II	ACCEPT	HRE-luciferase / Diap1 induction with Co-Sd; transcription-dependent phenotypes
NEW GO:0140297 DNA-binding transcription factor binding	IPI	co-IP with Co-Sd in S2R+ cells

Track C note (ORIGINS_OF_MULTICELLULARITY): none of the five TreeGrafter/ARBA rows is
an animal-specific process mis-propagated to a unicellular protein. "hippo signaling"
is a signalling-cassette term, not a multicellular process, and it is experimentally
supported in Capsaspora itself. No row asserts regulation of cell proliferation or
organ size, which the knockout data contradict. No process NEW terms proposed:
blebbing, cell-substrate adhesion and aggregate shape phenotypes are necessity
evidence downstream of an unidentified transcriptional program (fails participation
test as a direct process annotation).