pom1 (SPAC2F7.03c, Q09690) review notes

S. pombe DYRK-family dual-specificity protein kinase. Forms polar cortical gradients from cell tips; spatial cell-end marker coupling cell geometry to mitotic entry timing (cell-size control) and division-plane positioning, plus polarized (bipolar) growth.

Molecular function / catalysis

• DYRK / MNB-DYRK subfamily, CMGC group; kinase domain 699-995, ATP binding 705-713 + K728, active site D825. EC 2.7.12.1 (dual specificity). [UniProt Q09690]
• Dual-specificity: autophosphorylates on Tyr; phosphorylates substrates on Ser/Thr. PMID:22174761
• Pom1 kinase activity demonstrated; catalytic-domain point mutations cause asymmetry. PMID:11230130
• Direct in vitro phosphorylation of substrates. PMID:25720772
• Pom1 phosphorylates Cdr2 C-terminal domain reducing Cdr2-T166 activating phosphorylation by Ssp1. PMID:24508166

Cell-size control / mitotic entry (G2/M)

• Pom1 gradient measures cell length and controls mitotic entry; dose-dependent G2-M inhibitor; negatively regulates Cdr1/Cdr2 (Wee1 inhibitors). [PMID:19474792 "an intracellular gradient of the dual-specificity tyrosine-phosphorylation regulated kinase (DYRK) Pom1, which emanates from the ends of rod-shaped Schizosaccharomyces pombe cells, serves to measure cell length and control mitotic entry"; "Pom1 is also a dose-dependent G2-M inhibitor. Genetic analyses indicate that Pom1 negatively regulates Cdr1 and Cdr2"]
• Pom1 forms polar gradient, dose-dependent inhibitor of mitotic entry via Cdr2 pathway; as cells elongate Pom1 decreases at middle leading to mitotic entry. PMID:19474789
• Distinct Pom1 thresholds set timing vs positioning of division; Pom1 inhibits Cdr2 for mitotic commitment independently of regulating its localization. PMID:24316795
• Pom1 prevents activation of Cdr2 by CaMKK Ssp1. PMID:24508166
• Pom1 suppresses Wee1 node bursts in small cells. PMID:29514920
• Caveat: pom1Δ and nif1Δ have WT size homeostasis -> Pom1 is not the direct cell-size sensor. PMID:24047646

Division plane positioning / Mid1 / cytokinesis

• pom1 mutants misplace/misorient septa -> asymmetric division. PMID:9573052
• Pom1 required for proper placement of Mid1p ring; acts in pathway distinct from Plo1/Mid1. PMID:9852154
• Pom1 kinase prevents septation at cell tips even without Mid1; phosphorylates F-BAR Cdc15 to disrupt membrane/paxillin binding -> ensures medial division. [PMID:32101481 "Pom1's kinase activity prevents septation at cell tips even if Mid1 is absent or mislocalized"; "inhibition of Cdc15-scaffolded septum formation at cell poles is a key Pom1 mechanism that ensures medial division"]
• Multiple polarity kinases (incl. Pom1) phosphorylate Cdc15 IDR, inhibit phase separation/condensation, antagonize CR assembly. PMID:36749320
• Pom1 localizes at cortex of cell tip during cytokinesis; contributes to preventing tip septation. PMID:37746062
• Pom1 detected in contractile ring intermediate layer (super-res map). PMID:28914606

Polarized / bipolar growth (NETO), Cdc42, Rga4

• pom1 provides positional info for both growth and division; mutants fail to switch to bipolar growth. PMID:9573052
• Pom1 interacts with Rga4 (Cdc42 GAP); needed to remove Rga4 from nongrowing end -> bipolar GTP-Cdc42. [PMID:18328707 "Pom1 kinase physically interacts with Rga4"; "Pom1 kinase recruited to cell ends ... is essential for proper localization of a GAP for Cdc42, Rga4, which ensures bipolar localization of GTP-bound, active Cdc42"; deltapom1 brings about monopolar growth]
• Tea1-Tea4-Pom1 axis counteracts inappropriate Gef1 activity by regulating Rga4 localization. PMID:29930085
• Pom1 contributes to cell-end determination; pom1Δ has defective growth pattern/actin relocalization. PMID:14663827

Cell integrity MAPK (Pmk1)

• Pom1 is a negative regulator of the Pmk1 (cell integrity) pathway, via regulating Rga4 localization/phosphorylation (not via Rga4 Rho2-GAP). PMID:20164182

Localization / gradient mechanism

• Cell tip / cell cortex of cell tip / site of polarized growth / cell division site. [PMID:11230130; PMID:9573052; PMID:24047646]
• Tea4 recruits Pom1 to cortex; Pom1 binds PM via basic region (direct lipid interaction), diffuses laterally, autophosphorylates to release. PMID:21703453
• Interacts with Tea4; triggers PM association via Dis2-dependent dephosphorylation. PMID:21703453
• PIP binding: Pom1 binds plasma membrane lipids via basic region (phosphatidylinositol phosphate binding, IDA). [PMID:21703453, "direct lipid interaction"]
• Intermolecular autophosphorylation buffers gradient robustness. PMID:26150232
• Under glucose limitation Pom1 re-localizes to cell sides (lateral cell cortex) via MT destabilization/PKA-CLASP. PMID:26443240

Notes on specific annotations

• GO:0005515 protein binding (IPI to cdr2, tea4, rga4): uninformative MF; the underlying interactions are real but better captured by kinase MF + specific BP. Mark over-annotated / non-core.
• GO:0005856 cytoskeleton (IBA): Pom1 is cortical/PM, not a cytoskeletal component; over-annotation from phylo.
• GO:0005737 cytoplasm (IBA): broad; Pom1 acts at cortex/PM. Keep non-core.
• PMID:12206652 (Mac1) and PMID:20870879 (invasive filaments) and PMID:22174761 (Pom2): pom1 localization references, supportive of cell tip/division site CC.
• PMID:11950884 is now cached as an abstract-only record. Its abstract directly states
  that the analyzed morphological factors, including Pom1, concentrate at cell ends
  during vegetative growth and reports a Pom1 role early in the switch to shmooing growth.

2026-09-01 — current GOA and IBA refresh

• Refreshed the machine-sourced bundle with just fetch-gene SCHPO pom1 --force; current GOA adds an IBA GO:0004674 protein serine/threonine kinase activity at PAINT node PANTHER:PTN000624408.
• Removed the discontinued ARBA GO:0032878 regulation of establishment or maintenance of cell polarity row from existing_annotations; the experimentally supported polarity role remains synthesized in core_functions and represented by current, more specific experimental GOA rows.
• Accepted the new IBA. The PAINT node spans the conserved DYRK catalytic branch and includes Pom1 among its experimentally annotated descendants; this is expected experimental grounding for the ancestral placement, not circular evidence. Direct Pom1 substrate phosphorylation in PMID:25720772 independently supports the activity.
• Updated the PTHR24058 family review to separate this sound catalytic transfer from the deeper-node cytoplasm/cytoskeleton localization transfers, retaining the existing subfamily-aware localization decisions.
• Added structured failure metadata for the rejected cytoskeleton IBA and replaced the discontinued broad polarity term in core_functions with the current, experimentally supported GO:0061245 establishment or maintenance of bipolar cell polarity.