Nuclear localization sequence binding: obsoletion

GO:0008139 → GO:0140142 nucleocytoplasmic carrier activity, triaged per annotation

AI Gene Review · projects/NLS_BINDING_OBSOLETION · 2026

Bottom line

  • GO obsoleted GO:0008139 as "the same activity as" GO:0140142 nucleocytoplasmic carrier activity (OLS, 2026-09-26).
  • Of 34 curated rows, the karyopherins move cleanly; nucleoporins, NLS-masking and nucleolar proteins bind an NLS without carrying it and need case-by-case calls.
  • Scoped, not yet started: none of the ~25 affected gene products is reviewed here. The page was marked MATURE; it is now SCOPING.

Old term → replacement, by class

Carrying versus holding an NLS

Why a straight swap would be wrong

  • GO:0140142 is "binding to and carrying a cargo between the nucleus and the cytoplasm".
  • IκBα (IPI, PMID:1493333) masks the p65 NLS; Su(fu) holds Ci/Gli in the cytoplasm.
  • Nup58/98/153/214 (PMID:7878057, PMID:8707840) are pore components; likely GO:0017056 or removal.
  • NSR1, Nolc1 recognise nucleolar cargo; Lbr tethers at the nuclear envelope.
  • Cabp1 and BRAP need their pull-down and retention evidence re-read.
  • InterPro2GO IPR024882 (Nucleoporin p58/p45/NUP49) should not become carrier activity.

Review queue

Tier Genes Expected outcome
1 human KPNA2, KPNA4, KPNB1, IPO4 move to GO:0140142
2 yeast PSE1, KAP104, KAP123, MTR10, KAP120 move to GO:0140142
3 NFKBIA, Su(fu), Nup58/98/153/214, NSR1, ETP1, Lbr, Nolc1 triage: other MF or remove
4 BRAP, Cabp1, Arabidopsis IMPA1/IMPA2 triage / plant coverage

PINC's 5 TAS rows (KPNA1, KPNA3, KPNB1, TNPO1, TNPO2) are candidates for evidence-code modernisation.

Status and next steps

  • 2026-06-01/02: project created; 34 rows tallied by source; genes tiered.
  • 2026-09-26: GO:0008139 obsolete in OLS. No affected gene under genes/; no review uses GO:0008139.
  • Only repo review using GO:0140142: human NPM1 (core function), not in the affected set.
  • Next: review KPNA2 + KPNA4, then KPNB1, then one diagnostic case (NFKBIA or Su(fu)).

Upstream: go-annotation#6435 · go-ontology#31419
Read more: projects/NLS_BINDING_OBSOLETION.md