CTNNBL1 Is a Novel Nuclear Localization Sequence-binding Protein That Recognizes RNA-splicing Factors CDC5L and Prp31

Nuclear proteins typically contain short stretches of basic amino acids (nuclear localization sequences; NLSs) that bind karyopherin alpha family members, directing nuclear import. Here, we identify CTNNBL1 (catenin-beta-like 1), an armadillo motifcontaining nuclear protein that exhibits no detectable primary sequence homology to karyopherin alpha, as a novel, selective NLS-binding protein. CTNNBL1 (a single-copy gene conserved from fission yeast to man) was previously found associated with Prp19-containing RNA-splicing complexes as well as with the antibody-diversifying enzyme AID. We find that CTNNBL1 association with the Prp19 complex is mediated by recognition of the NLS of the CDC5L component of the complex and show that CTNNBL1 also interacts with Prp31 (another U4/U6. U5 tri-snRNP-associated splicing factor) through its NLS. As with karyopherin alpha s, CTNNBL1 binds NLSs via its armadillo (ARM) domain, but displays a separate, more selective NLS binding specificity. Furthermore, the CTNNBL1/AID interaction depends on amino acids forming the AID conformational NLS with CTNNBL1-deficient cells showing a partial defect in AID nuclear accumulation. However, in further contrast to karyopherin alpha s, the CTNNBL1 N-terminal region itself binds karyopherin alpha s (rather than karyopherin beta), suggesting a function divergent from canonical nuclear transport. Thus, CTNNBL1 is a novel NLS-binding protein, distinct from karyopherin alpha s, with the results suggesting a possible role in the selective intranuclear targeting or interactions of some splicing-associated complexes.