Sequence and structural rules define PY-NLS-dependent nuclear import by TRANSPORTIN 1 in plants

Nuclear localization signals (NLSs) direct proteins to the nucleus, but whether the non-classical proline-tyrosine NLS (PY-NLS), characterized mainly in animals and fungi, functions in plants is unknown. Here we identify a basic PY-NLS pathway in tobacco and Arabidopsis and show that TRANSPORTIN 1 (TRN1) is its receptor. TRN1 binds PY-NLS cargoes in vitro, whereas loss of TRN1 causes their cytoplasmic accumulation. Mutational, structural and quantitative localization analyses of motifs from the jasmonate signaling repressor JAZ1 and a PLA2-like protein reveal an extended linker between binding epitopes and a short -helix preceding the conserved PY dipeptide as features that distinguish plant PY-NLSs from established eukaryotic models. A validated prediction pipeline identifies 179 Arabidopsis proteins containing candidate PY-NLSs. Together, our findings establish TRN1-mediated PY-NLS recognition as a previously unrecognized plant nuclear import pathway and uncover a plant-specific signal architecture with broad implications for the nuclear control of gene expression, RNA metabolism and development.