NUP50c defines a conserved nuclear basket module with NUP82 and NUP136 to mediate mRNA export and gene regulation in plants

Abstract The nuclear basket (NB) is a key peripheral structure of the nuclear pore complex (NPC) that plays essential roles in eukaryotic mRNA surveillance and export, chromatin organization, and gene expression regulation. However, the architectural and functional mechanisms of plant NB remain poorly characterized. Here, we combined proximity labeling with fluorescence imaging to examine NUP50c, a paralog of NUP50 in Arabidopsis thaliana. Unlike its nucleoplasmic paralogs NUP50a/b, NUP50c localizes specifically to the NB at the nuclear periphery. Structural analysis revealed that NUP50c contains conserved α-helices that mediate its interaction with the β-sheets of NUP82, enabling its NPC anchoring. AlphaFold-Multimer modeling and protein-protein interaction assays using yeast and Nicotiana benthamiana confirmed the formation of an evolutionarily conserved NUP50c-NUP82-NUP136 complex in Arabidopsis, Oryza sativa, and Solanum lycopersicum. Notably, simultaneous disruption of NUP50c with NUP136 or with both NUP82 and NUP136 resulted in developmental defects and enhanced stress responses, accompanied by altered transcript profiles, and pronounced nuclear mRNA retention. These findings establish NUP50c as a bona fide NB component that cooperates with NUP82/NUP136 to mediate mRNA export and regulate gene expression, advancing our understanding of the assembly and function of the NB in plants.