Nuclear basket proteins regulate the distribution and mobility of nuclear pore complexes in budding yeast

Abstract

Nuclear pore complexes (NPCs) mediate all traffic between the nucleus and the cytoplasm and are among the most stable protein assemblies in cells. Intriguingly, budding yeast cells carry two variants of NPCs which differ in the presence or absence of the nuclear basket proteins Mlp1, Mlp2 and Pml39. The binding of this basket structure is the last step of NPC assembly and Mlp-positive NPCs are excluded from the region of the nuclear envelope that is associated with the nucleolus. Here, we use recombination-induced tag exchange (RITE) to investigate the stability of all the NPC subcomplexes within individual NPCs. We show that the nuclear basket proteins Mlp1, Mlp2 and Pml39 remain stably associated with NPCs through multiple cell-division cycles. Mlp1/2 are responsible for the exclusion of NPCs from the nucleolar territory, but an independent pathway via Nup2 also contributes to the depletion of Mlp-negative NPCs from this region. We developed a method for single NPC tracking in budding yeast and observed that NPCs exhibit increased mobility in the absence nuclear basket components. Our data suggest that the distribution of NPCs on the nucleus is governed by the nuclear basket proteins and is the result of interactions with chromatin or chromatin-associated factors.