Detecting Nuclear Pore Complex assembly in living cells

The formation of nuclear pore complexes (NPCs) — vital gateways regulating nuclear-cytoplasmic transport — is a highly orchestrated process requiring the integration of hundreds of nucleoporins into the nuclear envelope. A major challenge in studying this assembly process in living cells has been the difficulty to distinguish newly forming NPCs from their mature counterparts. Here, we present a powerful nanobody-based approach that overcomes this limitation. We demonstrate that a nanobody targeting the nucleoporin Nic96 from Saccharomyces cerevisiae selectively binds newly synthesized Nic96 subcomplexes prior to its incorporation into NPCs in vivo . Importantly, nanobody-bound Nic96 is incorporated in NPCs, and expression of the nanobody does not disrupt nuclear transport, cell growth, or lifespan, nor does it show genetic interactions with known NPC assembly surveillance pathways — making it an ideal, non-perturbing tool to study NPC biogenesis in yeast. Illustrating the use of the Nic96 nanobody we report novel aspects of the early stages of assembly, including co-recruitment of Kap121 and VHH[Nic96] to putative assembly sites. In addition, we show local enrichment of newly synthesized nucleoporins on nuclear envelope proximal lipid droplets, including a specific subset of Pdr16- and Ldo16-positive lipid droplets near the nucleus-vacuole junction. When NPC assembly is delayed, association of Nic96 subcomplexes with lipid droplets increases. These findings illustrate how the strategy to pulse-label newly forming NPCs opens new avenues for dissecting the spatiotemporal regulation of NPC assembly and misassembly.