Lipid analysis of S.c. cells expressing ProtA-ScNdc1 (261-655), ProtA-AHNdc1-ProtA, or ProtA-ScHmg1

Nuclear pore complexes (NPCs) are embedded in the nuclear envelope and
built from ∼30 different nucleoporins (Nups) in multiple copies, and few
are integral membrane proteins. One of these transmembrane nucleoporins,
Ndc1, is thought to function in NPC assembly at the fused inner and outer
nuclear membranes. Here, we show a direct interaction of Ndc1’s
transmembrane domain with Nup120 and Nup133, members of the pore membrane
coating Y-complex. We identify an amphipathic helix in Ndc1’s C-terminal
domain binding highly curved liposomes. Upon overexpression, this
amphipathic motif is toxic and dramatically alters the intracellular
membrane organization in yeast. Ndc1’s amphipathic motif functionally
interacts with related motifs in the C-terminus of the nucleoporins Nup53
and Nup59, important for pore membrane binding and interconnecting NPC
modules. The essential function of Ndc1 can be suppressed by deleting the
amphipathic helix from Nup53. Our data indicate that nuclear membrane and
presumably NPC biogenesis depends on a balanced ratio between amphipathic
motifs in diverse nucleoporins.