Nuclear pore basket proteins are tethered to the nuclear envelope and can regulate membrane curvature

Abstract

Nuclear pore complexes (NPCs) are selective transport channels embedded in the nuclear envelope. The cylindrical NPC core forms a protein coat lining a highly curved membrane opening and has a basket-like structure appended to the nucleoplasmic side. How NPCs interact with lipids, promoting membrane bending and NPC integrity, is poorly understood. Here we show that the NPC basket proteins Nup1 and Nup60 directly induce membrane curvature by amphipathic helix insertion into the lipid bilayer. In a cell-free system, both Nup1 and Nup60 transform spherical liposomes into highly curved membrane structures. In vivo, high levels of the Nup1/Nup60 amphipathic helices cause deformation of the yeast nuclear membrane, whereas adjacent helical regions contribute to anchoring the basket to the NPC core. Basket amphipathic helices are functionally linked to distinct transmembrane nucleoporins of the NPC core, suggesting a key contribution to the membrane remodeling events that underlie NPC assembly.

Graphical abstract

Figure 1

Basket Tethering to the NPC via the Nup1 and Nup60 N Termini (A) Nup1 and Nup60 motif organization based on secondary structure predictions and sequence conservation (https://www.predictprotein.org/). Predicted amphipathic helices (AH; yellow) and α-helical regions (HR; purple) are highlighted. Helical wheel projections (http://heliquest.ipmc.cnrs.fr/) of the Nup1 (16-27) and Nup60 (31-40) AHs. Boundaries are drawn to scale, gray boxes indicate other motifs. (B) Double-fluorescence microscopy of live nup1Δ cells expressing genomically tagged Nup188-GFP and plasmid-borne NUP1 alleles (endogenous promoter) with a C-terminal mCherry tag. Note that _NLSnup1Δ1-123 cells are frequently enlarged. NLS, SV40 large T-antigen NLS. Dashed lines mark the contour of cells. Scale bar represents 3 μm. (C) Growth analysis of the NUP1 alleles used in (B). A nup1Δ strain harboring wild-type NUP1 (URA plasmid) was transformed with wild-type NUP1, empty vector, or the indicated nup1 alleles (HIS plasmids). Growth was followed on SDC-His (loading control) and on SDC+5-fluoroorotic acid (5-FOA) plates to shuffle out the URA cover plasmid. Cells were spotted onto plates in 10-fold serial dilutions and incubated for 2 (SDC-His) or 3 days (5-FOA) at 30°C. (D) Double-fluorescence microscopy of live nup60Δ cells expressing genomically tagged Nup188-GFP and plasmid-borne NUP60 alleles with a C-terminal mCherry tag (endogenous promoter). Scale bar represents 3 μm.

Figure 2

The Nup1/Nup60 N Termini Are Sufficient to Associate with NPCs (A) A plasmid-borne NUP1 (1-123)-TAP construct (GAL promoter) was transformed into wild-type cells and tandem-affinity-purified following galactose-induced overexpression (4 hr). The calmodulin eluate was analyzed by SDS-PAGE and Coomassie staining. Assigned subunits were determined by mass spectrometry (roman numerals refer to cut-out bands, see Figure S2B). Asterisks indicate degradation products of endogenous full-length Nup1. Ssa1/Ssb1 are Hsp70-type chaperones, Kar2 is an ATPase involved in ER protein import. (B) Live imaging of NUP188-GFP nup133Δ cells expressing the indicated plasmid-borne NUP1 fragments (GAL promoter). Cells were grown in raffinose media to obtain low levels of Nup1 expression sufficient for depiction. Scale bar represents 2 μm. (C) Live imaging of wild-type and nup133Δ cells expressing the indicated NUP60 constructs (GAL promoter). As in (B), low level protein expression was achieved by growth in raffinose medium. Abnormally shaped nuclei were observed in nup133Δ cells expressing Nup60 (1-47). NLS, SV40 large T-antigen NLS. Scale bar represents 3 μm. (D) Coomassie-stained gel of a Nup60 (1-162) fragment purified and analyzed as in (A). Assigned subunits were determined by mass spectrometry (roman numerals refer to cut out bands, see Figure S2D). Asterisk indicates degradation products of the bait protein. Sse1/Ssc1/Ssa1 are chaperones. (E) Analysis of Nup60 (1-47) localization in kap123Δ NUP188-GFP cells. Cells were grown in raffinose as in (B) and (C). Also see Figure S2E. Scale bar represents 3 μm.

Figure 3

Nup1 Overproduction Induces Nuclear Membrane Deformation (A) Fluorescence imaging of cells expressing Nup188-GFP or Sec63-GFP (ER marker) and plasmid-borne Nup1 (1-123)-mCherry (GAL promoter). Induced refers to 4 hr of protein overproduction in galactose-containing medium. Black arrows indicate the site of nuclear membrane expansion; white arrows label NPC clusters. For protein expression levels, see Figure S3B. Scale bar represents 2 μm. (B) Transmission electron microscopy (TEM) of representative cells, which overproduced Nup1 (1-123)-mCherry for 2, 4, or 8 hr, respectively. N, nucleus; C, cytoplasm; E, expansion membrane; V, vacuole. White arrows label single NPCs; black arrows mark the tip of the expansion membrane (2 hr) and newly formed intranuclear membrane sheets (8 hr). Scale bar represents 1 μm. Inset shows higher magnification of aligned NPCs; scale bar represents 100 nm. (C) Live imaging of cells overexpressing the indicated Nup1 constructs for 4 hr in a NUP188-GFP background. See Figure S4B for Nup1 expression levels. Black arrows indicate expansion membrane; white arrows label NPC clusters. Note that Nup1 (1-76) overexpression in nup133Δ cells results in a similar NE phenotype, albeit with a more pronounced NPC clustering (Figure S3D). Scale bar represents 2 μm. (D) TEM analysis of the indicated Nup1 fragments after 4 hr of overproduction. White arrows label single NPCs, same nomenclature as in (B). Scale bar represents 1 μm.

Figure 4

High-Curvature Membrane Induction by Overexpressed Nup60 (A) Fluorescent imaging of cells expressing Nup188-GFP and plasmid-borne Nup60-mCherry constructs (GAL promoter). Induced refers to 4 hr of protein overproduction in galactose-containing medium. _NLSNup60 (1-47): black arrow indicates expansion membrane; white arrow indicates NPC clusters. For expression levels and toxicity, see Figure S5B and (C). Because Nup60 (48-162) was not imported into the nucleus, we added an SV40 NLS to all Nup60 constructs for comparability. Accelerated import also reduces targeting of Nup60 (1-47) to the plasma membrane (compare Figure 4A with Figure S5F left). Scale bar represents 2 μm. (B) TEM analysis of cells overproducing Nup60-mCherry constructs. _NLSNup60 (1-47): asterisk marks an intranuclear organelle of unknown origin, black arrow labels newly formed membrane sheet. _NLSNup60 (1-162): black arrows label membrane tubules in longitudinal and cross-section. N, nucleus; C, cytoplasm; E, expansion membrane; V, vacuole. Scale bar represents 500 nm. (C) Electron micrographs of _NLSNup60 (1-162) overproducing cells. Left and right images are TEM samples optimized for staining proteins or membranes, respectively. Left image shows membrane tubules in cross-section with a surrounding electron-dense coat (white arrow). Right image shows that tubules are made of a single lipid bilayer (black arrow, compare to INM/ONM). INM, inner nuclear membrane; ONM, outer nuclear membrane. Scale bar represents 100 nm.

Figure 5

Membrane Curvature Induction by Nup1 and Nup60 in a Reconstituted System (A) Coomassie-stained gel of a liposome co-sedimentation assay using Folch liposomes (0.5 mg/ml, size-filtered to 400 nm) and Strep-tagged recombinant Nup1 proteins. Liposome bound protein is pelleted upon centrifugation. S, supernatant; P, pellet. (B) In vitro liposome deformation assay showing a gallery of representative tubule shapes. Folch liposomes were mixed with purified wild-type or mutant Strep-Nup1 (1-32)-mCherry or Strep-mCherry (control) (final protein: 2.5 μM) and incubated at 22°C for 30 min prior to negative staining EM. For a protein control without liposomes, see Figure S6A. Outer diameters of liposomes and tubules are indicated. Scale bar represents 500 nm. (C) Liposome co-sedimentation assay as in (A). Recombinant wild-type and mutant 6His-Nup60 (27-47)-mCherry protein was used. (D) In vitro liposome deformation assay with 6His-Nup60 (27-47)-mCherry (final protein: 2.5 μM, 30 min incubation at 22°C) showing different types of tubules that are commonly observed by EM. For a Nup60 protein control without liposomes and further examples of tubule morphologies, see Figure S6C. Tubule diameters are indicated. Scale bar represents 500 nm. (E) Liposome co-sedimentation assay with recombinant Nup1, Nup60, and mCherry (control) proteins. Liposomes of varying sizes (0.5 mg/ml) were made by extrusion through membranes of different pore diameters (as indicated). The actual liposome diameters were determined by dynamic light scattering (Figure S6D). Pellet and supernatant fractions were analyzed by SDS-PAGE and Coomassie staining.

Figure 6

The N Terminus of Nup1 Is Required for NPC and NE Integrity (A) Double-fluorescence microscopy of cells expressing the indicated Nup1 mCherry constructs (endogenous promoter) in nup1Δ cells harboring different genomically GFP-tagged Nups. White arrows label cytoplasmically mislocalized Nup82/159. Note that some cells also contain cytoplasmic _NLSnup1Δ1-123 foci. Scale bar represents 2 μm. Appending an NLS to full-length Nup1 does not result in a similar mislocalization pattern (see Figure S7A). (B) TEM analysis of exponentially growing cells after 4hr treatment with 0.2% benzyl alcohol. The indicated Nup1 constructs (endogenous promoter) were expressed in nup1Δ cells. Inset shows higher magnification of a membrane herniation (black arrow). White arrows indicate NPCs. Scale bar represents 500 nm (100 nm for inset).

Figure 7

Functional Links between Basket and Other Lipid-Interacting Nups (A) Genetic interaction analysis. Double mutant strains harboring a wild-type NUP1 cover plasmid (URA marker) were co-transformed with the indicated NUP1 plasmids (HIS marker). Growth was followed on SDC-His (loading control) and on SDC+5-fluoroorotic acid (5-FOA) plates to shuffle out the URA cover plasmid. Cells were spotted in 10-fold serial dilutions and incubated for 2 (SDC-His) or 3 days (5-FOA) at 30°C. (B and C) A nup60Δnup1Δ mutant strain harboring a wild-type NUP1 cover plasmid (URA marker) was co-transformed with different NUP1 (HIS marker) and NUP60 plasmids (LEU marker) to yield the indicated genotypes. Growth was followed on SDC-His-Leu (loading control) and on 5-FOA plates to shuffle out the URA cover plasmid. (D) Genetic interaction analysis of the nup1Δ1-32 (HIS plasmid) / nup60Δ1-47 (LEU plasmid) mutant with the indicated Nups. Cells also contain a wild-type NUP1 cover plasmid (URA marker), which was shuffled out on 5-FOA plates (30°C). (E) Model depicting the hypothetical changes of pore membrane and NPC structure in cells lacking INM bending by Nup1/Nup60 (AH and HR). Destabilization of cytoplasmic Nups (Nup159/Nup82) and basket Nups (Nup1/Nup60/Mlps) is indicated by light colors. Membrane destabilization may result in sealed NPCs according to a mechanism proposed by (Wente and Blobel, 1993). Known lipid-interacting parts of the NPC are indicated in dark blue. For simplicity, only one bipartite N terminus representing Nup1/Nup60 is shown.