mRNA export from mammalian cell nuclei is dependent on GANP

Abstract

Bulk nuclear export of messenger ribonucleoproteins (mRNPs) through nuclear pore complexes (NPCs) is mediated by NXF1. It binds mRNPs through adaptor proteins such as ALY and SR splicing factors and mediates translocation through the central NPC transport channel via transient interactions with FG nucleoporins. Here, we show that mammalian cells require GANP (germinal center-associated nuclear protein) for efficient mRNP nuclear export and for efficient recruitment of NXF1 to NPCs. Separate regions of GANP show local homology to FG nucleoporins, the yeast mRNA export factor Sac3p, and the mammalian MCM3 acetyltransferase. GANP interacts with both NXF1 and NPCs and partitions between NPCs and the nuclear interior. GANP depletion inhibits mRNA export, with retention of mRNPs and NXF1 in punctate foci within the nucleus. The GANP N-terminal region that contains FG motifs interacts with the NXF1 FG-binding domain. Overexpression of this GANP fragment leads to nuclear accumulation of both poly(A)(+)RNA and NXF1. Treatment with transcription inhibitors redistributes GANP from NPCs into foci throughout the nucleus. These results establish GANP as an integral component of the mammalian mRNA export machinery and suggest a model whereby GANP facilitates the transfer of NXF1-containing mRNPs to NPCs.

Graphical abstract

Figure 1

GANP Combines Features Found in Nucleoporins and Components of the mRNA Export Machinery and Is Partitioned between Nuclear Pore Complexes and the Nuclear Interior (A) GANP (germinal center-associated nuclear protein) protein sequence compared to Drosophila Xmas-2, yeast Sac3p, and human Nups 153 and 214. Red bars indicate FG repeats typical of many nucleoporins. Percent identities to domains in GANP are indicated. (B) Immunofluorescence with anti-GANP (top) shows that it colocalizes with FG-repeat nucleoporins (stained with mAb414, middle) in SKOV-3 nuclei isolated with Triton X-100. Merged image with DAPI nuclear staining is shown at bottom (blue). (C) Immunofluorescence with anti-GANP on intact HCT116 cells shows that GANP is located at nuclear pore complexes (NPCs) and in the nucleus. Immunofluorescence showed negligible staining of small interfering RNA (siRNA) GANP-depleted HCT116 cells. Nuclei are indicated by DAPI staining. Scale bar represents 5 μm. Identical microscope settings were used to acquire each pair of images. (D) HCT116 cells were depleted of endogenous GANP as above and analyzed by immunoblotting for GANP and actin (loading control). Control cells were transfected with a siRNA differing from GANP siRNA by two bases. (E) Scanning analysis of GANP intensity in control siRNA-treated and GANP-depleted cells with ImageJ software. Nuclei used for scanning and the scanning axis are indicated by white lines. Pairs of nuclei of same scan width as determined by DAPI staining were used. Nuclear envelope (NE) and nuclear interior are indicated.

Figure 2

GANP Depletion Results in Nuclear Accumulation of poly(A)⁺RNA (A) Fluorescence in situ hybridization (FISH) showing nuclear accumulation of poly(A)⁺RNA in GANP-depleted cells 72 hr posttransfection. Merged image is shown in right panels. Scale bar represents 5 μm. (B) Scanning analysis of poly(A)⁺RNA intensity in control siRNA-treated and GANP-depleted cells. Pairs of cells with nuclei of same scan width as determined by DAPI staining were used for scanning, and the scanning axes are indicated by white lines. Scanning axis was chosen so as to bypass nucleoli in which poly(A)⁺RNA staining is not detected. Cytoplasm (Cyt) and nucleus are indicated. (C) Immunoblotting analysis of HCT116 cells depleted of Nup153, NXF1, and GANP. (D) FISH showing that poly(A)⁺RNA accumulates in punctate nuclear foci in GANP- and NXF1-depleted cells, but not in Nup153-depleted HCT116 cells 72 hr posttransfection. Poly(A)⁺RNA was identified with a Cy3-labeled oligo(dT) probe. Nuclei were stained with DAPI.

Figure 3

GANP Interactions with mRNA Nuclear Export Components (A) GANP interacts with nuclear poly(A)⁺RNPs. Nuclear poly(A)⁺RNA purified under nondenaturing conditions from soluble nuclear extract of HCT116 cells was analyzed by immunoblotting for associated proteins. (B) GANP interacts with NXF1 in vivo. Endogenous GANP was immunoprecipitated from nuclear extracts of HCT116 cells in the presence of RNase and blotted for GANP and NXF1. (C) NXF1 interacts with GANP in vivo. Endogenous NXF1 was immunoprecipitated from nuclear extract of HCT116 cells and blotted for GANP and NXF1. (D) GANP interacts with NXF1 through its nucleoporin homology region containing FG repeats (residues 1–313). CFP or CFP-GANP(1-313) was immunoprecipitated with GFP antibody from nuclear extracts of HCT116 cells expressing CFP or CFP-GANP(1-313) and blotted for GFP and NXF1. (E) GANP(1-313) can interact in vitro with NXF1(371-621). Recombinant GST-GANP(1-313) and His-NXF1(371-621) encoding the FG-repeat binding region of NXF1 were expressed and purified in E. coli. In vitro binding assays were performed with glutathione S-transferase (GST) alone or GST-GANP(1-313) incubated with His-NXF1(371-621) prebound to Ni-NTA agarose for 2 hr at 4°C. Resin was washed extensively and analyzed by SDS polyacrylamide gel electrophoresis and Coomassie staining. (F) GANP interacts with Nup153 and Nup358. Endogenous GANP was immunoprecipitated from cellular extract of HCT116 cells with anti-GANP antibody, mAb414 antibody, anti-Nup358 antibody, or sheep immunoglobin G (IgG) and blotted for GANP and mAb414. mAb414 recognizes Nup 358, 214, 153, and 62 (marked by arrows). (G) NXF1 localization is altered in GANP-depleted cells, but GANP localization is not altered in NXF1-depleted cells. Scanning analysis of NXF1 intensity in control siRNA-treated or GANP-depleted cells and also GANP intensity in control siRNA-treated or NXF1-depleted cells are shown. Nuclei used for scanning and the scanning axis are indicated by white lines. Pairs of nuclei of same scan width as determined by DAPI staining were used for scanning. Nuclear envelope (NE) and nuclear interior are indicated. Magnified view is shown in Figure S3.

Figure 4

Dynamic Role of GANP in the Mammalian mRNA Export Pathway (A) GANP colocalizes with NXF1. Immunofluorescence of HCT116 cells with anti-GANP and anti-NXF1, respectively, is shown. Scale bar represents 5 μm. HCT116 cells were also treated with Triton X-100 prior to fixation to remove soluble material. Scanning analysis of GANP or NXF1 intensity is also shown. Nuclear envelope (NE) and nuclear interior are indicated. (B) Treatment with transcription inhibitor DRB redistributes GANP into foci throughout the nucleus, with concomitant reduction in NPC staining. HCT116 cells were treated with RNA Pol II-specific transcription inhibitor DRB for 2 hr, and immunofluorescence was performed with anti-GANP and anti-NXF1, respectively. Scanning analysis of GANP intensity in untreated or DRB-treated HCT116 cells is also shown with the scanning axes indicated by white lines. Pairs of nuclei of same scan width were used for scanning. Nuclear envelope (NE) and nuclear interior are indicated. (C) A model of the role of GANP in mammalian mRNA export. We propose that GANP is recruited to messenger ribonucleoproteins (mRNPs) after NXF1 is bound and that it acts as a courier to collect and deliver these mRNPs to the NPC. At the NPC, FG nucleoporins displace GANP from the mRNP, freeing mRNP to pass through the NPC, facilitated by interactions between NXF1 and the FG repeats that line the channel.