Structural Characterization of the Chaetomium thermophilum TREX-2 Complex and its Interaction with the mRNA Nuclear Export Factor Mex67:Mtr2

Abstract

The TREX-2 complex integrates mRNA nuclear export into the gene expression pathway and is based on a Sac3 scaffold to which Thp1, Sem1, Sus1, and Cdc31 bind. TREX-2 also binds the mRNA nuclear export factor, Mex67:Mtr2, through the Sac3 N-terminal region (Sac3N). Here, we characterize Chaetomium thermophilum TREX-2, show that the in vitro reconstituted complex has an annular structure, and define the structural basis for interactions between Sac3, Sus1, Cdc31, and Mex67:Mtr2. Crystal structures show that the binding of C. thermophilum Sac3N to the Mex67 NTF2-like domain (Mex67(NTF2L)) is mediated primarily through phenylalanine residues present in a series of repeating sequence motifs that resemble those seen in many nucleoporins, and Mlp1 also binds Mex67:Mtr2 using a similar motif. Deletion of Sac3N generated growth and mRNA export defects in Saccharomyces cerevisiae, and we propose TREX-2 and Mlp1 function to facilitate export by concentrating mature messenger ribonucleoparticles at the nuclear pore entrance.

Figure 1

Identification and Characterization of ctTREX-2 Components (A) Schematic illustration of the structure of Sac3 from different organisms. Sac3 has an N-terminal domain of variable length (red), a conserved middle domain (blue) that interacts with Thp1 and Sem1, and a C-terminal domain (green) that contains a conserved CID motif. The N-terminal domains of human and C. thermophilum Sac3 have distinctive FG repeats (vertical lines). See also Figure S1. (B) Putative Sus1 binding domains in Sac3 sequences. (C) Repeating FG sequence motifs in ctSac3N. (D) Size-exclusion chromatography of the ctThp1:Sem1:Sac3^M complex reconstituted in vitro. (E) Tripartite ctSac3^CID:Sus1:Cdc31 complex. The CID region of ctSac3 was tagged with GST-TEV and co-expressed with Sus1 and Cdc31. GSH purification was followed by TEV cleavage and size-exclusion chromatography. Fractions were analyzed by SDS-PAGE.

Figure 2

C. thermophilum TREX-2 CID Region Complex (A) Crystal structure at 3.3-Å resolution of the C. thermophilum TREX-2 CID region in which Cdc31 (gold) and a single Sus1 chain (cyan) wrap around the Sac3 α helix (pink) that shows a distinct bend rather than the primarily straight conformation in other species (Jani et al., 2009, 2012). (B) Structure of the corresponding S. cerevisiae complex (PDB: 3FWB) with Sac3 colored red, Cdc31 yellow, and Sus1 sky blue. (C) Superposition of the C. thermophilum and S. cerevisiae complexes. (D and E) Superposition of the Cdc31 (D) and Sus1 (E) chains showing the conservation of each interaction. See also Figure S2.

Figure 3

Reconstitution of C. thermophilum TREX-2 (A) Purification of in vitro reconstituted ctTREX-2 based on Sac3 residues 1–1,191 using a 10%–30% glycerol gradient. Gradient fractions were analyzed by 4%–12% gradient SDS-PAGE gel and stained with Coomassie. (B) Electron micrograph of ctTREX-2 (from the boxed fraction in Figure 1A) negatively stained with uranyl formate. Fields contained particles that were generally 10–11 nm in diameter and which frequently had an annular appearance. (C) Class averages derived from analysis of 27,189 single particles. Many have an annular, ring-like appearance and frequently also have an additional small protuberance so that they resemble the letter “Q.” (D) SDS-PAGE of Dyn2-labeled TREX-2-DID complex purified by glycerol gradient centrifugation. (E) Class averages of electron micrographs of negatively stained Dyn2-labeled TREX-2-DID showed characteristic 20-nm rods formed by the Dyn2-bound DID label (red arrowheads in first panel) that had a 10-nm diameter ring at one end. (F) Highly schematic illustration of how an intermolecular interaction between the Sac3 N-terminal and CID regions could generate the annular TREX-2 particles observed on electron micrographs.

Figure 4

ctSac3N Interactions with ctMex67:Mtr2, ctKap104, and ctCRM1/Xpo1 (A) ctMex67:Mtr2 is recruited to the N-terminal region of ctSac3 that contains ten FG sequence motifs (residues 1–105). The Sac3 N-terminal truncations (upper right) were immobilized on GSH beads before addition of Mex67:Mtr2 or different truncations corresponding to its different functional domains (upper left). The purified proteins in lanes 2–4 were mixed with E. coli lysate (lanes 6–8) prior to addition to the immobilized baits. After incubation, washing, and elution with SDS loading buffer, the proteins were analyzed by SDS-PAGE with Coomassie staining. (B) Both the first five (residues 1–60) and second five FG motifs (residues 60–120) in ctSac3N bind to ctMex67:Mtr2, consistent with individual FG motifs having similar affinities. (C) The ctSac3N region provides a specific recruiting platform for Mex67:Mtr2. In vitro binding assay of ctMex67:Mtr2, ctKap104 and ctCrm1 pre-mixed with E. coli lysate (lanes 2, 3, and 4, respectively) to ctNup145N (lanes 5–8) and ctSac3N (residues 1–112). (D and E) Competition assay indicating that the binding sites for Sac3N and nucleoporin FG repeats on Mex67:Mtr2 overlap. The inputs are presented in (D). The same concentration of Mex67:Mtr2 complex was mixed with E. coli lysate and increasing concentration of Sac3N⁴³⁻⁹⁴ (D, lanes 4–7). The mixture was added to GST-ctSac3N¹⁻¹¹² (E), which contains ten sequential FG motifs (lanes 1–5), GST-ctNup145 (lanes 6–10), and GST (lanes 10–15) immobilized on GSH beads. Samples were incubated at 4°C for 1 hr, washed, eluted with sample buffer, and analyzed by SDS-PAGE. See also Figure S4.

Figure 5

Structure of Sac3N Peptides Bound to Mex67:Mtr2 (A) Overview of the binding sites on the NTF2L domain of FG-containing peptides derived from hsCAN (NUP214), and from C. thermophilum Sac3 residues 1–20 and 20–40 (for which density was observed only for ¹⁵QVNNPF²⁰ and ³⁰SSVFGAPA³⁷, respectively). The Sac3 peptides occupy the same hydrophobic pocket identified by Fribourg et al. (2001) occupied by a PGFGQ peptide derived from CAN/NUP214 in human NXF1, albeit with the chain direction reversed. (B) Details of the hydrophobic pocket in each case. The aromatic Phe side chain is central to the binding. (C and D) Schematic showing the interactions observed with the two Sac3 peptides. (E) Superposition of the two Sac3 peptides (pink: Sac3 1–20; blue: Sac3 20–40) and the CAN FG peptide (yellow). See also Figure S5.

Figure 6

Deletion of the N Terminus of Sac3 Causes Growth and mRNA Export Defects in S. cerevisiae (A) Serial dilutions of sac3Δ cells carrying plasmid-borne SAC3 (pRS314-SAC3) and sac3 residues140–1,301 (sac3^140−1301). Cells were plated on SDC-TRP plates and grown at 23°C, 30°C, and 37°C for 3 days. The deletion strain was transformed with empty pRS314 plasmid as a negative control. (B) In situ hybridization analysis of poly(A)⁺ mRNA in sac3Δ cells carrying plasmid-borne SAC3 and sac3^140−1301. The upper panels show poly(A)⁺ mRNA hybridized to an oligo-dT probe labeled with Cy3, whereas the lower panels show DAPI-stained DNA to identify nuclei. The fractions of cells showing nuclear accumulation of poly(A)⁺ RNA represent the means from three independent experiments in which 200 cells were scored for each. See also Figure S6.

Figure 7

Nuclear Basket Protein ctMlp1 Has Two NPFG Motifs in its C Terminus that Interact with ctMex67:Mtr2 (A) The FG motif is conserved in Pezyzomycotina and has been aligned to two repeats of the N terminus of ctSac3. (B) Different truncations of the ctMlp1 C terminus (upper panel) were immobilized on GSH beads to which E. coli lysate containing ctMex67:Mtr2 was added (lower panel). After incubation the beads were washed, eluted with SDS loading buffer, and analyzed by SDS-PAGE with Coomassie.

Figure 8

Schematic Illustration of the Interactions between TREX-2, Mex67, and NPC Components The FG motifs in Sac3N can bind to both the CID region (which contains Sus1 and Cdc31 bound to Sac3) and to the Mex67 NTF2-like domain, whereas Phe-containing motifs in nuclear basket components Mlp1 and Nup1 also bind to Mex67 and the CID region, respectively. These interactions function to localize mRNPs to the NPC nuclear face to facilitate export to the cytoplasm once processing has been completed.