Crystallographic analysis of polypyrimidine tract-binding protein-Raver1 interactions involved in regulation of alternative splicing

Abstract

The polypyrimidine tract-binding protein (PTB) is an important regulator of alternative splicing. PTB-regulated splicing of α-tropomyosin is enhanced by Raver1, a protein with four PTB-Raver1 interacting motifs (PRIs) that bind to the helical face of the second RNA recognition motif (RRM2) in PTB. We present the crystal structures of RRM2 in complex with PRI3 and PRI4 from Raver1, which--along with structure-based mutagenesis--reveal the molecular basis of their differential binding. High-affinity binding by Raver1 PRI3 involves shape-matched apolar contacts complemented by specific hydrogen bonds, a new variant of an established mode of peptide-RRM interaction. Our results refine the sequence of the PRI motif and place important structural constraints on functional models of PTB-Raver1 interactions. Our analysis indicates that the observed Raver1-PTB interaction is a general mode of binding that applies to Raver1 complexes with PTB paralogues such as nPTB and to complexes of Raver2 with PTB.

Figure 1

Structures of Raver1 PRIs Bound to PTB RRM2 (A) Schematic diagrams of PTB, Raver1, and Raver2 showing locations of RRMs and PRIs. Residue numbers are indicated above each protein. (B) Comparison of the crystal structure of Raver1 PRI3 (green) bound to RRM2 (tan) with the NMR-restrained docking model of the PRI3 peptide (gray). The structures are shown schematically as cartoon representations; the N and C termini of the peptides are colored blue and red, respectively. (C and D) Close-up views of the interactions of (C) Raver1 PRI3 and (D) Raver1 PRI4 with PTB RRM2. The Van der Waals surface of the RRM is depicted as a semitransparent skin. All structural figures were created using PyMOL (Delano, 2002). See also Figure S1.

Figure 2

Detailed Structural Comparison of Raver1 PRI3 and PRI4 Bound to PTB RRM2 (A and B) Close-up views of PRI3 bound to RRM2. Intramolecular hydrogen bonds are shown as orange dashes; intermolecular hydrogen bonds are yellow. (C and D) Equivalent views of PRI4 bound to RRM2.

Figure 3

Effect of Mutations of Raver1 PRIs on Binding to GST-PTB (A) Pull-down assays of binding of Raver1 PRI3 mutants to GST-PTB. Left: Loading controls for ³⁵S-Met-labeled PRI3-MS2 fusion proteins containing PRI3 wild-type (WT) and the mutants P6V, P6S, and P6A (see Experimental Procedures). Right: Autoradiogram of PRI3-MS2 proteins pulled down with GST (1 μg) or GST-PTB (3 μg). (B) Pull-down assays of binding of Raver1 PRI4 mutants to GST-PTB. Left: Loading controls for ³⁵S-Met-labeled PRI4-MS2 fusion proteins. Right: GST pull-down of PRI4 constructs with GST (5 μg) or GST-PTB (15 μg). Although PRI4 constructs migrate as a doublet (as observed previously [Rideau et al., 2006]), both products of the in vitro transcription-translation reaction contain the PRI since they bind PTB with the same affinity. (C) Comparison of binding of wild-type and mutant Raver1 PRIs to GST-PTB. Left: Loading controls. Right: GST pull-down of PRI4 constructs with GST (2 μg) or GST-PTB (6 μg). (D) PRI sequences from murine Raver1 (AAP33691), murine Raver2 (NP_898845), human matrin-3 (NP_001181884), and human hnRNP-L (NM_001533). Sequences shown for Raver1 are the 20 amino peptides used in pull-down assays; the shaded box indicates the sequences included in PRI-RRM2 chimeras for structural studies. Sequence similarity and identity within the PRI core are indicated. Residues in Raver1 PRI3 and PRI4 that were tested by mutagenesis are in boldface. See also Figure S3.

Figure 4

Mutation of PTB RRM2 RNA and PRI Interacting Surfaces Impairs Activity (A) Effects of RRM2 mutations on an MS2-tethered splicing regulation assay. The Tpm1 exon 1-3-4 splicing reporter, with the PTB site downstream of exon 3 replaced by a pair of MS2 coat protein binding sites, was transfected into HeLa cells, and splicing patterns were analyzed by RT-PCR. Lane 1: reporter alone. Lane 2: reporter cotransfected with MS2 coat protein. Lanes 3-6: reporter cotransfected with MS2-PTB2L expression constructs (wild-type [WT], Y247Q, K271A, K266A/Y267A/K271A, respectively). Percent exon skipping (±SD) is shown below each lane. (B) Western blots to show equivalence of expression of MS2-PTB2L tested in panel A (anti-FLAG). Loading control, anti-actin. (C) Electrophoretic mobility shift assay of 0.2-3.2 μM recombinant PTB RRM2 wild-type (lanes 2-6), K271A (lanes 7-11), and Y247Q (lanes 12-16). Lane 1: no protein. (D) Pull-down of in vitro translated full-length Raver1 with the indicated GST-fusion proteins.

Figure 5

Comparison of the PTB-Raver1 Interaction with Other Peptide-RRM Complexes A common mode of binding is revealed by superposition of the complex of Raver1 PRI3 and PTB RRM2 with the peptide/RRM complexes of U2AF65/U2AF35 (PDB-1jmt), SF3b155/SPF45 (PDB-2peh) and eIF3j/eIF3b (PDB-2krb). PTB RRM2 is colored tan; other RRMs are colored gray. The superposition was performed for the RRM domains using PyMOL (Delano, 2002). See also Figure S4.