Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen

Abstract

The nuclear phosphoprotein La was identified as an autoantigen in patients with systemic lupus erythematosus and Sjogren's syndrome. La binds to and protects the UUU(OH) 3' terminii of nascent RNA polymerase III transcripts from exonuclease digestion. We report the 1.85 angstroms crystal structure of the N-terminal domain of human La, consisting of La and RRM1 motifs, bound to r(U1-G2-C3-U4-G5-U6-U7-U8-U9OH). The U7-U8-U9OH 3' end, in a splayed-apart orientation, is sequestered within a basic and aromatic amino acid-lined cleft between the La and RRM1 motifs. The specificity-determining U8 residue bridges both motifs, in part through unprecedented targeting of the beta sheet edge, rather than the anticipated face, of the RRM1 motif. Our structural observations, supported by mutation studies of both La and RNA components, illustrate the principles behind RNA sequestration by a rheumatic disease autoantigen, whereby the UUU(OH) 3' ends of nascent RNA transcripts are protected during downstream processing and maturation events.

Figure 1. Structure of La NTD Bound to the r(U1-G2-C3-U4-G5-U6-U7-U8-U9) Sequence

(A) The domain architecture of the La protein. (B) The G2-C3-U4-G5-U6 segment of the 9 nt RNA forms a self-complementary duplex in the complex. (C) Ribbon and stick representation of the complex containing two La NTD domains and two 9 nt RNAs related by noncrystallographic 2-fold symmetry axis. The La (E8-R91) and RRM1 (D107-Y188) motifs are colored cyan and green, respectively, whereas the connecting linker (R92-N106) is colored gray. The two RNA strands are colored gold and magenta, with the backbone phosphorus atoms colored yellow and the nonbridging phosphate oxygens colored red. The U7-U8-U9 segment is sequestered at the interface between the La and RRM1 motifs. (D) An electrostatic view of the complex generated by using the GRASP program. The RNA is shown in a slab representation, with blue and red patches corresponding to basic and acidic segments on the protein surface. The bases on the two symmetry-related RNA strands are colored gold and magenta. (E) A stick and ribbon view of the intermolecular contacts between the U1-G2 and U6-U7-U8-U9 elements of the 9-mer RNA and La (in cyan) and RRM1 (in green) motifs of La NTD in the complex. The nucleotides of the RNA and the α helices and β strands of the protein are labeled. The U7 and U9 residues are directed toward the La motif, whereas the U8 residue is directed toward the RRM1 motif. (F) The same view as in (E) except for the protein is in a surface representation, with the same color code as in (C).

Figure 2. Overview of Protein-RNA Interactions in the Complex

(A) Simulated annealing omit map of the 3′-UUU_OH segment of the 9-mer in the complex. Electron density map (contoured at 2.5σ) calculated with a starting temperature of 5000 K and excluding UUU_OH from the model. (B) A view of the alignment of the U1 and U7-U8-U9 RNA 9-mer segments relative to the La and RRM1 motifs of the La NTD in the complex. A single intermolecular hydrogen bond was detected between Y23 on the La motif (in cyan) and N139 on the RRM1 motif (in green) across the interface between these two motifs in the complex. The figure labels the a helices and b strands within the La NTD and also highlights the bridging intermolecular hydrogen bonding contacts from U8 to both the La and RRM1 motifs. (C) A comparison between the extended conformations of the U6-U7, U7-U8, and U8-U9 steps in the complex. (D) Stereo view of the protein-RNA interface highlighting intermolecular contacts between 5′-U1-G2 and U7-U8-U9_OH 3′ ends and the La NTD. Stacking interactions between bases and aromatic residues as well as hydrogen-bonding contacts involving U8 and U9 are highlighted.

Figure 3. Details of RNA Architecture and Protein-RNA Contacts in the Complex

(A) Positioning of the O² of U7 with respect to the side chain amide of N56 of the La motif. Note stacking of the sugar ring of U9 on the aromatic ring of F55. (B) Hydrogen bonding of the O² of U8 with the side chain amide of Q20 of the La motif and the O⁴ of U8 with the backbone amide of I140 of the RRM1 motif. U8 also stacks with Y23 of the La motif. (C) Hydrogen bonding between the nonbridging phosphate oxygen linking the U8-U9 step and the backbone amide of R57 and the side chain hydroxyl of Y24, both from the La motif. (D) Hydrogen bonding between the 2′-OH and 3′-OH groups of U9 and the carboxylate oxygens of the side chain D33 of the La motif. U9 also stacks with F35 of the La motif. (E) Hydrogen bonding of the O⁴ of U1 with the side chains of R32 of the La motif and N139 of the RRM1 motif. (F) Hydrogen bonding of the 2′-OH of G2 with the side chain of Q141 of the RRM1 motif and hydrogen bonding of the nonbridging phosphate oxygen linking the G2-C3 step and the side chain of K185 of the RRM1 motif.

Figure 4. Gel Electrophoretic Mobility Shift Assays of Binding of Wild-Type and Mutant La NTD to the ³²P-labeled 9 nt 5′-UGCUG UUUU-3′ RNA

(A) Representative electrophoretic mobility gel shift assay data for binding of r(U-G-C-U-G-U-U-U-U) to La NTD point mutants. The specific La NTD point mutation under consideration is shown below each gel. Protein concentrations (nM) used are indicated above each lane and were identical for each protein construct. (B) Plots of radiolabeled RNA fraction bound as monitored by gel electrophoretic mobility shift binding assays against La NTD concentration. The polar La NTD point mutants include N56A and Q20A, whereas the aromatic point mutants include Y24A, Y24F, Y23A, and F35A. Solid lines indicate theoretical values of the best least squares analysis according to equation 1 in the Experimental Procedures section. Estimated dissociation constants for wild-type and mutant La NTD-rUGCUGUUUU 9-nt RNA complexes are listed in the boxes. Data represent mean ± standard deviation (SD) for at least two independent experiments. (C) Corresponding plots for complex formation between either wild-type or D33 single point mutants (D33E, D33A, and D33I) of La NTD and the 5′-UGCUGUUUU-3′ sequence. Data represent mean ± SD for at least two independent experiments.

Figure 5. Plots of Gel Electrophoretic Mobility Shift Competition Assays Monitoring Addition of Unlabeled 9 nt RNAs to a Complex of Either Wild-Type La NTD or D33A Mutant and ³²P-Labeled 9 nt 5′-UGCUGUUUU-3′ RNA

(A) Plots of competition assays with unlabeled competitor 9 nt RNAs, which include wild-type sequence as a control and U7C and U7A substitutions. (B) Plots of competition assays with unlabeled competitor 9 nt RNAs containing U8C and U8A substitutions. (C) Plots of competition assays with unlabeled competitor 9 nt RNAs containing U9C, U9A, and U9dT substitutions. (D) Complex contains wild-type La NTD. Plots of competition assays with unlabeled competitor 9-nt RNAs, which include the wild-type RNA sequence as a control and its U9U_m substitution. U_m stands for 2′-OmeU. (E) Complex contains D33A La NTD mutant. Plots of competition assays for the wild-type RNA sequence and its U9U_m substitution. The plots monitor a fraction of radiolabeled 9 nt wt-RNA bound to La LTD or D33A mutant against concentrations (nM) of unlabeled competitor 9 nt RNA containing either wild-type sequence, single point mutations in the 3′-UUU_OH segment, or U9U_m substitution. Solid lines plot theoretical values of the best least squares analysis according to equation (2) (Lin & Riggs, 1972). K_rel indicates the relative binding strength and is expressed as a ratio of the apparent dissociation constant (K_D) measured for the La NTD mutant 9 nt RNA complex to the K_D measured for the La NTD-wild-type RNA. Estimated K_rel values are listed in the box. The gel shift data are plotted in Figures S2 and S3. Data represent the mean ± SD for at least two independent experiments.

Figure 6. Comparison of Protein-RNA Interactions in the La NTD-RNA Complex with Those Reported for Classical RRM Motif-ssRNA and Winged-Helix Motif-DNA Duplex Complexes

(A) Protein-RNA recognition in the La NTD-9-mer RNA complex. Helix α5 within the La motif and β sheet composed of β7, β4, β6, and β5 in the RRM1 motif are colored red. (B) Protein-ssRNA recognition in the Sex-lethal protein-tra mRNA precursor complex (PDB code: 1B7F; Handa et al., 1999). The four-stranded β sheet of the first RRM of the Sex-lethal (SxL) protein, which interacts with a segment of ssRNA, is colored red. (C) Protein-DNA recognition in the heterodimeric cell cycle transcription factor E2F–DP bound to duplex DNA (PDB code: 1CF7; chains A, C, and D; Zheng et al., 1999). The α helix of the winged-helix motif of E2F domain, which interacts with a segment of duplex DNA, is colored red.