Structural Basis for NusA Stabilized Transcriptional Pausing

Abstract

Transcriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial transcription factor NusA stimulates both pausing and termination of transcription, thus playing a central role. Here, we report single-particle electron cryo-microscopy reconstructions of NusA bound to paused E. coli RNAP elongation complexes with and without a pause-enhancing hairpin in the RNA exit channel. The structures reveal four interactions between NusA and RNAP that suggest how NusA stimulates RNA folding, pausing, and termination. An asymmetric translocation intermediate of RNA and DNA converts the active site of the enzyme into an inactive state, providing a structural explanation for the inhibition of catalysis. Comparing RNAP at different stages of pausing provides insights on the dynamic nature of the process and the role of NusA as a regulatory factor.

Keywords: NusA; RNA polymerase structure; cryo-EM; his-pause; transcription; transcriptional pausing.

Graphical abstract

Figure 1

Schematics of Transcription and Cryo-EM Reconstruction of hisPEC-NusA (A) Transcription occurs in three distinct phases. During initiation bacterial RNAP binds Sigma factor to bind promoter DNA (top left). After initiation, RNAP enters the elongation phase (right). During elongation transcription factors like NusA (yellow) join. In bacteria, two pathways lead to termination (bottom). At intrinsic terminators, a hairpin in the nascent RNA destabilizes the EC. At Rho terminators, Rho ATPase causes transcript release. NusA stimulates both pathways. (B) In a post-translocated EC, the RNA 3′ end (position −1) occupies the i-site, while the i+1-site holds the +1 tDNA base and is open for the next NTP substrate to bind (left). Once the correct NTP substrate (red) is bound (top) catalysis can take place leading to a pre-translocated EC, where the RNA 3′ end now occupies the i+1-site (right). Translocation moves RNAP along the DNA by one base pair. When RNAP pauses, it enters an offline state that competes with elongation (green circle). (C) Overview of hisPEC-NusA cryo-EM structure with RNAP in gray, tDNA in orange, ntDNA in blue, RNA in black, and NusA in yellow envelope. (D) Representative cryo-EM density (blue mesh) for RNA-DNA hybrid and RNA hairpin is shown with cartoon model superimposed (tDNA orange, ntDNA blue, RNA black). (E) Representative cryo-EM density (blue mesh) for the active site revealed side chains of the bridge helix (pink) and nucleotides of tDNA (orange) and RNA (black). See also Table 1 and Figures S1, S2, and S4.

Figure 2

Conformational Changes in the hisPEC-NusA and Structural Heterogeneity of NusA (A) Superposition of hisPEC-NusA and EC (PDB ID 6ALH) (Kang et al., 2017). Difference in the RNAP clamp and shelf, β, β′ subunit pincers are shown (hisPEC-NusA clamp, light green; shelf, dark green; β, cyan; β′, pink; EC, gray). The RNAP clamp and shelf rotate by 4.8° relative to the core (left). The tips of the pincers are closer, possibly allowing interactions between the β and β′ subunits (right, β′ M1040 to L1053 identified in mutational study are highlighted). (B) Superposition of three reconstructions shows that RNAP is stable, while NusA and upstream DNA are flexible. (C) Overlay of three models of NusA orientations (from reconstruction 2, 3, 4) and NusA in antitermination complex (PDB ID 5MS0) (Said et al., 2017). NusA needs to rotate more than 40 degrees from hisPEC to antitermination complex. The rotation axis is highlighted. See also Figure S3.

Figure 3

Interactions between NusA and hisPEC (A) Surface representation of hisPEC-NusA. RNAP α1 subunit (forest), α2 subunit (lime), ω subunit (wheat), β flap tip helix (cyan), NusA (yellow), RNA hairpin (black), and upstream and downstream DNA (tDNA orange, ntDNA blue) are indicated. The four interaction points are (1) RNAP α1-CTD and NusA-AR2; (2) RNAP α2-CTD and NusA-NTD; (3) RNAP ω and NusA-KH1/KH2; (4) RNAP FTH and NusA-NTD. (B) Cartoon representation of the interaction between α2-CTD (lime), β-flap region (cyan), and NusA-NTD (yellow). Secondary structure elements and residues identified in mutational studies are labeled. (C) Comparison of NusA-NTD bound to the hisPEC (yellow) with the solution structure of NusA-NTD (gray) (PDB ID 2KWP). Dashed arrow indicates conformational changes of helix α4 as a result of binding to RNAP. (D) Cartoon representation of NusA-NTD and S1 domain (yellow) above the RNA stem (black) and modeled hairpin loop (gray). (E) Electrostatic surface potential of NusA above RNA hairpin (black) shows positively charged regions (blue). The modeled loop is shown in gray. (F) Like (E) but with the model of a terminator hairpin superimposed on the pause hairpin. A much longer terminator hairpin could be easily accommodated by NusA and would align with a positively charged surface of NusA. See also Figure S5.

Figure 4

Wild-Type RNAP and RNAP-Δα-CTD Respond Differently to NusA-NTD (A) Wild-type RNAP (RNAPwt) hisPECs were elongated with GTP in the absence (green) or presence (olive) of NusA-NTD. RNAP-Δα-CTD hisPECs were elongated with GTP in absence (pink) or presence (purple) of NusA-NTD. Assays were carried out as described in STAR Methods. Representative gels are shown. (B) The fraction of RNA29 remaining from at least three independent experiments was plotted as a function of reaction time. The rate of pause escape was determined by nonlinear regression of [U29] versus time using a double exponential decay. Double exponential decay suggested two kinetic species of RNAP with different pause half-lives (t_1/2) as seen in the table. For RNAPwt, NusA-NTD enhanced pausing for both species 3- to 4-fold, but this is not true for RNAP-Δα-CTD. Data are represented as mean ± SEM.

Figure 5

Conformational Changes in the RNA Exit Channel (A) Conformational changes of RNA exit channel from EC (gray) (PDB ID 6ALH) (Kang et al., 2017) to hisPEC-NusA (β flap, cyan; shelf, forest; clamp, lime). Dashed circle indicates clash between EC and hairpin stem (left). RNA exit channel (blue area) expands from EC to hisPEC-NusA (right). (B) Comparison of the FTH (cyan) in the hisPEC-NusA and EC structures. In ECs, the FTH is usually flexible (one possible orientation close to the RNA hairpin is shown here). Binding of NusA-NTD (yellow) to the FTH stabilizes it in a distal position to the RNA hairpin.

Figure 6

RNA-DNA Hybrid Comparison between hisPEC-NusA and EC Structures (A) Schematic illustration of polar interactions between RNAP and the RNA-DNA hybrid in pre- (top), and post-translocated states (bottom), and for the hisPEC-NusA (middle). Hybrid movement of the hisPEC-NusA was estimated using the ribose moieties of the pre- and post-translocation complex as references. Ribose sugars are shown as circles, bases, and phosphates are shown as lines. Arrows indicate polar interactions. Residues of the RNAP Switch 2 are underlined. (B) Comparison of Switch 2 (green), clamp helices (gray), lid loop (blue), and bridge helix (pink) between EC (transparent) and hisPEC-NusA (solid). A superposition of a modeled pre-translocated hybrid (gray transparent) and the hybrid of the hisPEC-NusA is also shown (color). In the hisPEC-NusA, the lid loop moved upstream providing space for the −10 base pair. Switch 2, connected to the lid loop through the clamp helices, also moved upstream but maintained contacts to the downstream tDNA and upstream RNA bases it would contact in the pre-translocated state. The bridge helix is slightly kinked. (C) Active site comparison between the post-translocated EC structure (hisPEC sequence modeled based on PDB ID 6ALH; (Kang et al., 2017) and the hisPEC-NusA. The substrate-binding site is highlighted (red). In contrast to a post-translocated state (EC, left), the next incoming tDNA base (C15) has not yet accommodated in the active site in the hisPEC-NusA because of the half-translocated hybrid. See also Figures S6 and S7.

Figure 7

Comparison with Other Paused Complexes and Model for the his-Pause (A) The shelf and clamp module rotate relative to their position in a EC (left). The extent of rotation is different for various intermediates determined in this work (PEC-NusA, hisPEC-NusA) and by Kang et al. (2018) (ePEC, hisPEC). (B) Model for RNAP entering the hairpin and NusA stabilized state at the his-pause. RNAP may convert to an ePEC when it encounters a pause sequence with a half-translocated RNA-DNA hybrid. Conformational changes in clamp and shelf module can be trapped by hairpin formation. Binding of NusA induces minimal additional changes and stabilizes paused conformation (top). Alternatively, NusA can bind an EC (resulting RNAP conformation unknown) or ePEC with half-translocated hybrid. RNAP adopts an intermediate conformation as a result of NusA binding. Hairpin formation (stimulated by NusA) leads to the final paused RNAP conformation (bottom). Active site schematics are shown (note that a pre-translocated EC was modeled based on 6ALH). See also Table S1.