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Structural basis of Rho-dependent transcription termination

Abstract

Rho is a ring-shaped hexameric ATP-dependent molecular motor. Together with the transcription elongation factor NusG, Rho mediates factor-dependent transcription termination and transcription–translation-coupling quality control in Escherichia coli1,2,3,4. Here we report the preparation of complexes that are functional in factor-dependent transcription termination from Rho, NusG, RNA polymerase (RNAP), and synthetic nucleic acid scaffolds, and we report cryogenic electron microscopy structures of the complexes. The structures show that functional factor-dependent pre-termination complexes contain a closed-ring Rho hexamer; have RNA threaded through the central channel of Rho; have 60 nucleotides of RNA interacting sequence-specifically with the exterior of Rho and 6 nucleotides of RNA interacting sequence-specifically with the central channel of Rho; have Rho oriented relative to RNAP such that ATP-dependent translocation by Rho exerts mechanical force on RNAP; and have NusG bridging Rho and RNAP. The results explain five decades of research on Rho and provide a foundation for understanding Rho’s function.

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Fig. 1: Rho-dependent termination.
Fig. 2: Structures of Rho pre-termination complexes.
Fig. 3: Protein–RNA interactions in Rho pre-termination complexes.
Fig. 4: Rho–TEC interactions and ATP-binding-site motor states in Rho pre-termination complexes.

Data availability

Cryo-EM maps have been deposited into the EMDB with the following accession codes: EMD-27928, EMD-27929, EMD-27930, EMD-27931, EMD-27932, EMD-27933, EMD-27864, EMD-27865, EMD-27897, EMD-27913, EMD-27914, EMD-27915, EMD-27916, EMD-27917 and EMD-27918. Atomic coordinates have been deposited into the PDB with the following accession codes: 8E3F, 8E3H, 8E5K, 8E5L, 8E5O, 8E5P, 8E6W, 8E6X, 8E6Z and 8E70. Specific biological materials will be made available to qualified investigators on request.

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Acknowledgements

We thank J. Berger and I. Artsimovitch for plasmids and discussion; staff at the Rutgers CryoEM and Nanoimaging Facility, the National Center for CryoEM Access and Training (supported by National Institutes of Health (NIH) grant GM129539, Simons Foundation grant SF349247 and New York state grants), and the Stanford-SLAC Cryo-EM Center (supported by NIH grant GM129541) for microscope access; and staff at the IPS CMDH Center (supported by Shanghai Municipal Science and Technology Major Project 2019SHZDZX02) for computer resources. This work was supported by NIH grant GM041376 to R.H.E.

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Authors and Affiliations

Authors

Contributions

V.M. and R.H.E. designed the experiments. V.M. prepared the proteins and nucleic acids and performed biochemical experiments. V.M., C.W., E.F. and J.T.K. performed cryo-EM data collection. V.M., C.W. and R.H.E. analysed the data. V.M., C.W. and R.H.E. prepared the figures. R.H.E. wrote the manuscript.

Corresponding authors

Correspondence to Chengyuan Wang or Richard H. Ebright.

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The authors declare no competing interests.

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Nature thanks Xiaodong Zhang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data figures and tables

Extended Data Fig. 1 Scaffold assay for Rho-dependent termination: additional data.

(a) Top, synthetic nucleic-acid scaffolds containing complementary nontemplate and template DNA strands (colours as in Fig. 1b). Bottom, RNA-release data assessing Rho-dependent termination in complexes containing NusG (left), NusG-N (center), or no NusG (right). Asterisks, released RNA products that exhibit increased levels relative to control reactions lacking Rho (lanes 6 and 7 of each subpanel). Termination is detected by an increase in released RNA products relative to control reactions lacking Rho. Assays were performed twice with consistent results. (b) As in (a), except that synthetic nucleic-acid scaffolds contain noncomplementary nontemplate and template DNA strands. The PBS ligands λtR1 rut and dC75 support efficient termination under these conditions (lanes 1 and 2 of each gel panel), but the shorter PBS ligands dC5 and dC15 do not (lanes 3 and 4 of each gel subpanel). It has been shown previously that dC15 and dC5 exhibit lower binding affinities for Rho than dC75, exhibiting half-maximally saturating concentrations 30-fold and 150-fold, respectively, the half-maximally saturating concentrations for dC7521. The PBS ligand λtR1 rut supports efficient and immediate termination under these conditions; with λtR1 rut, approximately 100 % of RNA is released before RNA extension (lane 1 of each gel panel). The PBS ligand dC75 supports efficient but less immediate termination under these conditions; with dC75, in the experiments of b, approximately 100% of RNA is released before RNA extension (lane 1 of each gel panel), but, in the experiments of a, approximately 30% of RNA is released before RNA extension, and approximately 70% of RNA is released only after RNA extension by 1 nt or 2 nt (lane 2 of each gel panel). The results indicate that both λtR1 rut and dC75 are effective PBS ligands and that λtR1 rut is a more effective PBS ligand than dC75 (see Extended Data Fig. 2).

Extended Data Fig. 2 Scaffold assay for Rho-dependent termination: additional data.

(a) Top, synthetic nucleic-acid scaffolds containing complementary nontemplate and template DNA strands (colours as in Fig. 1b; Extended Data Fig. 1). Bottom, RNA-extension data assessing Rho-dependent termination in complexes having λtR1 rut as PBS ligand (odd-numbered lanes) or dC75 as PBS ligand (even-numbered lanes) on scaffolds where the U-rich-RNA-segment length, n, is 4, 5, 6, 7, 8 or 9 codons (first, second, third, fourth, fifth, and sixth subpanels). Red asterisks, RNA products that exhibit increased levels compared to control reactions without PBS ligand; open circles, RNA products that exhibit decreased levels relative to control reactions without PBS ligand. Termination is detected by an increase in unextended and partly extended RNA products (lower and central bands), and a decrease in fully extended RNA products (top bands). Assays were performed twice with consistent results. (b) As in a, except that synthetic nucleic-acid scaffolds contain noncomplementary nontemplate and template DNA strands. The PBS ligand λtR1 rut supports efficient and immediate termination under these conditions; with λtR1 rut, approximately 100% of RNA synthesis ceases before RNA extension (lane 1 of each gel panel). The PBS ligand dC75 supports efficient but less immediate termination under these conditions; with dC75, approximately 30% of RNA synthesis ceases before RNA extension, and approximately 70% of RNA synthesis ceases only after RNA extension by 1 nt or 2 nt (lane 2 of each gel panel). The results indicate that both λtR1 rut and dC75 are effective PBS ligands and that λtR1 rut is a more effective PBS ligand than dC75 (see Extended Data Fig. 1). All six tested U-rich-RNA-segment lengths (n = 4, 5, 6, 7, 8, and 9 codons) support termination. In the experiments of a, the six tested U-rich-RNA-segment lengths support termination comparably efficiently. In the experiments of b, shorter lengths (n = 4, 5, and 6 codons) support termination more efficiently than longer lengths (n = 7, 8, and 9 codons).

Extended Data Fig. 3 Structure determination: λtR1-NusG-Rho-TEC (n = 6).

(a) Data processing scheme (Table S1). (b) Representative electron microphotograph and 2D class averages (50 nm scale bar in right subpanel). (c) Orientation distribution. (d) Fourier-shell correlation (FSC) plot. (e) EM density map coloured by local resolution (view orientation as in Fig. 2a, left). (f-i) Representative EM density (blue mesh) and fits (ribbons) for RNAP regions that interact with Rho, NusG, Rho protomer C, PBS ligand interacting with Rho protomer C, spacer RNA, and SBS ligand.

Extended Data Fig. 4 Structure determination: dC75-NusG-Rho-TEC (n = 6).

(a) Data processing scheme (Table S1). (b) Representative electron microphotograph and 2D class averages (50 nm scale bar in right subpanel). (c) Orientation distribution. (d) Fourier-shell correlation (FSC) plot. (e) EM density map coloured by local resolution (view orientation as in Fig. 2a, left). (f-i) Representative EM density (blue mesh) and fits (ribbons) for RNAP regions that interact with Rho, NusG, Rho protomer C, PBS ligand interacting with Rho protomer C, spacer RNA, and SBS ligand.

Extended Data Fig. 5 Structure determination: NusG-Rho-TEC (n = 6, 7, and 8).

(a) Data processing scheme (n = 8). (b) Representative electron microphotograph and 2D class averages (n = 8; 50 nm scale bar in right subpanel). (c) Orientation distribution (n = 8). (d) Fourier-shell correlation (FSC) plot. (e) EM density map coloured by local resolution (n = 8) (view orientation as in Fig. 2a, left). (f) EM density maps for NusG-Rho-TEC obtained using nucleic acid scaffolds with n = 6, 7, and 8 (view orientation as in Fig. 2a, left). (g-j) Representative EM density (blue mesh) and fits (ribbons) for RNAP regions that interact with Rho, NusG, Rho protomer C, spacer RNA, and SBS ligand.

Extended Data Fig. 6 Comparison of structure of λtR1-NusG-Rho-TEC to structures of Rho-TEC complexes of 30 and 31.

(a) Structure of λtR1-NusG-Rho-TEC. Rho N-terminal domain (Rho-N); cyan, and Rho C-terminal domain (Rho-C), slate blue, are shown in different colours to highlight orientation of Rho domains relative to the TEC. View orientation and other colours as in Fig. 2a, left. (b)-(c) Structures of Rho-TEC complexes of 30 (B; PDB 6Z9R) and 31 (C; PDB 6XAS; NusA omitted for clarity). View orientation that superimposes TEC atoms in b and c on TEC atoms in a. Colours as in a. The ring opening of the open-ring Rho hexamer in structures of 30 and 31 is indicated by a dashed line, and rotations and translation that relate the orientation of Rho relative to the TEC in structures of 30 and 31 to those in a are summarized below.

Extended Data Fig. 7 Protein-RNA interactions between PBS ligand and Rho PBS.

(a) Rho-(PBS ligand) interactions in dC75-NusG-Rho-TEC. View orientations and colours as in Fig. 3a, top right. (b) Rho-(PBS ligand) interactions in crystal structure of Rho hexamer interacting with six copies of oligoribonucleotide in absence of NusG and TEC (PDB 2HT1)17. View orientations and colours as in Fig. 3a, top. Oligoribonucleotides non-specifically interacting with Rho-C omitted for clarity. (c)-(d) Rho-(PBS ligand) interactions in structures of 30 (c; PDB 6Z9R) and 31 (d; PDB 6XAS). Dashed black lines, ring openings in open-ring Rho hexamers in structures of 30 and 31; black cylinders and black ribbons, RNAP or DNA structural elements of that occlude PBS-binding sites, preventing interaction with PBS ligand in structures of 30 and 31. View orientations and other colours as in Fig. 3a, top.

Extended Data Fig. 8 Protein-protein interactions between NusG-C and Rho.

(a) Rho-(NusG-C) interactions in λtR1-NusG-Rho-TEC. Colours as in Extended Data Fig. 6. (b) Superimposition of NusG-C and Rho protomer C of λtR1-NusG-Rho-TEC (coloured as in a) on structure of one NusG-C and one Rho protomer in crystal structure of Rho hexamer interacting with six copies of a NusG-C protein fragment in absence of TEC (PDB 6DUQ; grey)23. Dashed grey ribbon, disordered segment of NusG-C β8-β9 loop in crystal structure. The interaction between NusG-C and Rho protomer B (see a) is not present in the crystal structure of Rho hexamer interacting with six copies of NusG-C protein fragment23 (see b), apparently because steric clash between adjacent NusG-C protein fragments in that structure resulted in disorder of the NusG β8-β9 loop and disruption of interactions made by the NusG β8-β9 and β10-β11 loops (dashed lines in b).

Extended Data Fig. 9 Motor states of Rho hexamer.

(a) Left, superimposition of structure of λtR1-NusG-Rho-TEC (coloured as in Fig. 2a, left) on crystal structure of Rho hexamer interacting with SBS ligand and Mg-ADP-BeF3 in absence of NusG and TEC (PDB 5JJI; coloured grey)22. View orientation as in Fig. 2a, left. TEC omitted for clarity. Right, superimposition of Rho protomers A-F interacting with PBS ligand, SBS ligand, and Mg-ADP-BeF3 in structure of λtR1-NusG-Rho-TEC (coloured as in a) on crystal structure of Rho protomers A-F interacting with SBS ligand and Mg-ADP-BeF3 (PDB 5JJI; grey)22. (b) Occupancy and order of ATP-binding sites of λtR1-NusG-Rho-TEC. Figure presents EM density (blue mesh) and fit (cyan for Rho; orange, light orange, and yellow for Mg-ADP-BeF3 at high, low, and very low occupancies, respectively) for ATP binding sites between Rho protomers A and B, B and C, C and D, D and E, E and F, and F and A.

Extended Data Fig. 10 Comparison of structure of λtR1-NusG-Rho-TEC to structures of functional transcription-translation complexes NusG-TTC-B and NusA-NusG-TTC-B.

(a) Structure of λtR1-NusG-Rho-TEC. View orientation and colours as in Fig. 2a, left. (b)-(c) Structures of NusG-TTC-B (B; PDB 6XII)34,35 and NusA-NusG-TTC-B (C; PDB 6X7F)35. View orientation that superimposes TEC atoms in b and c on TEC atoms in a. Ribosome 30S subunit, yellow; ribosome 50S subunit, grey; P- and E-site tRNAs bound to ribosome, green and orange; NusA, light blue. Other colours as in a.

Extended Data Table 1 Cryo-EM data collection, refinement and validation statistics

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Supplementary Information

This file contains Supplementary Fig. 1 (unprocessed gel images) and Supplementary Table 1 (summary of cryo-EM data collection and data processing).

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Molodtsov, V., Wang, C., Firlar, E. et al. Structural basis of Rho-dependent transcription termination. Nature (2023). https://doi.org/10.1038/s41586-022-05658-1

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