Action of a minimal contractile bactericidal nanomachine

Abstract

R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics1,2,3,4. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded in a metastable state by a baseplate scaffold1,2. Fine-tuning of such nucleic acid-free protein machines for precision medicine calls for an atomic description of the entire complex and contraction mechanism, which is not available from baseplate structures of the (DNA-containing) T4 bacteriophage5. Here we report the atomic model of the complete R2 pyocin in its pre-contraction and post-contraction states, each containing 384 subunits of 11 unique atomic models of 10 gene products. Comparison of these structures suggests the following sequence of events during pyocin contraction: tail fibres trigger lateral dissociation of baseplate triplexes; the dissociation then initiates a cascade of events leading to sheath contraction; and this contraction converts chemical energy into mechanical force to drive the iron-tipped tube across the bacterial cell surface, killing the bacterium.

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Fig. 1: Cryo-EM and overall structure of pyocin in pre-contracted and post-contracted states.
Fig. 2: Architecture of the collar.
Fig. 3: Triplex expansion and lateral dimer dissociation.
Fig. 4: Baseplate transition from the pre-contracted to the post-contracted state.

Data availability

Cryo-EM maps and the associated atomic models have been deposited to the Electron Microscopy Data Bank (EMDB) and the PDB under the accession numbers EMD-20526/PDB: 6PYT (pre-contraction helical trunk), EMD-20643/PDB: 6U5B (pre-contraction baseplate), EMD-20646/PDB: 6U5H (pre-contraction hub in C3 symmetry), EMD-20644/PDB: 6U5F (pre-contraction collar), EMD-20647/PDB: 6U5J (post-contraction collar) and EMD-20648/PDB: 6U5K (post-contraction baseplate), respectively. X-ray crystal structures have been deposited to the PDB under the accession numbers 5CES (PA0618 C-terminal domain), 4S36 (PA0616 C-terminal domain) and 4S37 (full-length PA0616). All other data are available from the corresponding authors on reasonable request.

Code availability

The modified version of MotionCorr 1 is available on GitHub, licensed under GPLv3 (gepeng1983/motioncorr1exp). Relion 1.2 with helical reconstruction patch is available on GitHub, licensed under GPLv2 (gepeng1983/relion12exp). A later version of Relion (1.4) with the same patch is also available on GitHub (gepeng1983/relion14exp).

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Acknowledgements

We thank X. Yu for advice in sample purification; UCLA students K. Wang, L. Nguyen, R. Chi, N. Poweleit and P. Graybeal and Beverly Hills High School students J. Gunn and L. Wang for picking particles; UCLA student E. Brown for video editing support; and D. Martin of AvidBiotics for discussion and support throughout this project. This research was supported in part by the NIH (R01GM071940 to Z.H.Z. and R21AI085318 to D.S.), the Swiss National Science Foundation (31003A_146284 to P.G.L.), and the Schaffer Family Foundation and Kavli Endowment (to J.F.M.). P.G. was supported in part by the American Heart Association Western States Affiliates Postdoc Fellowship (13POST17340020). We acknowledge the use of resources at the Electron Imaging Center for Nanomachines (EICN; supported by UCLA and by instrumentation grants from the NIH (1S10OD018111 and 1U24GM116792) and the NSF (DBI-1338135 and DMR-1548924)) and computation resource at the Extreme Science and Engineering Discovery Environment (XSEDE grant MCB140140 to Z.H.Z.). Recharge fees for access to the EICN facility for imaging the pyocin samples were partially defrayed by an award to Z.H.Z. from the UCLA CTSI core voucher program.

Author information

Affiliations

Authors

Contributions

Z.H.Z., J.F.M., P.G. and P.G.L. conceived the project. D.S., J.A. and K.D. prepared pyocin R2 samples used for high-resolution cryo-EM. P.G. and J.A. recorded the cryo-EM data. P.G. and Z.H.Z. processed the cryo-EM data. P.G., J.A. and P.G.L. built the atomic models using cryo-EM data. P.G., P.G.L., J.A. and Z.H.Z. analysed and interpreted the models. D.S., N.S.P. and U.C. created the pyocin mutants and examined their assembly properties and phenotypes. N.S.P. designed the functional assays and circular dichroism experiments to measure the activation energy of sheath contraction. M.M.S. created the expression constructs used for crystallography. C.B. and P.G.L. determined the crystal structure of the PA0616 spike protein. S.A.B. and M.P. determined the crystal structure of the C-terminal domain of PA0618. P.G., Z.H.Z., J.A., P.G.L., D.S. and J.F.M. wrote the paper. All authors contributed to the editing of the manuscript.

Corresponding authors

Correspondence to Jeff F. Miller or Z. Hong Zhou.

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Competing interests

J.F.M. is a cofounder, equity holder and a member of the Board of Directors of Pylum Biosciences, Inc., a biotherapeutics company in South San Francisco, CA, USA. D.S. is an equity holder of the same company.

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Extended data figures and tables

Extended Data Fig. 1 Resolution assessment and model validation for the cryo-EM structures.

ResMap results for the collar and baseplate regions of the pyocin reconstructions in pre-contraction and post-contraction states. Listed in the table are model validation statistics for the collar, baseplate subunits and average. For the ‘Slices Through Input Volume’ and the ‘Slices Through ResMap Results’ panels, the units on the axes are indexes for pixels.

Extended Data Fig. 2 Model assessment of pre-contraction pyocin subunits.

For each of the collar and baseplate proteins, the cryo-EM density map is shown as semi-transparent grey superposed with its atomic model (ribbon). The close-up view of the box region shows the match of the density (wire frames) and the atomic model (sticks).

Extended Data Fig. 3 Types of sheath handshakes in pyocin.

Ribbon diagrams depicting the three types of handshake conformations in pyocin. a, Collar–sheath handshake. b, Sheath–sheath handshake. c, Sheath–sheath initiator handshake. All handshakes are composed of a four-stranded β-sheet.

Extended Data Fig. 4 Trunk transitioning into the baseplate.

a, Ribbon diagram depicting the lower portion of pyocin. The pink ribbons depict the expected positions of the sheath subunits according to the helical symmetry of the trunk. b, Schematic diagram depicting changes in the quaternary structure of the sheath subunits approaching the baseplate. The pink circles depict the expected positions of the sheath subunits according to helical symmetry of the trunk. The blue circles depict the actual positions with greater sequential helical turn, 4.4° at the last disc of the sheath.

Extended Data Fig. 5 Inspection of the baseplate.

a, Ribbon diagram of the ripcord hexamer with the tube hexamer. b, c, Ribbon diagram of the hub (b) and the spike (c) (with the chelating site of its iron ion highlighted). d, Binding of the ripcord into triplexes. e, Ribbon diagram of the baseplate with one-sixth of its sixfold symmetric part highlighted in colours as in Fig. 1, showing the relative positions of each subunit. f, Baseplate ribbon model superimposed with a blurred cryo-EM density map of the proximal region of the tail fibre.

Extended Data Fig. 6 Functional and morphogenetic implications of ripcord mutagenesis.

a, Overview of ripcord mutagenesis. b, Co-expression of the WT pyocin and mutant 626TEV with the TEV protease. Pyocin killing activity in the lysates was assessed with the help of a spot assay with the P. aeruginosa 13 s strain as prey. Both pyocin and protease expression levels are arabinose dependent, with the rate of protease production being proportional to arabinose concentration and pyocin expression reaching the maximum at the lowest concentrations of arabinose tested (0.01%). Each experiment was repeated biologically three times (also for cg). c, Representative negative staining EM images of the crude lysates shown in panel b induced with 0.01% arabinose. Despite showing killing activity in the lysates, no extended particles were found in the mutant 626TEV on EM grids. df, Temperature-dependent sheath contraction rates of the WT pyocins (d) and mutants (e and f) measured with the help of circular dichroism. g, The rate constants k(T) of WT pyocins, 626ΔWL and 626TEV fitted to the Arrhenius model k(T) = A exp(−Ea/RT) where T is the absolute temperature, A is a temperature independent constant, Ea is the activation energy and R is the ideal gas constant. The dots on the graph are individual values for three biologically independent measurements of ln k(T), and the error bars show the 95% confidence interval calculated for them.

Extended Data Fig. 7 Interactions important for triplex formation.

a, Ribbon diagram of the atomic model of the pyocin triplex. b–d, The ribbon model with the depicted side chains in the top (b), stem (c) and base (d) regions of the triplex. In panel d, the phenylalanine pi-stacking coordination between PA0618a (yellow, Phe89 and Phe125), PA0618b (red, Phe89 and Phe125) and PA0619 (blue, Phe72) is shown. e, Ribbon model diagram of the lateral dimer. f, Close-up of the ribbon model diagram of the lateral dimer, highlighting the key interacting residues (Phe253–Phe253, His257–Ser250 and Ser250–His257).

Extended Data Fig. 8 Electrostatic views of the ripcord handle.

a, Electrostatic surface diagram of the ripcord with adjacent triplexes. b, c, Electrostatic properties of the interfaces between the ripcord and triplexes 1 and 2, respectively. The colour code corresponds to positive (blue), neutral (white) and negative (red).

Extended Data Fig. 9 Comparison of related protein subunits from pyocin R2 and T4 phage.

a, Ribbon diagram of the pyocin triplex. b, Ribbon diagram of the T4 triplex equivalent with subunits marked by corresponding colour to panel a. c, Ribbon diagram of pyocin PA0618a (yellow) and T4 gp6A (grey). d, Ribbon diagram of pyocin PA0619 (blue) and T4 gp7 (grey). e, Ribbon diagram of pyocin PA0618b (red) and T4 gp6B (grey). f, Ribbon diagram of pyocin PA0627 (pink) and T4 gp53 (grey). g, Ribbon diagram of pyocin PA0617 (green) and T4 gp25 (grey).

Extended Data Table 1 Cryo-EM data statistics
Extended Data Table 2 Crystallographic data statistics
Extended Data Table 3 Pyocin protein identification by mass spectrometry

Supplementary information

41586_2020_2186_MOESM3_ESM.mp4

A flyby of the montage structure of the pre-contracted pyocin (coloured shaded surface), showing features including the groove of the sheath, collar, and the central channel.

41586_2020_2186_MOESM4_ESM.mp4

A representative α-helical region and a β-sheet region of the pre-contracted map (wire frames), fitted with its atomic model, is rotated about its helical axis.

41586_2020_2186_MOESM5_ESM.mp4

A low resolution montage model of the post-contracted pyocin (shaded surface) is rotated to highlight the post-contracted baseplate. The camera then zooms in while the full resolution model replaces the previous model, demonstrating the resolution of the reconstructions.

41586_2020_2186_MOESM6_ESM.mp4

Ribbon diagrams of individual subunits are put together to form the model of pre-contraction pyocin, with key structural features highlighted.

41586_2020_2186_MOESM7_ESM.mp4

A minimal pyocin consisting of the collar, 12 disks of sheath and tube and the baseplate is morphed between pre- and post-contraction states.

Supplementary Tables

This file contains Supplementary Table 1, a list of primers used for expression and Supplementary Table 2, a list of primers used to construct pyocin baseplate mutants.

Reporting Summary

Video 1: Overall structure of the pre-contracted pyocin

A flyby of the montage structure of the pre-contracted pyocin (coloured shaded surface), showing features including the groove of the sheath, collar, and the central channel.

Video 2: Validation of resolution for pre-contracted pyocin.

A representative α-helical region and a β-sheet region of the pre-contracted map (wire frames), fitted with its atomic model, is rotated about its helical axis.

Video 3: Overall structure of the post-contracted pyocin.

A low resolution montage model of the post-contracted pyocin (shaded surface) is rotated to highlight the post-contracted baseplate. The camera then zooms in while the full resolution model replaces the previous model, demonstrating the resolution of the reconstructions.

Video 4: Computer constellation of atomic models into a pre-contraction pyocin.

Ribbon diagrams of individual subunits are put together to form the model of pre-contraction pyocin, with key structural features highlighted.

Video 5: Morph movie between the models of pre- and post-contraction pyocin.

A minimal pyocin consisting of the collar, 12 disks of sheath and tube and the baseplate is morphed between pre- and post-contraction states.

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Ge, P., Scholl, D., Prokhorov, N.S. et al. Action of a minimal contractile bactericidal nanomachine. Nature 580, 658–662 (2020). https://doi.org/10.1038/s41586-020-2186-z

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