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Cited by 32Advanced Electron Microscopy Techniques and ApplicationsBacteriophages and microbial interactionsBacterial Genetics and Biotechnology

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CryoEM structure of the outer membrane secretin channel pIV from the f1 filamentous bacteriophage

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Conners, Rebecca, McLaren, Mathew, Łapińska, Urszula, Sanders, Kelly, Stone, M. Rhia L., Blaskovich, Mark A. T., Pagliara, Stefano, Daum, Bertram, Rakonjac, Jasna, Gold, Vicki A. M.·2021·Nature Communications
DOI 10.1038/s41467-021-26610-3PMC PMC8563730

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Abstract

The Ff family of filamentous bacteriophages infect gram-negative bacteria, but do not cause lysis of their host cell. Instead, new virions are extruded via the phage-encoded pIV protein, which has homology with bacterial secretins. Here, we determine the structure of pIV from the f1 filamentous bacteriophage at 2.7 Å resolution by cryo-electron microscopy, the first near-atomic structure of a phage secretin. Fifteen f1 pIV subunits assemble to form a gated channel in the bacterial outer membrane, with associated soluble domains projecting into the periplasm. We model channel opening and propose a mechanism for phage egress. By single-cell microfluidics experiments, we demonstrate the potential for secretins such as pIV to be used as adjuvants to increase the uptake and efficacy of antibiotics in bacteria. Finally, we compare the f1 pIV structure to its homologues to reveal similarities and differences between phage and bacterial secretins.

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Fig. 1 f1pIV cryoEM data and atomic model. a Left, 2D class averages from Relion. A red arrow highlights a hazy area, likely resulting from protein flexibility. Right, a cross-section through the initial 3D model from Relion (generated without symmetry applied), highlighting the observed C15 symmetry (yellow arrows), displayed using IMOD72. b Final 3D reconstruction shown from left to right as top view, side view and side view sliced through the centre. c f1pIV protein structure modelled into the experimental density map shown as a top view, side view and side view sliced through the centre. A single f1pIV subunit is shown as a cyan cartoon with the remaining 14 subunits in yellow; the EM map is shown in light grey. A band of 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulphonate (CHAPS) detergent molecules is shown as purple sticks.
Fig. 1 f1pIV cryoEM data and atomic model. a Left, 2D class averages from Relion. A red arrow highlights a hazy area, likely resulting from protein flexibility. Right, a cross-section through the initial 3D model from Relion (generated without symmetry applied), highlighting the observed C15 symmetry (yellow arrows), displayed using IMOD72. b Final 3D reconstruction shown from left to right as top view, side view and side view sliced through the centre. c f1pIV protein structure modelled into the experimental density map shown as a top view, side view and side view sliced through the centre. A single f1pIV subunit is shown as a cyan cartoon with the remaining 14 subunits in yellow; the EM map is shown in light grey. A band of 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulphonate (CHAPS) detergent molecules is shown as purple sticks.CC BY · PubMed Central
Fig. 2 Structural details of f1pIV. a Domain structure and amino acid sequence of f1pIV, showing the N0 domain (dark grey), the N3 domain (blue), and the β-barrel secretin domain (light grey). The regions forming the outer β-barrel are shown in pink, and that forming the inner β-barrel in cyan. Residues highlighted in yellow in the amino acid sequence were observed in the cryoEM map. Underlined residues were confirmed to be present in the cryoEM sample by mass spectrometry analysis. b Cartoon representation of the f1pIV multimer (top and side views) with a single molecule coloured as follows: N3 domain in blue, outer β-barrel in pink, inner β-barrel in cyan, Gate 1 in orange, Gate 2 in green, and CHAPS molecules as purple sticks. c Cartoon representation of the f1pIV multimer with all chains coloured as in b. CHAPS molecules have been removed for clarity. d Residues 292–303 (incorporating part of the Gate 1 loop and the inner β-barrel) showing representative density. e The interface between the inner and outer β-barrels is lined mostly with hydrophobic residues which are shown as sticks, and coloured by atom (N in blue, O in red, S in yellow). A salt bridge is formed at the edge of this interface between conserved residues Glu 185 and Arg 337 (dashed blue line). f Inter- (blue dashed lines) and intra- (red dashed lines) subunit hydrogen bonds are formed connecting the inner and outer β-barrels. One subunit (position 1) is coloured as in b, and the neighbouring subunits (in positions 2 and 15) are shown in grey. Only mainchain hydrogen bonds are shown; images have been clipped for clarity. g Composite model of a single f1pIV subunit shown as front and side views. The structure built into the EM map is coloured as in b, with a homology model of the N0 domain in dark grey.
Fig. 2 Structural details of f1pIV. a Domain structure and amino acid sequence of f1pIV, showing the N0 domain (dark grey), the N3 domain (blue), and the β-barrel secretin domain (light grey). The regions forming the outer β-barrel are shown in pink, and that forming the inner β-barrel in cyan. Residues highlighted in yellow in the amino acid sequence were observed in the cryoEM map. Underlined residues were confirmed to be present in the cryoEM sample by mass spectrometry analysis. b Cartoon representation of the f1pIV multimer (top and side views) with a single molecule coloured as follows: N3 domain in blue, outer β-barrel in pink, inner β-barrel in cyan, Gate 1 in orange, Gate 2 in green, and CHAPS molecules as purple sticks. c Cartoon representation of the f1pIV multimer with all chains coloured as in b. CHAPS molecules have been removed for clarity. d Residues 292–303 (incorporating part of the Gate 1 loop and the inner β-barrel) showing representative density. e The interface between the inner and outer β-barrels is lined mostly with hydrophobic residues which are shown as sticks, and coloured by atom (N in blue, O in red, S in yellow). A salt bridge is formed at the edge of this interface between conserved residues Glu 185 and Arg 337 (dashed blue line). f Inter- (blue dashed lines) and intra- (red dashed lines) subunit hydrogen bonds are formed connecting the inner and outer β-barrels. One subunit (position 1) is coloured as in b, and the neighbouring subunits (in positions 2 and 15) are shown in grey. Only mainchain hydrogen bonds are shown; images have been clipped for clarity. g Composite model of a single f1pIV subunit shown as front and side views. The structure built into the EM map is coloured as in b, with a homology model of the N0 domain in dark grey.CC BY · PubMed Central
Fig. 3 Positioning of the f1pIV multimer in the E. coli outer membrane. a The f1pIV cryoEM map in side view (yellow) shows density that was unaccounted for after the atomic model had been built (purple). b The f1pIV atomic model is shown as space-filled atoms in light grey with the CHAPS shown as purple sticks. There are two bands of aromatic residues shown in yellow (aromatic girdles). The enlarged panels (blue boxes) show the two girdles in greater detail with the aromatic residues labelled. One full molecule of CHAPS, and one consisting only of the aromatic rings (CHAPS*) were modelled in to the ring of density. CHAPS is shown as purple sticks, and the f1pIV subunits are coloured as in Fig. 2b. c f1pIV atomic model shown as surface representation is coloured by hydrophobicity, ranging from the most hydrophilic areas (dark cyan), through white, to the most hydrophobic areas (orange).
Fig. 3 Positioning of the f1pIV multimer in the E. coli outer membrane. a The f1pIV cryoEM map in side view (yellow) shows density that was unaccounted for after the atomic model had been built (purple). b The f1pIV atomic model is shown as space-filled atoms in light grey with the CHAPS shown as purple sticks. There are two bands of aromatic residues shown in yellow (aromatic girdles). The enlarged panels (blue boxes) show the two girdles in greater detail with the aromatic residues labelled. One full molecule of CHAPS, and one consisting only of the aromatic rings (CHAPS*) were modelled in to the ring of density. CHAPS is shown as purple sticks, and the f1pIV subunits are coloured as in Fig. 2b. c f1pIV atomic model shown as surface representation is coloured by hydrophobicity, ranging from the most hydrophilic areas (dark cyan), through white, to the most hydrophobic areas (orange).CC BY · PubMed Central
Fig. 4 The Gate region, channel opening, and interaction with phage. a Extensive inter- (blue dashed lines) and intra- (red dashed lines) gate hydrogen bonds are formed between neighbouring subunits and within Gate 1 and Gate 2, colouring as in Fig. 2b. Only main chain hydrogen bonds are shown. b Close up to show the hydrogen bonding interactions of Arg 293 and Asn 269 in Gate 1. Arg 293 forms intra-gate hydrogen bonds with Asn 269, and inter-gate hydrogen bonds with Val 332 in Gate 2 of the neighbouring subunit. Asn 269 forms intra-gate hydrogen bonds with Arg 293 and Asn 295 in Gate 1, and two inter-gate bonds with Thr 334 from the Gate 2 loop of the neighbouring subunit. Gate 1 from subunit 1 is shown in orange and Gate 2 from subunit 15 in grey, and coloured by atom (N in blue, O in red). c Structural superimposition of a single f1pIV subunit closed state structure (pink) with f1pIV modelled in the open gate position (green), shown in front, side and back views. d Close up showing the Gate 1 (Gly 267, Gly 297) and Gate 2 (Asp 321, Asn 335) hinge residues in blue. e The closed (pink) and open (green) multimers are shown as space-fill representation in top view. f Left, structure of an fd virion (2C0W) in cartoon form. Centre and right, manual docking of the fd virion (blue space-filled representation) into the open f1pIV secretin pore (green surface representation) in side and top views respectively. g Left, electrostatic surface potential of the fd virion coloured red for negative and blue for positive. Centre and right, electrostatic surface potential of the closed (pink) and open (green) states of the f1pIV pore, coloured as per the fd virion.
Fig. 4 The Gate region, channel opening, and interaction with phage. a Extensive inter- (blue dashed lines) and intra- (red dashed lines) gate hydrogen bonds are formed between neighbouring subunits and within Gate 1 and Gate 2, colouring as in Fig. 2b. Only main chain hydrogen bonds are shown. b Close up to show the hydrogen bonding interactions of Arg 293 and Asn 269 in Gate 1. Arg 293 forms intra-gate hydrogen bonds with Asn 269, and inter-gate hydrogen bonds with Val 332 in Gate 2 of the neighbouring subunit. Asn 269 forms intra-gate hydrogen bonds with Arg 293 and Asn 295 in Gate 1, and two inter-gate bonds with Thr 334 from the Gate 2 loop of the neighbouring subunit. Gate 1 from subunit 1 is shown in orange and Gate 2 from subunit 15 in grey, and coloured by atom (N in blue, O in red). c Structural superimposition of a single f1pIV subunit closed state structure (pink) with f1pIV modelled in the open gate position (green), shown in front, side and back views. d Close up showing the Gate 1 (Gly 267, Gly 297) and Gate 2 (Asp 321, Asn 335) hinge residues in blue. e The closed (pink) and open (green) multimers are shown as space-fill representation in top view. f Left, structure of an fd virion (2C0W) in cartoon form. Centre and right, manual docking of the fd virion (blue space-filled representation) into the open f1pIV secretin pore (green surface representation) in side and top views respectively. g Left, electrostatic surface potential of the fd virion coloured red for negative and blue for positive. Centre and right, electrostatic surface potential of the closed (pink) and open (green) states of the f1pIV pore, coloured as per the fd virion.CC BY · PubMed Central
Fig. 5 Antibiotic susceptibility in E. coli expressing leaky mutants of f1pIV. a Front and side views showing all mutants20 that were leaky to both maltopentaose and deoxycholate as magenta sticks. b Front and side views showing the mutations which caused sensitivity to the antibiotics vancomycin and bacitracin as green sticks. Mutations which caused sensitivity to vancomycin only are shown as orange sticks. In parts a and b the 15-residue loop from residues G275-Q289 (labelled), which is disordered in our structure, has been modelled in for representation purposes. The position of the Ser 324 mutation to Gly (S324G), analysed in part d, is also shown. c Gate 2 loop showing the key hydrogen bonds made by Ser 324. Subunit 1 is shown in purple, with neighbouring subunits 2 and 15 in red and green respectively. The close up shows that Ser 324 forms intra-gate hydrogen bonds with Ile 333 and Ser 326 (red dashed lines), and an inter-gate hydrogen bond with Gln 328 from a neighbouring subunit (blue dashed line) (N in blue, O in red). d Top, individual E. coli cells expressing f1pIVS324G take up fluorescently labelled roxithromycin. No fluorescence change was observed for the cells expressing wild type f1pIV (f1pIVWT). Scale bar, 5 μm. Bottom, scatter graph depicting the fluorescence change for f1pIVWT and f1pIVS324G samples, confirming roxithromycin uptake in the S324G mutant. Data were analysed using an unpaired t-test with Welch’s correction. **** = p ≤ 0.0001. n = 241 biologically independent cells for f1pIVWT and n = 260 for f1pIVS324G; error bars represent standard error of the mean.
Fig. 5 Antibiotic susceptibility in E. coli expressing leaky mutants of f1pIV. a Front and side views showing all mutants20 that were leaky to both maltopentaose and deoxycholate as magenta sticks. b Front and side views showing the mutations which caused sensitivity to the antibiotics vancomycin and bacitracin as green sticks. Mutations which caused sensitivity to vancomycin only are shown as orange sticks. In parts a and b the 15-residue loop from residues G275-Q289 (labelled), which is disordered in our structure, has been modelled in for representation purposes. The position of the Ser 324 mutation to Gly (S324G), analysed in part d, is also shown. c Gate 2 loop showing the key hydrogen bonds made by Ser 324. Subunit 1 is shown in purple, with neighbouring subunits 2 and 15 in red and green respectively. The close up shows that Ser 324 forms intra-gate hydrogen bonds with Ile 333 and Ser 326 (red dashed lines), and an inter-gate hydrogen bond with Gln 328 from a neighbouring subunit (blue dashed line) (N in blue, O in red). d Top, individual E. coli cells expressing f1pIVS324G take up fluorescently labelled roxithromycin. No fluorescence change was observed for the cells expressing wild type f1pIV (f1pIVWT). Scale bar, 5 μm. Bottom, scatter graph depicting the fluorescence change for f1pIVWT and f1pIVS324G samples, confirming roxithromycin uptake in the S324G mutant. Data were analysed using an unpaired t-test with Welch’s correction. **** = p ≤ 0.0001. n = 241 biologically independent cells for f1pIVWT and n = 260 for f1pIVS324G; error bars represent standard error of the mean.CC BY · PubMed Central
Fig. 6 Structural comparison of f1pIV with a selection of different classes of bacterial secretins. Secretins are aligned at the β-barrel domain. f1pIV is shown in pink (this study:7OFH), the Type III secretin InvG from Salmonella typhimurium in sea green (6PEE), the Type II secretin GspD from E. coli K12 in yellow (Klebsiella-type, 5WQ7), the Type II secretin GspD from Vibrio cholerae in blue (Vibrio-type, 5WQ8) and the Type IV pilus secretin PilQ from Vibrio cholerae in orange (6W6M). The secretins are shown in a) as multimers (with one subunit coloured lime green). Periplasmic N domains not observed in the maps are shown as grey boxes. b Electrostatic surface potential comparison of multimers cut-through to show the inner surface inside the pore. c Structural superimposition of the selected secretin subunits (shown individually in Supplementary Fig. 9) in front (left) and side (right) views. d Sequence conservation amongst the secretin family plotted on to the f1pIV structure, calculated using Consurf and based on 100 unique homologues from the UniProt database sharing 35–100% identity.
Fig. 6 Structural comparison of f1pIV with a selection of different classes of bacterial secretins. Secretins are aligned at the β-barrel domain. f1pIV is shown in pink (this study:7OFH), the Type III secretin InvG from Salmonella typhimurium in sea green (6PEE), the Type II secretin GspD from E. coli K12 in yellow (Klebsiella-type, 5WQ7), the Type II secretin GspD from Vibrio cholerae in blue (Vibrio-type, 5WQ8) and the Type IV pilus secretin PilQ from Vibrio cholerae in orange (6W6M). The secretins are shown in a) as multimers (with one subunit coloured lime green). Periplasmic N domains not observed in the maps are shown as grey boxes. b Electrostatic surface potential comparison of multimers cut-through to show the inner surface inside the pore. c Structural superimposition of the selected secretin subunits (shown individually in Supplementary Fig. 9) in front (left) and side (right) views. d Sequence conservation amongst the secretin family plotted on to the f1pIV structure, calculated using Consurf and based on 100 unique homologues from the UniProt database sharing 35–100% identity.CC BY · PubMed Central
Fig. 7 Model for filamentous phage egress. a f1pIV with the gate in the closed state (salmon pink). The N3 (blue) and N0 (yellow) domains project into the periplasm. N0 is attached to N3 via a long linker and is flexible. b N0 (now green, activated) is bound to the cytoplasmic membrane complex of pI/pXI (purple) with pIV (orange) primed to open. c Egressing phage (blue) interacts with the N3 domain (now green, activated), triggering opening of pIV (now green, open) by rearrangement of the gate. The pVIII phage capsid was drawn using the 2C0W structure, and the pVII/pIX cap added as a cartoon.
Fig. 7 Model for filamentous phage egress. a f1pIV with the gate in the closed state (salmon pink). The N3 (blue) and N0 (yellow) domains project into the periplasm. N0 is attached to N3 via a long linker and is flexible. b N0 (now green, activated) is bound to the cytoplasmic membrane complex of pI/pXI (purple) with pIV (orange) primed to open. c Egressing phage (blue) interacts with the N3 domain (now green, activated), triggering opening of pIV (now green, open) by rearrangement of the gate. The pVIII phage capsid was drawn using the 2C0W structure, and the pVII/pIX cap added as a cartoon.CC BY · PubMed Central

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Cites

Research works printed but not linked: 70

  1. Marvin, D. A., Symmons, M. F. & Straus, S. K. Structure and assembly of filamentous bacteriophages. Prog. Biophys. Mol. Biol. 114, 80–122 (2014). · DOI
  2. Rakonjac, J. Filamentous Bacteriophages: Biology and Applications. eLS, 1–13, https://doi.org/10.1002/9780470015902.a0000777 (2012). · DOI
  3. Szot-Karpińska, K. et al. Modified filamentous bacteriophage as a scaffold for carbon nanofiber. Bioconjugate Chem. 27, 2900–2910 (2016). · DOI
  4. Mao, C. et al. Virus-based toolkit for the directed synthesis of magnetic and semiconducting nanowires. Science 303, 213–217 (2004). · DOI
  5. Nathan, C. Resisting antimicrobial resistance. Nat. Rev. Microbiol. 18, 259–260 (2020). · DOI
  6. McKenna, M. The antibiotic paradox: why companies can’t afford to create life-saving drugs. Nature 584, 338–341 (2020). · DOI
  7. Brives, C. & Pourraz, J. Phage therapy as a potential solution in the fight against AMR: obstacles and possible futures. Palgrave Commun. 6, 1–11 (2020). · DOI
  8. Hampton, H. G., Watson, B. N. J. & Fineran, P. C. The arms race between bacteria and their phage foes. Nature 577, 327–336 (2020). · DOI
  9. Rakonjac, J., Bennett, N. J., Spagnuolo, J., Gagic, D. & Russel, M. Filamentous bacteriophage: biology, phage display and nanotechnology applications. Curr. issues Mol. Biol. 13, 51–76 (2011).
  10. Riechmann, L. & Holliger, P. The C-terminal domain of TolA is the coreceptor for filamentous phage infection of E. coli. Cell 90, 351–360 (1997). · DOI
  11. Hay, I. D. & Lithgow, T. Filamentous phages: masters of a microbial sharing economy. EMBO Rep. 20, https://doi.org/10.15252/embr.201847427 (2019). · DOI
  12. Feng, J. N., Model, P. & Russel, M. A trans-envelope protein complex needed for filamentous phage assembly and export. Mol. Microbiol. 34, 745–755 (1999). · DOI
  13. Russel, M. & Kazmierczak, B. Analysis of the structure and subcellular location of filamentous phage pIV. J. Bacteriol. 175, 3998–4007 (1993). · DOI
  14. Green, E. R. & Mecsas, J. Bacterial secretion systems: an overview. Microbiol. Spectr. 4, 1–32 (2016). · DOI
  15. Filloux, A. & Voulhoux, R. Multiple structures disclose the secretins’ secrets. J. Bacteriol. 200, 1–5 (2018). · DOI
  16. Majewski, D. D., Worrall, L. J. & Strynadka, N. C. J. Secretins revealed: structural insights into the giant gated outer membrane portals of bacteria. Curr. Opin. Struct. Biol. 51, 61–72 (2018). · DOI
  17. Naskar, S., Hohl, M., Tassinari, M. & Low, H. H. The structure and mechanism of the bacterial type II secretion system. Mol. Microbiol. 115, 412–424 (2021). · DOI
  18. Opalka, N. et al. Structure of the filamentous phage pIV multimer by cryo-electron microscopy. J. Mol. Biol. 325, 461–470 (2003). · DOI
  19. Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, 1–22 (2018). · DOI
  20. Spagnuolo, J. et al. Identification of the gate regions in the primary structure of the secretin pIV. Mol. Microbiol. 76, 133–150 (2010). · DOI
  21. Chernyatina, A. A. & Low, H. H. Core architecture of a bacterial type II secretion system. Nat. Commun. 10, 1–10 (2019). · DOI
  22. Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018). · DOI
  23. Yang, J. et al. The I-TASSER suite: protein structure and function prediction. Nat. Methods 12, 7–8 (2014). · DOI · Paper page
  24. Russel, M. Protein-protein interactions during filamentous phage assembly. J. Mol. Biol. 231, 689–697 (1993). · DOI
  25. Daefler, S., Russel, M. & Model, P. Module swaps between related translocator proteins pIV(f1), pIV(IKe) and PulD: identification of a specificity domain. J. Mol. Biol. 266, 978–992 (1997). · DOI
  26. Vollmer, W. & Seligman, S. J. Architecture of peptidoglycan: more data and more models. Trends Microbiol. 18, 59–66 (2010). · DOI
  27. Chaptal, V. et al. Quantification of detergents complexed with membrane proteins. Sci. Rep. 7, 1–12 (2017). · DOI
  28. Schulz, G. E. β-barrel membrane proteins. Curr. Opin. Struct. Biol. 10, 443–447 (2000). · DOI
  29. Yan, Z., Yin, M., Xu, D., Zhu, Y. & Li, X. Structural insights into the secretin translocation channel in the type II secretion system. Nat. Struct. Mol. Biol. 24, 177–183 (2017). · DOI
  30. Hu, J. et al. T3S injectisome needle complex structures in four distinct states reveal the basis of membrane coupling and assembly. Nat. Microbiol. 4, 2010–2019 (2019). · DOI
  31. Marvin, D. A., Welsh, L. C., Symmons, M. F., Scott, W. R. P. & Straus, S. K. Molecular structure of fd (f1, M13) filamentous bacteriophage refined with respect to X-ray fibre diffraction and solid-state NMR data supports specific models of phage assembly at the bacterial membrane. J. Mol. Biol. 355, 294–309 (2006). · DOI
  32. Russel, M. Mutants at conserved positions in gene IV, a gene required for assembly and secretion of filamentous phages. Mol. Microbiol. 14, 357–369 (1994). · DOI
  33. Russel, M., Linderoth, N. A. & Šali, A. Filamentous phage assembly: Variation on a protein export theme. Gene 192, 23–32 (1997). · DOI
  34. Marciano, D. K., Russel, M. & Simon, S. M. An aqueous channel for filamentous phage export. Science 284, 1516–1519 (1999). · DOI
  35. Stone, M. R. L. et al. Fluorescent macrolide probes – synthesis and use in evaluation of bacterial resistance. RSC Chem. Biol. 1, 395–404 (2020). · DOI
  36. Bryskier, A. Roxithromycin: review of its antimicrobial activity. J. Antimicrobial Chemother. 41, 1–21 (1998). · DOI
  37. Łapińska, U., Glover, G., Capilla-Lasheras, P., Young, A. J. & Pagliara, S. Bacterial ageing in the absence of external stressors. Philos. Trans. R. Soc. B: Biol. Sci. 374, 1–13 (2019). · DOI
  38. Bamford, R. A. et al. Investigating the physiology of viable but non-culturable bacteria by microfluidics and time-lapse microscopy. BMC Biol. 15, 1–12 (2017). · DOI
  39. Cama, J. et al. Single-cell microfluidics facilitates the rapid quantification of antibiotic accumulation in Gram-negative bacteria. Lab a Chip 20, 2765–2775 (2020). · DOI
  40. Weaver, S. J. et al. CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae. Nat. Commun. 11, 1–13 (2020). · DOI · Paper page
  41. Ashkenazy, H. et al. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic acids Res. 44, W344–W350 (2016). · DOI · Paper page
  42. Linderoth, N. A., Model, P. & Russel, M. Essential role of a sodium dodecyl sulfate-resistant protein IV multimer in assembly-export of filamentous phage. J. Bacteriol. 178, 1962–1970 (1996). · DOI
  43. Feng, J. N., Russel, M. & Model, P. A permeabilized cell system that assembles filamentous bacteriophage. Proc. Natl Acad. Sci. USA 94, 4068–4073 (1997). · DOI
  44. Hu, J. et al. Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin. Nat. Commun. 9, 1–11 (2018). · DOI
  45. Worrall, L. J. et al. Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body. Nature 540, 597–601 (2016). · DOI
  46. Iannolo, G., Minenkova, O., Petruzzelli, R. & Cesareni, G. Modifying filamentous phage capsid: limits in the size of the major capsid protein. J. Mol. Biol. 248, 835–844 (1995). · DOI
  47. Yamaguchi, T. et al. Structure of the molecular bushing of the bacterial flagellar motor. Nat. Commun. 12, 4469 (2021). · DOI
  48. Davis, B. M. et al. Convergence of the secretory pathways for cholera toxin and the filamentous phage, CTXφ. Science 288, 333–335 (2000). · DOI
  49. Bille, E. et al. A chromosomally integrated bacteriophage in invasive meningococci. J. Exp. Med. 201, 1905–1913 (2005). · DOI
  50. Hay, I. D., Belousoff, M. J., Dunstan, R. A., Bamert, R. S. & Lithgow, T. Structure and membrane topography of the vibrio-type secretin complex from the type 2 secretion system of enteropathogenic Escherichia coli. J. Bacteriol. 200, 1–15 (2018). · DOI
  51. McCallum, M., Tammam, S., Rubinstein, J. L., Burrows, L. L. & Howell, P. L. CryoEM map of Pseudomonas aeruginosa PilQ enables structural characterization of TsaP. Structure 29, 457–466 (2021). · DOI
  52. Daefler, S., Guilvout, I., Hardie, K. R., Pugsley, A. P. & Russel, M. The C-terminal domain of the secretin PulD contains the binding site for its cognate chaperone, PulS, and confers PulS dependence on pIV(f1) function. Mol. Microbiol. 24, 465–475 (1997). · DOI
  53. Daefler, S. & Russel, M. The Salmonella typhimurium InvH protein is an outer membrane lipoprotein required for the proper localization of InvG. Mol. Microbiol. 28, 1367–1380 (1998). · DOI
  54. Baron, C. & Coombes, B. Targeting bacterial secretion systems: benefits of disarmament in the microcosm. Infect. Disord. - Drug Targets 7, 19–27 (2008). · DOI
  55. McShan, A. C. & De Guzman, R. N. The bacterial type III secretion system as a target for developing new antibiotics. Chem. Biol. Drug Des. 85, 30–42 (2015). · DOI
  56. Hagens, S. & Bläsi, U. Genetically modified filamentous phage as bactericidal agents: a pilot study. Lett. Appl. Microbiol. 37, 318–323 (2003). · DOI
  57. Moradpour, Z. et al. Genetically engineered phage harbouring the lethal catabolite gene activator protein gene with an inducer-independent promoter for biocontrol of Escherichia coli. FEMS Microbiol. Lett. 296, 67–71 (2009). · DOI
  58. Westwater, C. et al. Use of genetically engineered phage to deliver antimicrobial agents to bacteria: an alternative therapy for treatment of bacterial infections. Antimicrobial Agents Chemother. 47, 1301–1307 (2003). · DOI
  59. Linderoth, N. A., Simon, M. N. & Russel, M. The filamentous phage pIV multimer visualized by scanning transmission electron microscopy. Science 278, 1635–1638 (1997). · DOI
  60. Tegunov, D. & Cramer, P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods 16, 1146–1152 (2019). · DOI
  61. Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014). · DOI
  62. Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. Sect. D: Struct. Biol. 75, 861–877 (2019). · DOI · Paper page
  63. Pettersen, E. F. et al. UCSF Chimera - A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). · DOI
  64. Emsley, P. & Cowtan, K. Coot: Model-building tools for molecular graphics. Acta Crystallogr. Sect. D: Biol. Crystallogr. 60, 2126–2132 (2004). · DOI · Paper page
  65. Wood, C. et al. Collaborative computational project for electron cryo-microscopy. Acta Crystallogr. Sect. D: Biol. Crystallogr. 71, 123–126 (2015). · DOI
  66. Williams, C. J. et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018). · DOI · Paper page
  67. Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun Biol, 4 874 https://doi.org/10.1038/s42003-021-02399-1 (2021). · DOI
  68. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990). · DOI · Paper page
  69. Simossis, V. A. & Heringa, J. PRALINE: A multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res. 33, W289–W294 (2005). · DOI
  70. Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996). · DOI

Metadata

Authors
Conners, R., McLaren, M., Łapińska, U., Sanders, K., Stone, M. R. L., Blaskovich, M. A. T., Pagliara, S., Daum, B., Rakonjac, J., & Gold, V. A. M.
Affiliations
  • University of Exeter (GB)
  • The University of Queensland (AU)
  • Massey University (NZ)
Corresponding author
Gold, Vicki A. M.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2021-11-02
Volume
12
Issue
1
Pages
6316-6316
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-021-26610-3
PMC
PMC8563730
OpenAlex
W3209565305
Cited by
32
References
2
Citations by year
2025: 9 · 2024: 3 · 2023: 10 · 2022: 6 · 2021: 4
FWCI
2.41
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Massey Research Online (Massey University) (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
  • Open Research Exeter (University of Exeter) (submittedVersion, cc-by)
Funders
  • Wellcome Trust (210363/Z/18/Z)
  • RCUK | Biotechnology and Biological Sciences Research Council (BB/R008639/1, BB/V008021/1)
  • Gordon and Betty Moore Foundation (GBMF5514)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
outer membrane, channel gating, phage assembly, periplasmic domain, antibiotic adjuvants, phage-bacteria interactions
MeSH terms
Protein Structural Elements, Amino Acid Sequence, Biological Transport, Secretin, Sequence Alignment, Viral Nonstructural Proteins, Inovirus, Cryoelectron Microscopy

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