Colicin E1 opens its hinge to plug TolC
- University of Kansas, United States
- University of Michigan, United States
- Rutgers University, United States
- Rutgers, The State University of New Jersey, United States
Abstract
The double membrane architecture of Gram-negative bacteria forms a barrier that is impermeable to most extracellular threats. Bacteriocin proteins evolved to exploit the accessible, surface-exposed proteins embedded in the outer membrane to deliver cytotoxic cargo. Colicin E1 is a bacteriocin produced by, and lethal to, Escherichia coli that hijacks the outer membrane proteins TolC and BtuB to enter the cell. Here we capture the colicin E1 translocation domain inside its membrane receptor, TolC, by high-resolution cryoEM to obtain the first reported structure of a bacteriocin bound to TolC. Colicin E1 binds stably to TolC as an open hinge through the TolC pore-an architectural rearrangement from colicin E1's unbound conformation. This binding is stable in live E. coli cells as indicated by single-molecule fluorescence microscopy. Finally, colicin E1 fragments binding to TolC plug the channel, inhibiting its native efflux function as an antibiotic efflux pump and heightening susceptibility to three antibiotic classes. In addition to demonstrating that these protein fragments are useful starting points for developing novel antibiotic potentiators, this method could be expanded to other colicins to inhibit other outer membrane protein functions.
Data availability
The manuscript has been deposited in BioRXiv BIORXIV/2019/692251CryoEM maps and models have been deposited with accession codes EMD-21960, EMD-21959, PDB ID 6WXI, and PDB ID 6WXH. The following data are publically available for the two structures:6WXH TolC + colE1Structure: https://files.rcsb.org/download/6WXH.cifEM map: https://ftp.wwpdb.org/pub/emdb/structures/EMD-21959/map/emd_21959.map.gzValidation report: https://files.rcsb.org/pub/pdb/validation_reports/wx/6wxh/6wxh_full_validation.pdf6WXI TolC aloneStructure: https://files.rcsb.org/download/6WXI.cifEM map: https://ftp.wwpdb.org/pub/emdb/structures/EMD-21960/map/emd_21960.map.gzValidation report: https://files.rcsb.org/pub/pdb/validation_reports/wx/6wxi/6wxi_full_validation.pdf
Article and author information
Author details
Jacqueline J Stevens
Ayotunde P Ikujuni
Virangika K Wimalasena
Funding
National Institute of General Medical Sciences (DP2GM128201)
- Joanna SG Slusky
National Institute of General Medical Sciences (P20GM113117)
- Joanna SG Slusky
National Institute of General Medical Sciences (P20GM103638)
- Joanna SG Slusky
Gordon and Betty Moore Foundation (Moore Inventor Fellowship)
- Joanna SG Slusky
National Institute of General Medical Sciences (P20 GM103418)
- S Jimmy Budiardjo
National Institute of General Medical Sciences (2K12GM063651)
- S Jimmy Budiardjo
National Institute of General Medical Sciences (R21-GM128022)
- Julie S Biteen
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Budiardjo et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Colicin E1 opens its hinge to plug TolC
eLife 11:e73297.
https://doi.org/10.7554/eLife.73297
Further reading
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Glutamine synthetases (GS) are central enzymes essential for the nitrogen metabolism across all domains of life. Consequently, they have been extensively studied for more than half a century. Based on the ATP-dependent ammonium assimilation generating glutamine, GS expression and activity are strictly regulated in all organisms. In the methanogenic archaeon Methanosarcina mazei, it has been shown that the metabolite 2-oxoglutarate (2-OG) directly induces the GS activity. Besides, modulation of the activity by interaction with small proteins (GlnK1 and sP26) has been reported. Here, we show that the strong activation of M. mazei GS (GlnA1) by 2-OG is based on the 2-OG dependent dodecamer assembly of GlnA1 by using mass photometry (MP) and single particle cryo-electron microscopy (cryo-EM) analysis of purified strep-tagged GlnA1. The dodecamer assembly from dimers occurred without any detectable intermediate oligomeric state and was not affected in the presence of GlnK1. The 2.39 Å cryo-EM structure of the dodecameric complex in the presence of 12.5 mM 2-OG demonstrated that 2-OG is binding between two monomers. Thereby, 2-OG appears to induce the dodecameric assembly in a cooperative way. Furthermore, the active site is primed by an allosteric interaction cascade caused by 2-OG-binding towards an adaption of an open active state conformation. In the presence of additional glutamine, strong feedback inhibition of GS activity was observed. Since glutamine dependent disassembly of the dodecamer was excluded by MP, feedback inhibition most likely relies on the binding of glutamine to the catalytic site. Based on our findings, we propose that under nitrogen limitation the induction of M. mazei GS into a catalytically active dodecamer is not affected by GlnK1 and crucially depends on the presence of 2-OG.
