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Francis MLR, Webby MN, Housden NG, Kaminska R, Elliston E, Chinthammit B, Lukoyanova N, Kleanthous C. Porin threading drives receptor disengagement and establishes active colicin transport through Escherichia coli OmpF. EMBO J 2021; 40:e108610. [PMID: 34515361 PMCID: PMC8561637 DOI: 10.15252/embj.2021108610] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022] Open
Abstract
Bacteria deploy weapons to kill their neighbours during competition for resources and to aid survival within microbiomes. Colicins were the first such antibacterial system identified, yet how these bacteriocins cross the outer membrane (OM) of Escherichia coli is unknown. Here, by solving the structures of translocation intermediates via cryo‐EM and by imaging toxin import, we uncover the mechanism by which the Tol‐dependent nuclease colicin E9 (ColE9) crosses the bacterial OM. We show that threading of ColE9’s disordered N‐terminal domain through two pores of the trimeric porin OmpF causes the colicin to disengage from its primary receptor, BtuB, and reorganises the translocon either side of the membrane. Subsequent import of ColE9 through the lumen of a single OmpF subunit is driven by the proton‐motive force, which is delivered by the TolQ‐TolR‐TolA‐TolB assembly. Our study answers longstanding questions, such as why OmpF is a better translocator than OmpC, and reconciles the mechanisms by which both Tol‐ and Ton‐dependent bacteriocins cross the bacterial outer membrane.
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Affiliation(s)
| | - Melissa N Webby
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emma Elliston
- Department of Biochemistry, University of Oxford, Oxford, UK
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Lee S, Housden NG, Ionescu SA, Zimmer MH, Kaminska R, Kleanthous C, Bayley H. Transmembrane Epitope Delivery by Passive Protein Threading through the Pores of the OmpF Porin Trimer. J Am Chem Soc 2020; 142:12157-12166. [PMID: 32614588 PMCID: PMC7366379 DOI: 10.1021/jacs.0c02362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Trimeric porins in the outer membrane (OM) of Gram-negative bacteria are the conduits by which nutrients and antibiotics diffuse passively into cells. The narrow gateways that porins form in the OM are also exploited by bacteriocins to translocate into cells by a poorly understood process. Here, using single-channel electrical recording in planar lipid bilayers in conjunction with protein engineering, we explicate the mechanism by which the intrinsically unstructured N-terminal translocation domain (IUTD) of the endonuclease bacteriocin ColE9 is imported passively across the Escherichia coli OM through OmpF. We show that the import is dominated by weak interactions of OmpF pores with binding epitopes within the IUTD that are orientationally biased and result in the threading of over 60 amino acids through 2 subunits of OmpF. Single-molecule kinetic analysis demonstrates that the IUTD enters from the extracellular side of OmpF and translocates to the periplasm where the polypeptide chain does an about turn in order to enter a neighboring subunit, only for some of these molecules to pop out of this second subunit before finally re-entering to form a stable complex. These intimately linked transport/binding processes generate an essentially irreversible, hook-like assembly that constrains an import activating peptide epitope between two subunits of the OmpF trimer.
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Affiliation(s)
- Sejeong Lee
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | | | - Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Matthew H Zimmer
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
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Atanaskovic I, Kleanthous C. Tools and Approaches for Dissecting Protein Bacteriocin Import in Gram-Negative Bacteria. Front Microbiol 2019; 10:646. [PMID: 31001227 PMCID: PMC6455109 DOI: 10.3389/fmicb.2019.00646] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022] Open
Abstract
Bacteriocins of Gram-negative bacteria are typically multi-domain proteins that target and kill bacteria of the same or closely related species. There is increasing interest in protein bacteriocin import; from a fundamental perspective to understand how folded proteins are imported into bacteria and from an applications perspective as species-specific antibiotics to combat multidrug resistant bacteria. In order to translocate across the cell envelope and cause cell death, protein bacteriocins hijack nutrient uptake pathways. Their import is energized by parasitizing intermembrane protein complexes coupled to the proton motive force, which delivers a toxic domain into the cell. A plethora of genetic, structural, biochemical, and biophysical methods have been applied to find cell envelope components involved in bacteriocin import since their discovery almost a century ago. Here, we review the various approaches that now exist for investigating how protein bacteriocins translocate into Gram-negative bacteria and highlight areas of research that will need methodological innovations to fully understand this process. We also highlight recent studies demonstrating how bacteriocins can be used to probe organization and architecture of the Gram-negative cell envelope itself.
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Affiliation(s)
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Benoni R, Beck CM, Garza-Sánchez F, Bettati S, Mozzarelli A, Hayes CS, Campanini B. Activation of an anti-bacterial toxin by the biosynthetic enzyme CysK: mechanism of binding, interaction specificity and competition with cysteine synthase. Sci Rep 2017; 7:8817. [PMID: 28821763 PMCID: PMC5562914 DOI: 10.1038/s41598-017-09022-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) is a wide-spread mechanism of inter-bacterial competition. CDI+ bacteria deliver CdiA-CT toxins into neighboring bacteria and produce specific immunity proteins that protect against self-intoxication. The CdiA-CT toxin from uropathogenic Escherichia coli 536 is a latent tRNase that is only active when bound to the cysteine biosynthetic enzyme CysK. Remarkably, the CysK:CdiA-CT binding interaction mimics the ‘cysteine synthase’ complex of CysK:CysE. The C-terminal tails of CysE and CdiA-CT each insert into the CysK active-site cleft to anchor the respective complexes. The dissociation constant for CysK:CdiA-CT (Kd ~ 11 nM) is comparable to that of the E. coli cysteine synthase complex (Kd ~ 6 nM), and both complexes bind through a two-step mechanism with a slow isomerization phase after the initial encounter. However, the second-order rate constant for CysK:CdiA-CT binding is two orders of magnitude slower than that of the cysteine synthase complex, suggesting that CysE should outcompete the toxin for CysK occupancy. However, we find that CdiA-CT can effectively displace CysE from pre-formed cysteine synthase complexes, enabling toxin activation even in the presence of excess competing CysE. This adventitious binding, coupled with the very slow rate of CysK:CdiA-CT dissociation, ensures robust nuclease activity in target bacteria.
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Affiliation(s)
- Roberto Benoni
- Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
| | - Christina M Beck
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Stefano Bettati
- Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy.,Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy
| | - Andrea Mozzarelli
- Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy.,Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA. .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy.
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