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Jansen KB, Inns PG, Housden NG, Hopper JTS, Kaminska R, Lee S, Robinson CV, Bayley H, Kleanthous C. Bifurcated binding of the OmpF receptor underpins import of the bacteriocin colicin N into Escherichia coli. J Biol Chem 2020; 295:9147-9156. [PMID: 32398259 PMCID: PMC7335789 DOI: 10.1074/jbc.ra120.013508] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/04/2020] [Indexed: 11/14/2022] Open
Abstract
Colicins are Escherichia coli-specific bacteriocins that translocate across the outer bacterial membrane by a poorly understood mechanism. Group A colicins typically parasitize the proton-motive force-linked Tol system in the inner membrane via porins after first binding an outer membrane protein receptor. Recent studies have suggested that the pore-forming group A colicin N (ColN) instead uses lipopolysaccharide as a receptor. Contrary to this prevailing view, using diffusion-precipitation assays, native state MS, isothermal titration calorimetry, single-channel conductance measurements in planar lipid bilayers, and in vivo fluorescence imaging, we demonstrate here that ColN uses OmpF both as its receptor and translocator. This dual function is achieved by ColN having multiple distinct OmpF-binding sites, one located within its central globular domain and another within its disordered N terminus. We observed that the ColN globular domain associates with the extracellular surface of OmpF and that lipopolysaccharide (LPS) enhances this binding. Approximately 90 amino acids of ColN then translocate through the porin, enabling the ColN N terminus to localize within the lumen of an OmpF subunit from the periplasmic side of the membrane, a binding mode reminiscent of that observed for the nuclease colicin E9. We conclude that bifurcated engagement of porins is intrinsic to the import mechanism of group A colicins.
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Affiliation(s)
| | | | | | | | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sejeong Lee
- Chemistry Research laboratory, University of Oxford, Oxford, United Kingdom
| | - Carol V Robinson
- Chemistry Research laboratory, University of Oxford, Oxford, United Kingdom
| | - Hagan Bayley
- Chemistry Research laboratory, University of Oxford, Oxford, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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2
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Hahn-Löbmann S, Stephan A, Schulz S, Schneider T, Shaverskyi A, Tusé D, Giritch A, Gleba Y. Colicins and Salmocins - New Classes of Plant-Made Non-antibiotic Food Antibacterials. FRONTIERS IN PLANT SCIENCE 2019; 10:437. [PMID: 31024601 PMCID: PMC6465592 DOI: 10.3389/fpls.2019.00437] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
Recently, several plant-made recombinant proteins received favorable regulatory review as food antibacterials in the United States through the Generally Recognized As Safe (GRAS) regulatory procedure, and applications for others are pending. These food antimicrobials, along with approved biopharmaceuticals and vaccines, represent new classes of products manufactured in green plants as production hosts. We present results of new research and development and summarize regulatory, economic and business aspects of the antibacterial proteins colicins and salmocins as new food processing aids.
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Affiliation(s)
| | | | | | | | | | - Daniel Tusé
- DT/Consulting Group, Sacramento, CA, United States
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3
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On mechanisms of colicin import: the outer membrane quandary. Biochem J 2018; 475:3903-3915. [PMID: 30541793 DOI: 10.1042/bcj20180477] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/02/2018] [Accepted: 11/12/2018] [Indexed: 01/09/2023]
Abstract
Current problems in the understanding of colicin import across the Escherichia coli outer membrane (OM), involving a range of cytotoxic mechanisms, are discussed: (I) Crystal structure analysis of colicin E3 (RNAase) with bound OM vitamin B12 receptor, BtuB, and of the N-terminal translocation (T) domain of E3 and E9 (DNAase) inserted into the OM OmpF porin, provide details of the initial interaction of the colicin central receptor (R)- and N-terminal T-domain with OM receptors/translocators. (II) Features of the translocon include: (a) high-affinity (K d ≈ 10-9 M) binding of the E3 receptor-binding R-domain E3 to BtuB; (b) insertion of disordered colicin N-terminal domain into the OmpF trimer; (c) binding of the N-terminus, documented for colicin E9, to the TolB protein on the periplasmic side of OmpF. Reinsertion of the colicin N-terminus into the second of the three pores in OmpF implies a colicin anchor site on the periplasmic side of OmpF. (III) Studies on the insertion of nuclease colicins into the cytoplasmic compartment imply that translocation proceeds via the C-terminal catalytic domain, proposed here to insert through the unoccupied third pore of the OmpF trimer, consistent with in vitro occlusion of OmpF channels by the isolated E3 C-terminal domain. (IV) Discussion of channel-forming colicins focuses mainly on colicin E1 for which BtuB is receptor and the OM TolC protein the proposed translocator. The ability of TolC, part of a multidrug efflux pump, for which there is no precedent for an import function, to provide a trans-periplasmic import pathway for colicin E1, is questioned on the basis of an unfavorable hairpin conformation of colicin N-terminal peptides inserted into TolC.
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Patel DS, Re S, Wu EL, Qi Y, Klebba PE, Widmalm G, Yeom MS, Sugita Y, Im W. Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability. Biophys J 2016; 110:930-8. [PMID: 26910429 DOI: 10.1016/j.bpj.2016.01.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
The asymmetric outer membrane of Gram-negative bacteria is formed of the inner leaflet with phospholipids and the outer leaflet with lipopolysaccharides (LPS). Outer membrane protein F (OmpF) is a trimeric porin responsible for the passive transport of small molecules across the outer membrane of Escherichia coli. Here, we report the impact of different levels of heterogeneity in LPS environments on the structure and dynamics of OmpF using all-atom molecular dynamics simulations. The simulations provide insight into the flexibility and dynamics of LPS components that are highly dependent on local environments, with lipid A being the most rigid and O-antigen being the most flexible. Increased flexibility of O-antigen polysaccharides is observed in heterogeneous LPS systems, where the adjacent O-antigen repeating units are weakly interacting and thus more dynamic, compared to homogeneous LPS systems in which LPS interacts strongly with each other with limited overall flexibility due to dense packing. The model systems were validated by comparing molecular-level details of interactions between OmpF surface residues and LPS core sugars with experimental data, establishing the importance of LPS core oligosaccharides in shielding OmpF surface epitopes recognized by monoclonal antibodies. There are LPS environmental influences on the movement of bulk ions (K(+) and Cl(-)), but the ion selectivity of OmpF is mainly affected by bulk ion concentration.
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Affiliation(s)
- Dhilon S Patel
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Suyong Re
- RIKEN Theoretical Molecular Science Laboratory, Hirosawa, Wako, Saitama, Japan; RIKEN Quantitative Biology Center (QBiC), IMDA 6F, Chuo-ku, Kobe, Hyogo Prefecture, Japan; RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo Prefecture, Japan
| | - Emilia L Wu
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas
| | - Göran Widmalm
- Department of Organic Chemistry and Stockholm Center for Biomembrane Research, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information, Yuseong-gu, Daejeon, Korea
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, Hirosawa, Wako, Saitama, Japan; RIKEN Quantitative Biology Center (QBiC), IMDA 6F, Chuo-ku, Kobe, Hyogo Prefecture, Japan; RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo Prefecture, Japan
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
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Lim JA, Hong J, Kim J, Heu S, Roh E. OmpF of Pectobacterium carotovorum subsp. carotovorum Pcc3 is required for carocin D sensitivity. FEMS Microbiol Lett 2016; 363:fnw258. [PMID: 27915254 DOI: 10.1093/femsle/fnw258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/04/2016] [Accepted: 11/21/2016] [Indexed: 11/14/2022] Open
Abstract
Carocin D is a bacteriocin produced by Pectobacterium carotovorum subsp. carotovorum Pcc21. Carocin D inhibits the growth of P carotovorum subsp. carotovorum and closely related strains. Pectobacterium carotovorum subsp. carotovorum is a causative bacterium for soft rot disease and leads to severe economic losses. Bacteriocins recognize and interact with a specific membrane protein of target bacteria as a receptor. To identify the receptor responsible for carocin D recognition, mutants that underwent a phenotypic change from carocin D sensitivity to carocin D insensitivity were screened. Based on Tn5 insertions, carocin D sensitivity was dependent on expression of the outer membrane protein OmpF. The insensitivity of the mutant (Pcc3MR) to carocin D was complemented with ompF from carocin D-sensitive strains, not from carocin D-resistant strains. The selectivity between sensitive and resistant strains could be attributed to variation in OmpFs in the cell-surface-exposed regions. Based on sequence analysis and complementation assays, it appears that carocin D uses OmpF as a receptor and is translocated by the TonB system. According to previously reported translocation mechanisms of colicins, OmpF works along with the TolA system rather than the TonB system. Therefore, the current findings suggest that carocin D is imported by a unique colicin-like bacteriocin translocation system.
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Affiliation(s)
- Jeong-A Lim
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun 55365, Republic of Korea
| | - Jisoo Hong
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun 55365, Republic of Korea
| | - Jonguk Kim
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun 55365, Republic of Korea
| | - Sunggi Heu
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun 55365, Republic of Korea
| | - Eunjung Roh
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun 55365, Republic of Korea
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Ridley H, Lakey JH. Antibacterial toxin colicin N and phage protein G3p compete with TolB for a binding site on TolA. MICROBIOLOGY-SGM 2014; 161:503-15. [PMID: 25536997 PMCID: PMC4339652 DOI: 10.1099/mic.0.000024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Most colicins kill Escherichia coli cells by membrane pore formation or nuclease activity and, superficially, the mechanisms are similar: receptor binding, translocon recruitment, periplasmic receptor binding and membrane insertion. However, in detail, they employ a wide variety of molecular interactions that reveal a high degree of evolutionary diversification. Group A colicins bind to members of the TolQRAB complex in the periplasm and heterotrimeric complexes of colicin–TolA–TolB have been observed for both ColA and ColE9. ColN, the smallest and simplest pore-forming colicin, binds only to TolA and we show here that it uses the binding site normally used by TolB, effectively preventing formation of the larger complex used by other colicins. ColN binding to TolA was by β-strand addition with a KD of 1 µM compared with 40 µM for the TolA–TolB interaction. The β-strand addition and ColN activity could be abolished by single proline point mutations in TolA, which each removed one backbone hydrogen bond. By also blocking TolA–TolB binding these point mutations conferred a complete tol phenotype which destabilized the outer membrane, prevented both ColA and ColE9 activity, and abolished phage protein binding to TolA. These are the only point mutations known to have such pleiotropic effects and showed that the TolA–TolB β-strand addition is essential for Tol function. The formation of this simple binary ColN–TolA complex provided yet more evidence of a distinct translocation route for ColN and may help to explain the unique toxicity of its N-terminal domain.
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Affiliation(s)
- Helen Ridley
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jeremy H Lakey
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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Ghequire MGK, Dingemans J, Pirnay JP, De Vos D, Cornelis P, De Mot R. O serotype-independent susceptibility of Pseudomonas aeruginosa to lectin-like pyocins. Microbiologyopen 2014; 3:875-84. [PMID: 25224846 PMCID: PMC4263511 DOI: 10.1002/mbo3.210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 11/08/2022] Open
Abstract
Lectin-like bacteriocins of the LlpA family, originally identified in plant-associated bacteria, are narrow-spectrum antibacterial proteins composed of two tandemly organized monocot mannose-binding lectin (MMBL) domains. The LlpA-like bacteriocin of Pseudomonas aeruginosa C1433, pyocin L1, lacks any similarity to known P. aeruginosa bacteriocins. The initial interaction of pyocin L1 with target cells is mediated by binding to d-rhamnose, present in the common polysaccharide antigen of lipopolysaccharides (LPS), but the actual cytotoxic mechanism is unknown. In this study, we characterized the activity range of pyocin L1 and two additional L pyocins revealed by genome mining, representing two highly diverged LlpA groups in P. aeruginosa. The recombinant proteins exhibit species-specific antagonistic activities down to nanomolar concentrations against clinical and environmental P. aeruginosa strains, including several multidrug-resistant isolates. The overlap in target strain spectrum between two close homologues of the pyocin L1 group is only minimal, contrasting with the considerable spectral redundancy of LlpA proteins reported for other Pseudomonas species. No correlation was found between L pyocin susceptibility and phylogenetic relatedness of P. aeruginosa isolates. Sensitive strains were retrieved in 13 out of 15 O serotypes tested, excluding the possibility that the highly variable and immunogenic O serotype antigen of the LPS coating would represent a dominant susceptibility-discriminating factor.
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Affiliation(s)
- Maarten G K Ghequire
- Centre of Microbial and Plant Genetics, University of Leuven, 3001, Heverlee, Belgium
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8
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Kim YC, Tarr AW, Penfold CN. Colicin import into E. coli cells: a model system for insights into the import mechanisms of bacteriocins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1717-31. [PMID: 24746518 DOI: 10.1016/j.bbamcr.2014.04.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/04/2014] [Accepted: 04/06/2014] [Indexed: 01/03/2023]
Abstract
Bacteriocins are a diverse group of ribosomally synthesized protein antibiotics produced by most bacteria. They range from small lanthipeptides produced by lactic acid bacteria to much larger multi domain proteins of Gram negative bacteria such as the colicins from Escherichia coli. For activity bacteriocins must be released from the producing cell and then bind to the surface of a sensitive cell to instigate the import process leading to cell death. For over 50years, colicins have provided a working platform for elucidating the structure/function studies of bacteriocin import and modes of action. An understanding of the processes that contribute to the delivery of a colicin molecule across two lipid membranes of the cell envelope has advanced our knowledge of protein-protein interactions (PPI), protein-lipid interactions and the role of order-disorder transitions of protein domains pertinent to protein transport. In this review, we provide an overview of the arrangement of genes that controls the synthesis and release of the mature protein. We examine the uptake processes of colicins from initial binding and sequestration of binding partners to crossing of the outer membrane, and then discuss the translocation of colicins through the cell periplasm and across the inner membrane to their cytotoxic site of action. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Young Chan Kim
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK
| | - Alexander W Tarr
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK
| | - Christopher N Penfold
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK.
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