1
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Webby MN, Oluwole AO, Pedebos C, Inns PG, Olerinyova A, Prakaash D, Housden NG, Benn G, Sun D, Hoogenboom BW, Kukura P, Mohammed S, Robinson CV, Khalid S, Kleanthous C. Lipids mediate supramolecular outer membrane protein assembly in bacteria. Sci Adv 2022; 8:eadc9566. [PMID: 36322653 PMCID: PMC9629720 DOI: 10.1126/sciadv.adc9566] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
β Barrel outer membrane proteins (OMPs) cluster into supramolecular assemblies that give function to the outer membrane (OM) of Gram-negative bacteria. How such assemblies form is unknown. Here, through photoactivatable cross-linking into the Escherichia coli OM, coupled with simulations, and biochemical and biophysical analysis, we uncover the basis for OMP clustering in vivo. OMPs are typically surrounded by an annular shell of asymmetric lipids that mediate higher-order complexes with neighboring OMPs. OMP assemblies center on the abundant porins OmpF and OmpC, against which low-abundance monomeric β barrels, such as TonB-dependent transporters, are packed. Our study reveals OMP-lipid-OMP complexes to be the basic unit of supramolecular OMP assembly that, by extending across the entire cell surface, couples the requisite multifunctionality of the OM to its stability and impermeability.
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Affiliation(s)
- Melissa N. Webby
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Abraham O. Oluwole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QZ, UK
| | - Conrado Pedebos
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Patrick G. Inns
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Anna Olerinyova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Dheeraj Prakaash
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Nicholas G. Housden
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Georgina Benn
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Dawei Sun
- Structural Biology, Genentech Inc., South San Francisco, USA
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
- Department of Physics and Astronomy, University College London, WC1E 6BT London, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Shabaz Mohammed
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3QZ, UK
- Mechanistic Proteomics, Rosalind Franklin Institute, Harwell Campus, Didcot OX11 OFA, UK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QZ, UK
| | - Syma Khalid
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
| | - Colin Kleanthous
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford OX1 3QU, UK
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2
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Mamou G, Corona F, Cohen-Khait R, Housden NG, Yeung V, Sun D, Sridhar P, Pazos M, Knowles TJ, Kleanthous C, Vollmer W. Peptidoglycan maturation controls outer membrane protein assembly. Nature 2022; 606:953-959. [PMID: 35705811 PMCID: PMC9242858 DOI: 10.1038/s41586-022-04834-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/05/2022] [Indexed: 11/12/2022]
Abstract
Linkages between the outer membrane of Gram-negative bacteria and the peptidoglycan layer are crucial for the maintenance of cellular integrity and enable survival in challenging environments1–5. The function of the outer membrane is dependent on outer membrane proteins (OMPs), which are inserted into the membrane by the β-barrel assembly machine6,7 (BAM). Growing Escherichia coli cells segregate old OMPs towards the poles by a process known as binary partitioning, the basis of which is unknown8. Here we demonstrate that peptidoglycan underpins the spatiotemporal organization of OMPs. Mature, tetrapeptide-rich peptidoglycan binds to BAM components and suppresses OMP foldase activity. Nascent peptidoglycan, which is enriched in pentapeptides and concentrated at septa9, associates with BAM poorly and has little effect on its activity, leading to preferential insertion of OMPs at division sites. The synchronization of OMP biogenesis with cell wall growth results in the binary partitioning of OMPs as cells divide. Our study reveals that Gram-negative bacteria coordinate the assembly of two major cell envelope layers by rendering OMP biogenesis responsive to peptidoglycan maturation, a potential vulnerability that could be exploited in future antibiotic design. Peptidoglycan stem peptides in the Gram-negative bacterial cell wall regulate the insertion of essential outer membrane proteins, thus representing a potential target for antibiotic design.
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Affiliation(s)
- Gideon Mamou
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford, UK
| | - Federico Corona
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ruth Cohen-Khait
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford, UK
| | - Nicholas G Housden
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford, UK
| | - Vivian Yeung
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford, UK
| | - Dawei Sun
- Structural Biology, Genentech, South San Francisco, CA, USA
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Manuel Pazos
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.,Department of Molecular Biology, Center of Molecular Biology 'Severo Ochoa' (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | | | - Colin Kleanthous
- Department of Biochemistry, South Parks Road, University of Oxford, Oxford, UK.
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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3
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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: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Carpena N, Richards K, Bello Gonzalez TDJ, Bravo-Blas A, Housden NG, Gerasimidis K, Milling SWF, Douce G, Malik DJ, Walker D. Targeted Delivery of Narrow-Spectrum Protein Antibiotics to the Lower Gastrointestinal Tract in a Murine Model of Escherichia coli Colonization. Front Microbiol 2021; 12:670535. [PMID: 34721311 PMCID: PMC8551963 DOI: 10.3389/fmicb.2021.670535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 09/21/2021] [Indexed: 12/26/2022] Open
Abstract
Bacteriocins are narrow-spectrum protein antibiotics that could potentially be used to engineer the human gut microbiota. However, technologies for targeted delivery of proteins to the lower gastrointestinal (GI) tract in preclinical animal models are currently lacking. In this work, we have developed methods for the microencapsulation of Escherichia coli targeting bacteriocins, colicin E9 and Ia, in a pH responsive formulation to allow their targeted delivery and controlled release in an in vivo murine model of E. coli colonization. Membrane emulsification was used to produce a water-in-oil emulsion with the water-soluble polymer subsequently cross-linked to produce hydrogel microcapsules. The microcapsule fabrication process allowed control of the size of the drug delivery system and a near 100% yield of the encapsulated therapeutic cargo. pH-triggered release of the encapsulated colicins was achieved using a widely available pH-responsive anionic copolymer in combination with alginate biopolymers. In vivo experiments using a murine E. coli intestinal colonization model demonstrated that oral delivery of the encapsulated colicins resulted in a significant decrease in intestinal colonization and reduction in E. coli shedding in the feces of the animals. Employing controlled release drug delivery systems such as that described here is essential to enable delivery of new protein therapeutics or other biological interventions for testing within small animal models of infection. Such approaches may have considerable value for the future development of strategies to engineer the human gut microbiota, which is central to health and disease.
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Affiliation(s)
- Nuria Carpena
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kerry Richards
- Chemical Engineering Department, Loughborough University, Loughborough, United Kingdom
| | | | - Alberto Bravo-Blas
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Konstantinos Gerasimidis
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon W. F. Milling
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gillian Douce
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Danish J. Malik
- Chemical Engineering Department, Loughborough University, Loughborough, United Kingdom
| | - Daniel Walker
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Atanaskovic I, Mosbahi K, Sharp C, Housden NG, Kaminska R, Walker D, Kleanthous C. Targeted Killing of Pseudomonas aeruginosa by Pyocin G Occurs via the Hemin Transporter Hur. J Mol Biol 2020; 432:3869-3880. [PMID: 32339530 PMCID: PMC7322526 DOI: 10.1016/j.jmb.2020.04.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 01/20/2023]
Abstract
Pseudomonas aeruginosa is a priority pathogen for the development of new antibiotics, particularly because multi-drug-resistant strains of this bacterium cause serious nosocomial infections and are the leading cause of death in cystic fibrosis patients. Pyocins, bacteriocins of P. aeruginosa, are potent and diverse protein antibiotics that are deployed during bacterial competition. Pyocins are produced by more than 90% of P. aeruginosa strains and may have utility as last resort antibiotics against this bacterium. In this study, we explore the antimicrobial activity of a newly discovered pyocin called pyocin G (PyoG). We demonstrate that PyoG has broad killing activity against a collection of clinical P. aeruginosa isolates and is active in a Galleria mellonella infection model. We go on to identify cell envelope proteins that are necessary for the import of PyoG and its killing activity. PyoG recognizes bacterial cells by binding to Hur, an outer-membrane TonB-dependent transporter. Both pyocin and Hur interact with TonB1, which in complex with ExbB-ExbD links the proton motive force generated across the inner membrane with energy-dependent pyocin translocation across the outer membrane. Inner-membrane translocation of PyoG is dependent on the conserved inner-membrane AAA+ ATPase/protease, FtsH. We also report a functional exploration of the PyoG receptor. We demonstrate that Hur can bind to hemin in vitro and that this interaction is blocked by PyoG, confirming the role of Hur in hemin acquisition.
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Affiliation(s)
- Iva Atanaskovic
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Khedidja Mosbahi
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, G12 8QQ Glasgow, UK
| | - Connor Sharp
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, UK
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Daniel Walker
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, G12 8QQ Glasgow, UK
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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7
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Behrens HM, Lowe ED, Gault J, Housden NG, Kaminska R, Weber TM, Thompson CMA, Mislin GLA, Schalk IJ, Walker D, Robinson CV, Kleanthous C. Pyocin S5 Import into Pseudomonas aeruginosa Reveals a Generic Mode of Bacteriocin Transport. mBio 2020; 11:e03230-19. [PMID: 32156826 PMCID: PMC7064778 DOI: 10.1128/mbio.03230-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/28/2020] [Indexed: 11/20/2022] Open
Abstract
Pyocin S5 (PyoS5) is a potent protein bacteriocin that eradicates the human pathogen Pseudomonas aeruginosa in animal infection models, but its import mechanism is poorly understood. Here, using crystallography, biophysical and biochemical analyses, and live-cell imaging, we define the entry process of PyoS5 and reveal links to the transport mechanisms of other bacteriocins. In addition to its C-terminal pore-forming domain, elongated PyoS5 comprises two novel tandemly repeated kinked 3-helix bundle domains that structure-based alignments identify as key import domains in other pyocins. The central domain binds the lipid-bound common polysaccharide antigen, allowing the pyocin to accumulate on the cell surface. The N-terminal domain binds the ferric pyochelin transporter FptA while its associated disordered region binds the inner membrane protein TonB1, which together drive import of the bacteriocin across the outer membrane. Finally, we identify the minimal requirements for sensitizing Escherichia coli toward PyoS5, as well as other pyocins, and suggest that a generic pathway likely underpins the import of all TonB-dependent bacteriocins across the outer membrane of Gram-negative bacteria.IMPORTANCE Bacteriocins are toxic polypeptides made by bacteria to kill their competitors, making them interesting as potential antibiotics. Here, we reveal unsuspected commonalities in bacteriocin uptake pathways, through molecular and cellular dissection of the import pathway for the pore-forming bacteriocin pyocin S5 (PyoS5), which targets Pseudomonas aeruginosa In addition to its C-terminal pore-forming domain, PyoS5 is composed of two tandemly repeated helical domains that we also identify in other pyocins. Functional analyses demonstrate that they have distinct roles in the import process. One recognizes conserved sugars projected from the surface, while the other recognizes a specific outer membrane siderophore transporter, FptA, in the case of PyoS5. Through engineering of Escherichia coli cells, we show that pyocins can be readily repurposed to kill other species. This suggests basic ground rules for the outer membrane translocation step that likely apply to many bacteriocins targeting Gram-negative bacteria.
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Affiliation(s)
- Hannah M Behrens
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Edward D Lowe
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Joseph Gault
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - T Moritz Weber
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Catriona M A Thompson
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gaëtan L A Mislin
- UMR 7242, Biotechnologie et Signalisation Cellulaire, ESBS, Illkirch, France
| | - Isabelle J Schalk
- UMR 7242, Biotechnologie et Signalisation Cellulaire, ESBS, Illkirch, France
| | - Daniel Walker
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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8
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Sharp C, Boinett C, Cain A, Housden NG, Kumar S, Turner K, Parkhill J, Kleanthous C. O-Antigen-Dependent Colicin Insensitivity of Uropathogenic Escherichia coli. J Bacteriol 2019; 201:e00545-18. [PMID: 30510143 PMCID: PMC6351738 DOI: 10.1128/jb.00545-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
The outer membrane of Gram-negative bacteria presents a significant barrier for molecules entering the cell. Nevertheless, colicins, which are antimicrobial proteins secreted by Escherichia coli, can target other E. coli cells by binding to cell surface receptor proteins and activating their import, resulting in cell death. Previous studies have documented high rates of nonspecific resistance (insensitivity) of various E. coli strains toward colicins that is independent of colicin-specific immunity and is instead associated with lipopolysaccharide (LPS) in the outer membrane. This observation poses a contradiction: why do E. coli strains have colicin-expressing plasmids, which are energetically costly to retain, if cells around them are likely to be naturally insensitive to the colicin they produce? Here, using a combination of transposon sequencing and phenotypic microarrays, we show that colicin insensitivity of uropathogenic E. coli sequence type 131 (ST131) is dependent on the production of its O-antigen but that minor changes in growth conditions render the organism sensitive toward colicins. The reintroduction of O-antigen into E. coli K-12 demonstrated that it is the density of O-antigen that is the dominant factor governing colicin insensitivity. We also show, by microscopy of fluorescently labelled colicins, that growth conditions affect the degree of occlusion by O-antigen of outer membrane receptors but not the clustered organization of receptors. The result of our study demonstrate that environmental conditions play a critical role in sensitizing E. coli toward colicins and that O-antigen in LPS is central to this role.IMPORTANCEEscherichia coli infections can be a major health burden, especially with the organism becoming increasingly resistant to "last-resort" antibiotics such as carbapenems. Although colicins are potent narrow-spectrum antimicrobials with potential as future antibiotics, high levels of naturally occurring colicin insensitivity have been documented which could limit their efficacy. We identify O-antigen-dependent colicin insensitivity in a clinically relevant uropathogenic E. coli strain and show that this insensitivity can be circumvented by minor changes to growth conditions. The results of our study suggest that colicin insensitivity among E. coli organisms has been greatly overestimated, and as a consequence, colicins could in fact be effective species-specific antimicrobials targeting pathogenic E. coli such as uropathogenic E. coli (UPEC).
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Affiliation(s)
- Connor Sharp
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Amy Cain
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Macquarie University, Sydney, Australia
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sandip Kumar
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Keith Turner
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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9
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Kumar S, Housden NG, Inns P, Kleanthous C. Imaging Organization in the Escherichia coli Outer Membrane. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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10
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Housden NG, Rassam P, Lee S, Samsudin F, Kaminska R, Sharp C, Goult JD, Francis ML, Khalid S, Bayley H, Kleanthous C. Correction to “Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm”. Biochemistry 2018; 57:5270. [PMID: 30137977 PMCID: PMC6128617 DOI: 10.1021/acs.biochem.8b00864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Housden NG, Rassam P, Lee S, Samsudin F, Kaminska R, Sharp C, Goult JD, Francis ML, Khalid S, Bayley H, Kleanthous C. Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm. Biochemistry 2018; 57:4374-4381. [PMID: 29949342 PMCID: PMC6093495 DOI: 10.1021/acs.biochem.8b00621] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Protein
bacteriocins are potent narrow spectrum antibiotics that
exploit outer membrane porins to kill bacteria by poorly understood
mechanisms. Here, we determine how colicins, bacteriocins specific
for Escherichia coli, engage the trimeric porin OmpF
to initiate toxin entry. The N-terminal ∼80 residues of the
nuclease colicin ColE9 are intrinsically unstructured and house two
OmpF binding sites (OBS1 and OBS2) that reside within the pores of
OmpF and which flank an epitope that binds periplasmic TolB. Using
a combination of molecular dynamics simulations, chemical trimerization,
isothermal titration calorimetry, fluorescence microscopy, and single
channel recording planar lipid bilayer measurements, we show that
this arrangement is achieved by OBS2 binding from the extracellular
face of OmpF, while the interaction of OBS1 occurs from the periplasmic
face of OmpF. Our study shows how the narrow pores of oligomeric porins
are exploited by colicin disordered regions for direction-specific
binding, which ensures the constrained presentation of an activating
signal within the bacterial periplasm.
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Affiliation(s)
- Nicholas G Housden
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Patrice Rassam
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Sejeong Lee
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , U.K
| | - Firdaus Samsudin
- Department of Chemistry , University of Southampton , University Road , Southampton SO17 1BJ , U.K
| | - Renata Kaminska
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Connor Sharp
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Jonathan D Goult
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Marie-Louise Francis
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Syma Khalid
- Department of Chemistry , University of Southampton , University Road , Southampton SO17 1BJ , U.K
| | - Hagan Bayley
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , U.K
| | - Colin Kleanthous
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
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12
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Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen H, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV. Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces. Angew Chem Int Ed Engl 2017; 56:14463-14468. [PMID: 28884954 PMCID: PMC5813186 DOI: 10.1002/anie.201704849] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/07/2017] [Indexed: 12/19/2022]
Abstract
Mass spectrometry (MS) applications for intact protein complexes typically require electrospray (ES) ionization and have not been achieved via direct desorption from surfaces. Desorption ES ionization (DESI) MS has however transformed the study of tissue surfaces through release and characterisation of small molecules. Motivated by the desire to screen for ligand binding to intact protein complexes we report the development of a native DESI platform. By establishing conditions that preserve non-covalent interactions we exploit the surface to capture a rapid turnover enzyme-substrate complex and to optimise detergents for membrane protein study. We demonstrate binding of lipids and drugs to membrane proteins deposited on surfaces and selectivity from a mix of related agonists for specific binding to a GPCR. Overall therefore we introduce this native DESI platform with the potential for high-throughput ligand screening of some of the most challenging drug targets including GPCRs.
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Affiliation(s)
- Stephen Ambrose
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | | | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Jieyuan Fan
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Paul White
- Department of BiochemistryUniversity of OxfordOxfordUK
| | - Hsin‐Yung Yen
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Julien Marcoux
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
- Current address: IPBSCNRS, UMR 5089205 Route de Narbonne31077ToulouseFrance
| | | | - Jonathan T. S. Hopper
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
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13
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Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen HY, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV. Inside Back Cover: Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces (Angew. Chem. Int. Ed. 46/2017). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201710562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephen Ambrose
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | | | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Jieyuan Fan
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Paul White
- Department of Biochemistry; University of Oxford; Oxford UK
| | - Hsin-Yung Yen
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Julien Marcoux
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
- Current address: IPBS; CNRS, UMR 5089; 205 Route de Narbonne 31077 Toulouse France
| | | | - Jonathan T. S. Hopper
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
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14
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Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen HY, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV. Innenrücktitelbild: Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces (Angew. Chem. 46/2017). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stephen Ambrose
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | | | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Jieyuan Fan
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Paul White
- Department of Biochemistry; University of Oxford; Oxford UK
| | - Hsin-Yung Yen
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Julien Marcoux
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
- Current address: IPBS; CNRS, UMR 5089; 205 Route de Narbonne 31077 Toulouse France
| | | | - Jonathan T. S. Hopper
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
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15
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Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen HY, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV. Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704849] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stephen Ambrose
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | | | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Jieyuan Fan
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Paul White
- Department of Biochemistry; University of Oxford; Oxford UK
| | - Hsin-Yung Yen
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Julien Marcoux
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
- Current address: IPBS; CNRS, UMR 5089; 205 Route de Narbonne 31077 Toulouse France
| | | | - Jonathan T. S. Hopper
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
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16
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Ionescu SA, Lee S, Housden NG, Kaminska R, Kleanthous C, Bayley H. Orientation of the OmpF Porin in Planar Lipid Bilayers. Chembiochem 2017; 18:554-562. [PMID: 28094462 DOI: 10.1002/cbic.201600644] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Indexed: 12/27/2022]
Abstract
The outer-membrane protein OmpF is an abundant trimeric general diffusion porin that plays a central role in the transport of antibiotics and colicins across the outer membrane of E. coli. Individual OmpF trimers in planar lipid bilayers (PLBs) show one of two current-voltage asymmetries, thus implying that insertion occurs with either the periplasmic or the extracellular end first. A method for establishing the orientation of OmpF in PLB was developed, based on targeted covalent modification with membrane-impermeant reagents of peripheral cysteine residues introduced near the periplasmic or the extracellular entrance. By correlating the results of the modification experiments with measurements of current asymmetry or the sidedness of binding of the antibiotic enrofloxacin, OmpF orientation could be quickly determined in subsequent experiments under a variety of conditions. Our work will allow the precise interpretation of past and future studies of antibiotic permeation and protein translocation through OmpF and related porins.
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Affiliation(s)
- Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Sejeong Lee
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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17
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Rassam P, Copeland NA, Birkholz O, Tóth C, Chavent M, Duncan AL, Cross SJ, Housden NG, Kaminska R, Seger U, Quinn DM, Garrod TJ, Sansom MSP, Piehler J, Baumann CG, Kleanthous C. Supramolecular assemblies underpin turnover of outer membrane proteins in bacteria. Nature 2015; 523:333-6. [PMID: 26061769 PMCID: PMC4905513 DOI: 10.1038/nature14461] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 04/08/2015] [Indexed: 12/24/2022]
Abstract
Gram-negative bacteria inhabit a broad range of ecological niches. For Escherichia coli, this includes river water as well as humans and animals where it can be both a commensal and a pathogen1–3. Intricate regulatory mechanisms ensure bacteria have the right complement of β-barrel outer membrane proteins (OMPs) to enable adaptation to a particular habitat4,5. Yet no mechanism is known for replacing OMPs in the outer membrane (OM), a biological enigma further confounded by the lack of an energy source and the high stability6 and abundance of OMPs5. Here, we uncover the process underpinning OMP turnover in E. coli and show it to be passive and binary in nature wherein old OMPs are displaced to the poles of growing cells as new OMPs take their place. Using fluorescent colicins as OMP-specific probes, in combination with ensemble and single-molecule fluorescence microscopy in vivo and in vitro, as well as molecular dynamics (MD) simulations, we established the mechanism for binary OMP partitioning. OMPs clustered to form islands of ~0.5 μm diameter where their diffusion was restricted by promiscuous interactions with other OMPs. OMP islands were distributed throughout the cell and contained the Bam complex, which catalyses the insertion of OMPs in the OM7,8. However, OMP biogenesis occurred as a gradient that was highest at mid-cell but largely absent at cell poles. The cumulative effect is to push old OMP islands towards the poles of growing cells, leading to a binary distribution when cells divide. Hence the OM of a Gram-negative bacterium is a spatially and temporally organised structure and this organisation lies at the heart of how OMPs are turned over in the membrane.
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Affiliation(s)
- Patrice Rassam
- 1] Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK [2] Department of Biology, University of York, York YO10 5DD, UK
| | | | - Oliver Birkholz
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Csaba Tóth
- Department of Biology, University of York, York YO10 5DD, UK
| | - Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Stephen J Cross
- Department of Biology, University of York, York YO10 5DD, UK
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Urban Seger
- Department of Biology, University of York, York YO10 5DD, UK
| | - Diana M Quinn
- Department of Biology, University of York, York YO10 5DD, UK
| | - Tamsin J Garrod
- Department of Biology, University of York, York YO10 5DD, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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18
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Farrance OE, Kaminska R, Housden NG, Derrington SR, Kleanthous C, Radford SE, Brockwell DJ. Investigating Protein-Protein Interaction Networks with Force Spectroscopy. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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19
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Vankemmelbeke M, Housden NG, James R, Kleanthous C, Penfold CN. Immunity protein release from a cell-bound nuclease colicin complex requires global conformational rearrangement. Microbiologyopen 2013; 2:853-61. [PMID: 24039240 PMCID: PMC3831645 DOI: 10.1002/mbo3.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 07/12/2013] [Accepted: 07/21/2013] [Indexed: 11/24/2022] Open
Abstract
Nuclease colicins bind their target receptor BtuB in the outer membrane of sensitive Escherichia coli cells in the form of a high-affinity complex with their cognate immunity proteins. The release of the immunity protein from the colicin complex is a prerequisite for cell entry of the colicin and occurs via a process that is still relatively poorly understood. We have previously shown that an energy input in the form of the cytoplasmic membrane proton motive force is required to promote immunity protein (Im9) release from the colicin E9/Im9 complex and colicin cell entry. We report here that engineering rigidity in the structured part of the colicin translocation domain via the introduction of disulfide bonds prevents immunity protein release from the colicin complex. Reduction of the disulfide bond by the addition of DTT leads to immunity protein release and resumption of activity. Similarly, the introduction of a disulfide bond in the DNase domain previously shown to abolish channel formation in planar bilayers also prevented immunity protein release. Importantly, all disulfide bonds, in the translocation as well as the DNase domain, also abolished the biological activity of the Im9-free colicin E9, the reduction of which led to a resumption of activity. Our results show, for the first time, that conformational flexibility in the structured translocation and DNase domains of a nuclease colicin is essential for immunity protein release, providing further evidence for the hypothesis that global structural rearrangement of the colicin molecule is required for disassembly of this high-affinity toxin-immunity protein complex prior to outer membrane translocation.
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Affiliation(s)
- Mireille Vankemmelbeke
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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20
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Housden NG, Hopper JT, Lukoyanova N, Rodriguez-Larrea D, Wojdyla JA, Klein A, Kaminska R, Bayley H, Saibil HR, Robinson CV, Kleanthous C. Intrinsically disordered protein threads through the bacterial outer-membrane porin OmpF. Science 2013; 340:1570-4. [PMID: 23812713 PMCID: PMC3856478 DOI: 10.1126/science.1237864] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Porins are β-barrel outer-membrane proteins through which small solutes and metabolites diffuse that are also exploited during cell death. We have studied how the bacteriocin colicin E9 (ColE9) assembles a cytotoxic translocon at the surface of Escherichia coli that incorporates the trimeric porin OmpF. Formation of the translocon involved ColE9's unstructured N-terminal domain threading in opposite directions through two OmpF subunits, capturing its target TolB on the other side of the membrane in a fixed orientation that triggers colicin import. Thus, an intrinsically disordered protein can tunnel through the narrow pores of an oligomeric porin to deliver an epitope signal to the cell to initiate cell death.
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Affiliation(s)
- Nicholas G. Housden
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jonathan T.S. Hopper
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Natalya Lukoyanova
- Department of Crystallography and Institute of Structural Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - David Rodriguez-Larrea
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Justyna A. Wojdyla
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Alexander Klein
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Helen R. Saibil
- Department of Crystallography and Institute of Structural Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Carol V. Robinson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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21
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Farrance OE, Hann E, Kaminska R, Housden NG, Derrington SR, Kleanthous C, Radford SE, Brockwell DJ. A force-activated trip switch triggers rapid dissociation of a colicin from its immunity protein. PLoS Biol 2013; 11:e1001489. [PMID: 23431269 PMCID: PMC3576412 DOI: 10.1371/journal.pbio.1001489] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 01/09/2013] [Indexed: 01/24/2023] Open
Abstract
A single-molecule force study shows that rapid dissociation of a high-affinity protein interaction can be triggered by site-specific remodelling of one protein partner, and that prevention of remodelling maintains avidity. Colicins are protein antibiotics synthesised by Escherichia coli strains to target and kill related bacteria. To prevent host suicide, colicins are inactivated by binding to immunity proteins. Despite their high avidity (Kd≈fM, lifetime ≈4 days), immunity protein release is a pre-requisite of colicin intoxication, which occurs on a timescale of minutes. Here, by measuring the dynamic force spectrum of the dissociation of the DNase domain of colicin E9 (E9) and immunity protein 9 (Im9) complex using an atomic force microscope we show that application of low forces (<20 pN) increases the rate of complex dissociation 106-fold, to a timescale (lifetime ≈10 ms) compatible with intoxication. We term this catastrophic force-triggered increase in off-rate a trip bond. Using mutational analysis, we elucidate the mechanism of this switch in affinity. We show that the N-terminal region of E9, which has sparse contacts with the hydrophobic core, is linked to an allosteric activator region in E9 (residues 21–30) whose remodelling triggers immunity protein release. Diversion of the force transduction pathway by the introduction of appropriately positioned disulfide bridges yields a force resistant complex with a lifetime identical to that measured by ensemble techniques. A trip switch within E9 is ideal for its function as it allows bipartite complex affinity, whereby the stable colicin:immunity protein complex required for host protection can be readily converted to a kinetically unstable complex whose dissociation is necessary for cellular invasion and competitor death. More generally, the observation of two force phenotypes for the E9:Im9 complex demonstrates that force can re-sculpt the underlying energy landscape, providing new opportunities to modulate biological reactions in vivo; this rationalises the commonly observed discrepancy between off-rates measured by dynamic force spectroscopy and ensemble methods. Many proteins interact with other proteins as part of their function. One method of modulating the activity of protein complexes is to break them apart. Some complexes, however, are extremely kinetically stable and it is unclear how these can dissociate on a biologically relevant timescale. In this study we address this question using protein complexes between colicin E9 (a bacterial toxin) and its immunity protein Im9. These highly avid complexes (with a lifetime of days) must be broken apart for colicin to be activated. By using single-molecule force methods we show that pulling on one end of colicin E9 drastically destabilises the complex so that it dissociates a million-fold faster than its intrinsic rate. We then show that preventing this destabilisation (by the insertion of cross-links that pin the N-terminus of E9 in place) yields a kinetically stable complex. It has previously been postulated that force can destabilise a protein complex by partially unfolding one or more binding partners. Our work provides new experimental evidence that shows this is the case and provides a mechanism for this phenomenon, which we term a trip bond. For the E9:Im9 complex, trip bond behaviour allows a stable complex to be rapidly dissociated by application of a surprisingly small force.
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Affiliation(s)
- Oliver E. Farrance
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - Eleanore Hann
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Sasha R. Derrington
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sheena E. Radford
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - David J. Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
- * E-mail:
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22
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Papadakos G, Housden NG, Lilly KJ, Kaminska R, Kleanthous C. Kinetic Basis for the Competitive Recruitment of TolB by the Intrinsically Disordered Translocation Domain of Colicin E9. J Mol Biol 2012; 418:269-80. [DOI: 10.1016/j.jmb.2012.01.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/11/2012] [Accepted: 01/24/2012] [Indexed: 11/15/2022]
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23
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Bonsor DA, Hecht O, Vankemmelbeke M, Sharma A, Krachler AM, Housden NG, Lilly KJ, James R, Moore GR, Kleanthous C. Allosteric β-propeller signalling in TolB and its manipulation by translocating colicins. EMBO J 2009. [DOI: 10.1038/emboj.2009.266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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24
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Bonsor DA, Hecht O, Vankemmelbeke M, Sharma A, Krachler AM, Housden NG, Lilly KJ, James R, Moore GR, Kleanthous C. Allosteric beta-propeller signalling in TolB and its manipulation by translocating colicins. EMBO J 2009; 28:2846-57. [PMID: 19696740 PMCID: PMC2750012 DOI: 10.1038/emboj.2009.224] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 07/13/2009] [Indexed: 01/09/2023] Open
Abstract
The Tol system is a five-protein assembly parasitized by colicins and bacteriophages that helps stabilize the Gram-negative outer membrane (OM). We show that allosteric signalling through the six-bladed beta-propeller protein TolB is central to Tol function in Escherichia coli and that this is subverted by colicins such as ColE9 to initiate their OM translocation. Protein-protein interactions with the TolB beta-propeller govern two conformational states that are adopted by the distal N-terminal 12 residues of TolB that bind TolA in the inner membrane. ColE9 promotes disorder of this 'TolA box' and recruitment of TolA. In contrast to ColE9, binding of the OM lipoprotein Pal to the same site induces conformational changes that sequester the TolA box to the TolB surface in which it exhibits little or no TolA binding. Our data suggest that Pal is an OFF switch for the Tol assembly, whereas colicins promote an ON state even though mimicking Pal. Comparison of the TolB mechanism to that of vertebrate guanine nucleotide exchange factor RCC1 suggests that allosteric signalling may be more prevalent in beta-propeller proteins than currently realized.
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Affiliation(s)
| | - Oliver Hecht
- Centre for Molecular and Structural Biochemistry, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, UK
| | - Mireille Vankemmelbeke
- School of Molecular Medical Sciences, Institute of Infection, Inflammation and Immunity, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Amit Sharma
- Department of Biology, University of York, York, UK
| | | | | | | | - Richard James
- School of Molecular Medical Sciences, Institute of Infection, Inflammation and Immunity, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Geoffrey R Moore
- Centre for Molecular and Structural Biochemistry, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, UK
| | - Colin Kleanthous
- Department of Biology, University of York, York, UK,Department of Biology (Area 10), University of York, Heslington, PO Box 373, York, YO10 5YW, UK. Tel.: +44 0 1904 328820; Fax: +44 0 1904 328825; E-mail:
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25
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Harrison SL, Housden NG, Bottomley SP, Cossins AJ, Gore MG. Generation and expression of a minimal hybrid Ig-receptor formed between single domains from proteins L and G. Protein Expr Purif 2008; 58:12-22. [DOI: 10.1016/j.pep.2007.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 11/09/2007] [Accepted: 11/12/2007] [Indexed: 11/25/2022]
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26
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Housden NG, Loftus SR, Moore GR, James R, Kleanthous C. Cell entry mechanism of enzymatic bacterial colicins: porin recruitment and the thermodynamics of receptor binding. Proc Natl Acad Sci U S A 2005; 102:13849-54. [PMID: 16166265 PMCID: PMC1236540 DOI: 10.1073/pnas.0503567102] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Binding of enzymatic E colicins to the vitamin B12 receptor, BtuB, is the first stage in a cascade of events that culminate in the translocation of the cytotoxic nuclease into the Escherichia coli cytoplasm and release of its tightly bound immunity protein. A dogma of colicin biology is that the toxin coiled-coil connecting its functional domains must unfold or unfurl to span the periplasm, with recent reports claiming this reaction is initiated by receptor binding. We report isothermal titration calorimetry data of BtuB binding the endonuclease toxin ColE9 and a disulfide form (ColE9S-S) where unfolding of the coiled-coil is prevented and, as a consequence, the toxin is biologically inactive. Contrary to expectation, the thermodynamics of receptor binding, characterized by large negative values for TDeltaS, are identical for the two colicins, arguing against any form of BtuB-induced unfolding. We go on to delineate key features of the "colicin translocon" that assembles at the cell surface after BtuB binding by using a complex of histidine-tagged Im9 bound to ColE9S-S. First, we show that the porin OmpF is recruited directly to the BtuB.colicin complex to form the translocon. Second, recruitment is through the natively unfolded region of the colicin translocation domain, with this domain likely having two contact points for OmpF. Finally, the immunity protein is not released during its assembly. Our study demonstrates that although colicin unfolding is undoubtedly a prerequisite for E. coli cell death, it must occur after assembly of the translocon.
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Affiliation(s)
- Nicholas G Housden
- Department of Biology (Area 10), P.O. Box 373, University of York, York YO10 5YW, United Kingdom
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Granata V, Housden NG, Harrison S, Jolivet-Reynaud C, Gore MG, Stura EA. Comparison of the crystallization and crystal packing of two Fab single-site mutant protein L complexes. Acta Crystallogr D Biol Crystallogr 2005; 61:750-4. [PMID: 15930633 DOI: 10.1107/s0907444905007110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2004] [Accepted: 03/07/2005] [Indexed: 11/10/2022]
Abstract
Protein L from Peptostreptococcus magnus (PpL) is a multidomain protein composed of four or five immunoglobulin-binding domains that target the kappa light chain of a large repertoire of human and murine antibodies. Thus, a single domain of this protein can be used to aid the crystallization of Fab, free or complexed to their antigen when it is not possible to obtain crystals without it. Each wild-type PpL domain has two light-chain binding sites that target the same region of the light chain and can thus bring together two Fab-antigen complexes within the crystal lattice. In this context the small PpL domain is sandwiched between two Fab and cannot participate in crystal contacts, thus mutants are unlikely to increase the chances of crystallizing a particular complex. However, it is possible to design mutants that can bind at only one site by making use of the crystal structures obtained so far. Such mutants will have a free surface that can participate in crystal contacts and that can be modified to improve its crystal contact-forming properties. Here, a comparison of two single-site mutants that differ at three different positions is reported. In both mutants two different tryptophan residues participate in crystal-packing interactions, suggesting that this residue may be particularly interesting for enhancing crystal-contact formation.
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Affiliation(s)
- Vincenzo Granata
- Università Federico II, Dipartimento di Chimica Biologica, Via Mezzocannone, Napoli, Italy
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Ménez R, Housden NG, Harrison S, Jolivet-Reynaud C, Gore MG, Stura EA. Different crystal packing in Fab–protein L semi-disordered peptide complex. Acta Crystallogr D Biol Crystallogr 2005; 61:744-9. [PMID: 15930632 DOI: 10.1107/s0907444905006724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2004] [Accepted: 03/03/2005] [Indexed: 05/02/2023]
Abstract
Proteins and peptides with variable degrees of disorder are a challenge for protein crystallization. These may be completely disordered or just contain regions with a high degree of mobility that may be represented by a multitude of discretely defined conformations. These difficulties are not insurmountable, but it may be unreasonable to expect a clean result from a structural point of view. The complex between a murine monoclonal antibody (19D9D6) and a synthetic peptide that encompasses the first 45 residues of the core protein of Hepatitis C virus that is poorly structured in solution has been crystallized. In order to make the crystallization possible, use was made of a single immunoglobulin-binding domain of protein L from Peptostreptococcus magnus (PpL), a bacterial protein that can bind the variable region (Fv) of a large population of antibodies through its light chain with no interference with antibody-antigen recognition. Crystals were obtained in different space groups where the size of the cavity that accommodates the peptide is different, although many of the crystal contacts and the overall lattice are preserved. The peptide can be considered to be semi-disordered and the larger cavity accommodates a better ordered peptide than the smaller one. The lattice is of interest for the design of a scaffold system for the crystallization of peptide-tagged proteins since a cavity that accommodates a disordered entity might be able to host ordered proteins of the same size and shape as the cavity. Here, the differences between the lattices formed by this trimolecular complex are described and it is discussed how such a system may be adapted to the crystallization of peptide-tagged proteins.
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Affiliation(s)
- Renée Ménez
- Département R&D Immuno-essais et Protéomique, BioMerieux, Marcy l'Etoile, France
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Penfold CN, Healy B, Housden NG, Boetzel R, Vankemmelbeke M, Moore GR, Kleanthous C, James R. Flexibility in the receptor-binding domain of the enzymatic colicin E9 is required for toxicity against Escherichia coli cells. J Bacteriol 2004; 186:4520-7. [PMID: 15231784 PMCID: PMC438598 DOI: 10.1128/jb.186.14.4520-4527.2004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The events that occur after the binding of the enzymatic E colicins to Escherichia coli BtuB receptors that lead to translocation of the cytotoxic domain into the periplasmic space and, ultimately, cell killing are poorly understood. It has been suggested that unfolding of the coiled-coil BtuB receptor binding domain of the E colicins may be an essential step that leads to the loss of immunity protein from the colicin and immunity protein complex and then triggers the events of translocation. We introduced pairs of cysteine mutations into the receptor binding domain of colicin E9 (ColE9) that resulted in the formation of a disulfide bond located near the middle or the top of the R domain. After dithiothreitol reduction, the ColE9 protein with the mutations L359C and F412C (ColE9 L359C-F412C) and the ColE9 protein with the mutations Y324C and L447C (ColE9 Y324C-L447C) were slightly less active than equivalent concentrations of ColE9. On oxidation with diamide, no significant biological activity was seen with the ColE9 L359C-F412C and the ColE9 Y324C-L447C mutant proteins; however diamide had no effect on the activity of ColE9. The presence of a disulfide bond was confirmed in both of the oxidized, mutant proteins by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The loss of biological activity of the disulfide-containing mutant proteins was not due to an indirect effect on the properties of the translocation or DNase domains of the mutant colicins. The data are consistent with a requirement for the flexibility of the coiled-coil R domain after binding to BtuB.
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Affiliation(s)
- Christopher N Penfold
- School of Molecular Medical Sciences and Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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Housden NG, Harrison S, Housden HR, Thomas KA, Beckingham JA, Roberts SE, Bottomley SP, Graille M, Stura E, Gore MG. Observation and characterization of the interaction between a single immunoglobulin binding domain of protein L and two equivalents of human kappa light chains. J Biol Chem 2003; 279:9370-8. [PMID: 14668335 DOI: 10.1074/jbc.m312938200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Detailed stopped-flow studies in combination with site-directed mutagenesis, isothermal titration calorimetry data and x-ray crystallographic knowledge have revealed that the biphasic pre-equilibrium fluorescence changes reported for a single Ig-binding domain of protein L from Peptostreptococcus magnus binding to kappa light chain are due to the binding of the kappa light chain at two separate sites on the protein L molecule. Elimination of binding site 2 through the mutation A66W has allowed the K(d) for kappa light chain binding at site 1 to be measured by stopped-flow fluorescence and isothermal titration calorimetry techniques, giving values of 48.0 +/- 8.0 nM and 37.5 +/- 7.3 nM respectively. Conversely, a double mutation Y53F/L57H eliminates binding at site 1 and has allowed the K(d) for binding at site 2 to be determined. Stopped-flow fluorimetry suggests this to be 3.4 +/- 0.8 microM in good agreement with the value of 4.6 +/- 0.8 microM determined by isothermal titration calorimetry. The mutation Y53F reduces the affinity of site 1 to approximately that of site 2.
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Affiliation(s)
- Nicholas G Housden
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, Hants SO16 7PX, United Kingdom
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Housden NG, Harrison S, Roberts SE, Beckingham JA, Graille M, Stura E, Gore MG. Immunoglobulin-binding domains: Protein L from Peptostreptococcus magnus. Biochem Soc Trans 2003; 31:716-8. [PMID: 12773190 DOI: 10.1042/bst0310716] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Protein L is a multidomain cell-wall protein isolated from Peptostreptococcus magnus. It belongs to a group of proteins that contain repeated domains that are able to bind to Igs without stimulating an immune response, the most characterized of this group being Protein A ( Staphylococcus aureus ) and Protein G ( Streptococcus ). Both of these proteins bind predominantly to the interface of C(H)2-C(H)3 heavy chains, while Protein L binds exclusively to the V(L) domain of the kappa -chain. The function of these proteins in vivo is not clear but it is thought that they enable the bacteria to evade the host's immune system. Two binding sites for kappa -chain on a single Ig-binding domain from Protein L have recently been reported and we give evidence that one site has a 25-55-fold higher affinity for kappa -chain than the second site.
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Affiliation(s)
- N G Housden
- Division of Biochemistry and Molecular Biology, Institute of Biomolecular Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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Graille M, Harrison S, Crump MP, Findlow SC, Housden NG, Muller BH, Battail-Poirot N, Sibaï G, Sutton BJ, Taussig MJ, Jolivet-Reynaud C, Gore MG, Stura EA. Evidence for plasticity and structural mimicry at the immunoglobulin light chain-protein L interface. J Biol Chem 2002; 277:47500-6. [PMID: 12221088 DOI: 10.1074/jbc.m206105200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The multidomain bacterial surface protein L (PpL) is a virulence factor expressed by only 10% of Peptostreptococcus magnus strains, and its expression is correlated with bacterial vaginosis. The molecular basis for its ability to recognize 60% of mammalian immunoglobulin light chain variable regions (V(L)) has been described recently by x-ray crystallography, which suggested the presence of two V(L) binding sites on each protein L domain (Graille, M., Stura, E. A., Housden, N. G., Beckingham, J. A., Bottomley, S. P., Beale, D., Taussig, M. J., Sutton, B. J., Gore, M. G., and Charbonnier, J. (2001) Structure 9, 679-687). Here, we report the crystal structure at 2.1 A resolution of a protein L mutant complexed to an Fab' fragment with only 50% of the V(L) residues interacting with PpL site 1 conserved. Comparison of the site 1 interface from both structures shows how protein L is able to accommodate these sequence differences and therefore bind to a large repertoire of Ig. The x-ray structure and NMR results confirm the existence of two V(L) binding sites on a single protein L domain. These sites exhibit a remarkable structural mimicry of growth factors binding to their receptors. This could explain the protein L superantigenic activity on human B lymphocytes.
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Affiliation(s)
- Marc Graille
- Laboratoire de Structure des Protéines, Département d'Ingénierie et d'Etudes des Protéines (DIEP), Commissariat à l'Energie Atomique, Centre d'Etudes de Saclay, Gif-sur-Yvette, France
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Stura EA, Graille M, Housden NG, Gore MG. Protein L mutants for the crystallization of antibody fragments. Acta Crystallogr D Biol Crystallogr 2002; 58:1744-8. [PMID: 12351898 DOI: 10.1107/s0907444902012805] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2002] [Accepted: 07/16/2002] [Indexed: 11/10/2022]
Abstract
In many cases, antibody and their complexes can be crystallized and their structure determined without major difficulties. The remaining problematic cases may be approached through techniques such as of combinatorial complex crystallization which uses immunoglobulin binding proteins (IBP). The range of lattices that can be made using this method can be expanded by engineering mutants of IBP domains. We have designed Peptostreptococcus magnus protein L (PpL) mutants with altered immunoglobulin light chain binding characteristics. While the wild type PpL has two binding sites, some of the mutants contact the light chain via only one site. Other mutants have combinations of weakened first and second binding sites that modify their crystallization properties and their packing mode. In this study, we have selected PpL mutants with different behavior and that are most useful for crystallization and we present the various packing modes obtained so far.
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Affiliation(s)
- Enrico A Stura
- CEA, Département d'Ingénierie et d'Etudes des Protéines (DIEP), CE Saclay, 91191 Gif-sur-Yvette Cedex, France.
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Graille M, Stura EA, Housden NG, Beckingham JA, Bottomley SP, Beale D, Taussig MJ, Sutton BJ, Gore MG, Charbonnier JB. Complex between Peptostreptococcus magnus protein L and a human antibody reveals structural convergence in the interaction modes of Fab binding proteins. Structure 2001; 9:679-87. [PMID: 11587642 DOI: 10.1016/s0969-2126(01)00630-x] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Peptostreptococcus magnus protein L (PpL) is a multidomain, bacterial surface protein whose presence correlates with virulence. It consists of up to five homologous immunoglobulin binding domains that interact with the variable (VL) regions of kappa light chains found on two thirds of mammalian antibodies. RESULTS We refined the crystal structure of the complex between a human antibody Fab fragment (2A2) and a single PpL domain (61 residues) to 2.7 A. The asymmetric unit contains two Fab molecules sandwiching a single PpL domain, which contacts similar VL framework regions of two light chains via independent interfaces. The residues contacted on VL are remote from the hypervariable loops. One PpL-Vkappa interface agrees with previous biochemical data, while the second is novel. Site-directed mutagenesis and analytical-centrifugation studies suggest that the two PpL binding sites have markedly different affinities for VL. The PpL residues in both interactions are well conserved among different Peptostreptococcus magnus strains. The Fab contact positions identified in the complex explain the high specificity of PpL for antibodies with kappa rather than lambda chains. CONCLUSIONS The PpL-Fab complex shows the first interaction of a bacterial virulence factor with a Fab light chain outside the conventional combining site. Structural comparison with two other bacterial proteins interacting with the Fab heavy chain shows that PpL, structurally homologous to streptococcal SpG domains, shares with the latter a similar binding mode. These two bacterial surface proteins interact with their respective immunoglobulin regions through a similar beta zipper interaction.
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Affiliation(s)
- M Graille
- Département d'Ingénierie et d'Etudes des Protéines, Commissariat à l'Energie Atomique, Centre d'Etudes Saclay, F-91191, Gif-sur-Yvette, France
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Beckingham JA, Housden NG, Muir NM, Bottomley SP, Gore MG. Studies on a single immunoglobulin-binding domain of protein L from Peptostreptococcus magnus: the role of tyrosine-53 in the reaction with human IgG. Biochem J 2001; 353:395-401. [PMID: 11139405 PMCID: PMC1221583 DOI: 10.1042/0264-6021:3530395] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Chemical modification experiments with tetranitromethane (TNM) have been used to investigate the role of tyrosine residues in the formation of the complex between PpL (the single Ig-binding domain of protein L, isolated from P. magnus strain 3316) and the kappa light chain (kappa-chain). Reaction of PpL with TNM causes the modification of 1.9 equiv. of tyrosine (Tyr(51) and Tyr(53)) and results in an approx. 140-fold decrease in affinity for human IgG. Similar experiments with mutated PpL proteins suggest that nitration predominantly inactivates the protein by modification of Tyr(53). Reduction of the nitrotyrosine groups to aminotyrosine by incubation with sodium hydrosulphite does not restore high affinity for IgG. Modification of kappa-chain by TNM resulted in the nitration of 3.1+/-0.09 tyrosine residues. When the PpL-kappa-chain complex was incubated with TNM, 4.1+/-0.04 tyrosine residues were nitrated, indicating that one tyrosine residue previously modified by the reagent was protected from TNM when the proteins are in complex with each other. The K(d) for the equilibrium between PpL, human IgG and their complex has been shown by ELISA to be 112+/-20 nM. A similar value (153+/-33 nM) was obtained for the complex formed between IgG and the Tyr(64)-->Trp mutant (Y64W). However, the K(d) values for the equilibria involving the PpL mutants Y53F and Y53F,Y64W were found to be 3.2+/-0.2 and 4.6+/-1 microM respectively. These suggest that the phenol group of Tyr(53) in PpL is important to the stability of the PpL-kappa-chain complex.
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Affiliation(s)
- J A Beckingham
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, Hants. SO16 7PX, U.K
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