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Zhao X, Wang W, Zeng X, Xu R, Yuan B, Yu W, Wang M, Jia R, Chen S, Zhu D, Liu M, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Sun D, Cheng A. Klebicin E, a pore-forming bacteriocin of Klebsiella pneumoniae, exploits the porin OmpC and the Ton system for translocation. J Biol Chem 2024; 300:105694. [PMID: 38301890 PMCID: PMC10906532 DOI: 10.1016/j.jbc.2024.105694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriocins, which have narrow-spectrum activity and limited adverse effects, are promising alternatives to antibiotics. In this study, we identified klebicin E (KlebE), a small bacteriocin derived from Klebsiella pneumoniae. KlebE exhibited strong efficacy against multidrug-resistant K. pneumoniae isolates and conferred a significant growth advantage to the producing strain during intraspecies competition. A giant unilamellar vesicle leakage assay demonstrated the unique membrane permeabilization effect of KlebE, suggesting that it is a pore-forming toxin. In addition to a C-terminal toxic domain, KlebE also has a disordered N-terminal domain and a globular central domain. Pulldown assays and soft agar overlay experiments revealed the essential role of the outer membrane porin OmpC and the Ton system in KlebE recognition and cytotoxicity. Strong binding between KlebE and both OmpC and TonB was observed. The TonB-box, a crucial component of the toxin-TonB interaction, was identified as the 7-amino acid sequence (E3ETLTVV9) located in the N-terminal region. Further studies showed that a region near the bottom of the central domain of KlebE plays a primary role in recognizing OmpC, with eight residues surrounding this region identified as essential for KlebE toxicity. Finally, based on the discrepancies in OmpC sequences between the KlebE-resistant and sensitive strains, it was found that the 91st residue of OmpC, an aspartic acid residue, is a key determinant of KlebE toxicity. The identification and characterization of this toxin will facilitate the development of bacteriocin-based therapies targeting multidrug-resistant K. pneumoniae infections.
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Affiliation(s)
- Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Wenyu Wang
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Zeng
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Rong Xu
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Wenyao Yu
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China.
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Skutel M, Andriianov A, Zavialova M, Kirsanova M, Shodunke O, Zorin E, Golovshchinskii A, Severinov K, Isaev A. T5-like phage BF23 evades host-mediated DNA restriction and methylation. MICROLIFE 2023; 4:uqad044. [PMID: 38025991 PMCID: PMC10644984 DOI: 10.1093/femsml/uqad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/15/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
Bacteriophage BF23 is a close relative of phage T5, a prototypical Tequintavirus that infects Escherichia coli. BF23 was isolated in the middle of the XXth century and was extensively studied as a model object. Like T5, BF23 carries long ∼9.7 kb terminal repeats, injects its genome into infected cell in a two-stage process, and carries multiple specific nicks in its double-stranded genomic DNA. The two phages rely on different host secondary receptors-FhuA (T5) and BtuB (BF23). Only short fragments of the BF23 genome, including the region encoding receptor interacting proteins, have been determined. Here, we report the full genomic sequence of BF23 and describe the protein content of its virion. T5-like phages represent a unique group that resist restriction by most nuclease-based host immunity systems. We show that BF23, like other Tequintavirus phages, resist Types I/II/III restriction-modification host immunity systems if their recognition sites are located outside the terminal repeats. We also demonstrate that the BF23 avoids host-mediated methylation. We propose that inhibition of methylation is a common feature of Tequintavirus and Epseptimavirus genera phages, that is not, however, associated with their antirestriction activity.
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Affiliation(s)
- Mikhail Skutel
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, 143028, Moscow, Russia
| | - Aleksandr Andriianov
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, 143028, Moscow, Russia
| | - Maria Zavialova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, 143028, Moscow, Russia
- Institute of Biomedical Chemistry (IBMC), Pogodinskaya 10/8, 119435, Moscow, Russia
| | - Maria Kirsanova
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, 143028, Moscow, Russia
| | - Oluwasefunmi Shodunke
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, 143028, Moscow, Russia
- Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, 141701, Dolgoprudny, Russia
| | - Evgenii Zorin
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, 143028, Moscow, Russia
| | | | - Konstantin Severinov
- Waksman Institute of Microbiology, 190 Frelinghuysen Rd, NJ 08854, Piscataway, United States
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, 143028, Moscow, Russia
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Young JW, Zhao Z, Wason IS, Duong van Hoa F. A Dual Detergent Strategy to Capture a Bacterial Outer Membrane Proteome in Peptidiscs for Characterization by Mass Spectrometry and Binding Assays. J Proteome Res 2022; 22:1537-1545. [PMID: 36516475 DOI: 10.1021/acs.jproteome.2c00560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The outer membrane of Gram-negative bacteria plays a critical role in protecting the cell against external stressors, including antibiotics, and therefore is a prime target for antimicrobial discovery. To facilitate the discovery efforts, a precise knowledge of the outer membrane proteome, and possible variations during pathogenesis, is important. Characterization of the bacterial outer membrane remain challenging, however, and low throughput, due to the high hydrophobicity and relatively low abundance of this cell compartment. Here we adapt our peptidisc-based method to selectively isolate the outer membrane proteome before analysis by mass spectrometry. Using a dual detergent membrane solubilization approach, followed by protein purification in peptidiscs, we capture over 70 outer membrane proteins, including 26 integral β-barrels and 26 lipoproteins. Many of these proteins are present at high peptide intensities, indicative of a high abundance in the library sample. We further show that the isolated outer membrane proteome can be employed in downstream ligand-binding assays. This peptidisc library made of outer membrane proteins may therefore be useful to systematically survey other bacterial outer membrane proteomes, but also as a nanoparticle format able to support the discovery of next-generation antimicrobials. Data are available via ProteomeXchange identifier PXD036749.
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Affiliation(s)
- John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Irvinder Singh Wason
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Budiardjo SJ, Stevens JJ, Calkins AL, Ikujuni AP, Wimalasena VK, Firlar E, Case DA, Biteen JS, Kaelber JT, Slusky JSG. Colicin E1 opens its hinge to plug TolC. eLife 2022; 11:73297. [PMID: 35199644 PMCID: PMC9020818 DOI: 10.7554/elife.73297] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/21/2022] [Indexed: 12/02/2022] Open
Abstract
The double membrane architecture of Gram-negative bacteria forms a barrier that is impermeable to most extracellular threats. Bacteriocin proteins evolved to exploit the accessible, surface-exposed proteins embedded in the outer membrane to deliver cytotoxic cargo. Colicin E1 is a bacteriocin produced by, and lethal to, Escherichia coli that hijacks the outer membrane proteins (OMPs) TolC and BtuB to enter the cell. Here, we capture the colicin E1 translocation domain inside its membrane receptor, TolC, by high-resolution cryo-electron microscopy to obtain the first reported structure of a bacteriocin bound to TolC. Colicin E1 binds stably to TolC as an open hinge through the TolC pore—an architectural rearrangement from colicin E1’s unbound conformation. This binding is stable in live E. coli cells as indicated by single-molecule fluorescence microscopy. Finally, colicin E1 fragments binding to TolC plug the channel, inhibiting its native efflux function as an antibiotic efflux pump, and heightening susceptibility to three antibiotic classes. In addition to demonstrating that these protein fragments are useful starting points for developing novel antibiotic potentiators, this method could be expanded to other colicins to inhibit other OMP functions. Bacteria are constantly warring with each other for space and resources. As a result, they have developed a range of molecular weapons to poison, damage or disable other cells. For instance, bacteriocins are proteins that can latch onto structures at the surface of enemy bacteria and push toxins through their outer membrane. Bacteria are increasingly resistant to antibiotics, representing a growing concern for modern healthcare. One way that they are able to survive is by using ‘efflux pumps’ studded through their external membranes to expel harmful drugs before these can cause damage. Budiardjo et al. wanted to test whether bacteriocins could interfere with this defence mechanism by blocking efflux pumps. Bacteriocins are usually formed of binding elements (which recognise specific target proteins) and of a ‘killer tail’ that can stab the cell. Experiments showed that the binding parts of a bacteriocin could effectively ‘plug’ efflux pumps in Escherichia coli bacteria: high-resolution molecular microscopy revealed how the bacteriocin fragment binds to the pump, while fluorescent markers showed that it attached to the surface of E. coli and stopped the efflux pumps from working. As a result, lower amounts of antibiotics were necessary to kill the bacteria when bacteriocins were present. The work by Budiardjo et al. could lead to new ways to combat bacteria that will reduce the need for current antibiotics. In the future, bacteriocins could also be harnessed to target other proteins than efflux pumps, allowing scientists to manipulate a range of bacterial processes.
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Affiliation(s)
- S Jimmy Budiardjo
- Center for Computational Biology, University of Kansas, Lawrence, United States
| | - Jacqueline J Stevens
- Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Anna L Calkins
- Department of Chemistry, University of Michigan, Ann Arbor, United States
| | - Ayotunde P Ikujuni
- Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | | | - Emre Firlar
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, United States
| | - David A Case
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, United States
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, United States
| | - Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, United States
| | - Joanna S G Slusky
- Center for Computational Biology, University of Kansas, Lawrence, United States
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5
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Calcuttawala F, Pal A, Nath P, Kar R, Hazra D, Pal R. Structural and functional insights into colicin: a new paradigm in drug discovery. Arch Microbiol 2021; 204:37. [PMID: 34928429 DOI: 10.1007/s00203-021-02689-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 11/28/2022]
Abstract
Colicins are agents of allelopathic interactions produced by certain enterobacteria which give them a competitive advantage in the environment. These protein molecules are mostly encoded by plasmids. The colicin operon consists of the activity, immunity and the lysis genes. The activity protein is responsible for the killing activity, the immunity protein protects the producer cell from the lethal action of colicin and the lysis protein facilitates its release. Colicins are primarily composed of three domains, namely the receptor-binding domain, the translocation domain and the cytotoxic domain. The protein molecule binds to its cognate receptor on the target cell via the receptor-binding domain and undergoes translocation into the cell either via the Tol system or the Ton system. After gaining entry into the target cell, there are various mechanisms by which colicins exert their lethality. These comprise DNase activity, RNase activity and pore formation in the target cell membrane or peptidoglycan synthesis inhibition. This review gives a detailed insight into the structural and functional aspect of colicins and their mode of action. This knowledge is of immense significance because colicins are being considered as very useful alternatives to conventional antibiotics in the treatment of multidrug-resistant infections. Besides, they also have a negligible harmful impact on the commensals. Thus, before tapping their therapeutic potential, it is imperative to know their structure and mechanism of action in detail.
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Affiliation(s)
- Fatema Calcuttawala
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India.
| | - Ankita Pal
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India
| | - Papri Nath
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India
| | - Riya Kar
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India
| | - Debraj Hazra
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India
| | - Rajat Pal
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India
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Francis MLR, Webby MN, Housden NG, Kaminska R, Elliston E, Chinthammit B, Lukoyanova N, Kleanthous C. Porin threading drives receptor disengagement and establishes active colicin transport through Escherichia coli OmpF. EMBO J 2021; 40:e108610. [PMID: 34515361 PMCID: PMC8561637 DOI: 10.15252/embj.2021108610] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022] Open
Abstract
Bacteria deploy weapons to kill their neighbours during competition for resources and to aid survival within microbiomes. Colicins were the first such antibacterial system identified, yet how these bacteriocins cross the outer membrane (OM) of Escherichia coli is unknown. Here, by solving the structures of translocation intermediates via cryo‐EM and by imaging toxin import, we uncover the mechanism by which the Tol‐dependent nuclease colicin E9 (ColE9) crosses the bacterial OM. We show that threading of ColE9’s disordered N‐terminal domain through two pores of the trimeric porin OmpF causes the colicin to disengage from its primary receptor, BtuB, and reorganises the translocon either side of the membrane. Subsequent import of ColE9 through the lumen of a single OmpF subunit is driven by the proton‐motive force, which is delivered by the TolQ‐TolR‐TolA‐TolB assembly. Our study answers longstanding questions, such as why OmpF is a better translocator than OmpC, and reconciles the mechanisms by which both Tol‐ and Ton‐dependent bacteriocins cross the bacterial outer membrane.
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Affiliation(s)
| | - Melissa N Webby
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emma Elliston
- Department of Biochemistry, University of Oxford, Oxford, UK
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7
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Johnstone BA, Christie MP, Morton CJ, Parker MW. X-ray crystallography shines a light on pore-forming toxins. Methods Enzymol 2021; 649:1-46. [PMID: 33712183 DOI: 10.1016/bs.mie.2021.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A common form of cellular attack by pathogenic bacteria is to secrete pore-forming toxins (PFTs). Capable of forming transmembrane pores in various biological membranes, PFTs have also been identified in a diverse range of other organisms such as sea anemones, earthworms and even mushrooms and trees. The mechanism of pore formation by PFTs is associated with substantial conformational changes in going from the water-soluble to transmembrane states of the protein. The determination of the crystal structures for numerous PFTs has shed much light on our understanding of these proteins. Other than elucidating the atomic structural details of PFTs and the conformational changes that must occur for pore formation, crystal structures have revealed structural homology that has led to the discovery of new PFTs and new PFT families. Here we review some key crystallographic results together with complimentary approaches for studying PFTs. We discuss how these studies have impacted our understanding of PFT function and guided research into biotechnical applications.
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Affiliation(s)
- Bronte A Johnstone
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Michelle P Christie
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Craig J Morton
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia; St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia.
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8
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Bhattacharyya S, Walker DM, Harshey RM. Dead cells release a 'necrosignal' that activates antibiotic survival pathways in bacterial swarms. Nat Commun 2020; 11:4157. [PMID: 32814767 PMCID: PMC7438516 DOI: 10.1038/s41467-020-17709-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 07/14/2020] [Indexed: 01/06/2023] Open
Abstract
Swarming is a form of collective bacterial motion enabled by flagella on the surface of semi-solid media. Swarming populations exhibit non-genetic or adaptive resistance to antibiotics, despite sustaining considerable cell death. Here, we show that antibiotic-induced death of a sub-population benefits the swarm by enhancing adaptive resistance in the surviving cells. Killed cells release a resistance-enhancing factor that we identify as AcrA, a periplasmic component of RND efflux pumps. The released AcrA interacts on the surface of live cells with an outer membrane component of the efflux pump, TolC, stimulating drug efflux and inducing expression of other efflux pumps. This phenomenon, which we call 'necrosignaling', exists in other Gram-negative and Gram-positive bacteria and displays species-specificity. Given that adaptive resistance is a known incubator for evolving genetic resistance, our findings might be clinically relevant to the rise of multidrug resistance.
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Affiliation(s)
- Souvik Bhattacharyya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - David M Walker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Rasika M Harshey
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
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9
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Horne JE, Brockwell DJ, Radford SE. Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria. J Biol Chem 2020; 295:10340-10367. [PMID: 32499369 PMCID: PMC7383365 DOI: 10.1074/jbc.rev120.011473] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/03/2020] [Indexed: 01/09/2023] Open
Abstract
β-Barrel outer membrane proteins (OMPs) represent the major proteinaceous component of the outer membrane (OM) of Gram-negative bacteria. These proteins perform key roles in cell structure and morphology, nutrient acquisition, colonization and invasion, and protection against external toxic threats such as antibiotics. To become functional, OMPs must fold and insert into a crowded and asymmetric OM that lacks much freely accessible lipid. This feat is accomplished in the absence of an external energy source and is thought to be driven by the high thermodynamic stability of folded OMPs in the OM. With such a stable fold, the challenge that bacteria face in assembling OMPs into the OM is how to overcome the initial energy barrier of membrane insertion. In this review, we highlight the roles of the lipid environment and the OM in modulating the OMP-folding landscape and discuss the factors that guide folding in vitro and in vivo We particularly focus on the composition, architecture, and physical properties of the OM and how an understanding of the folding properties of OMPs in vitro can help explain the challenges they encounter during folding in vivo Current models of OMP biogenesis in the cellular environment are still in flux, but the stakes for improving the accuracy of these models are high. OMP folding is an essential process in all Gram-negative bacteria, and considering the looming crisis of widespread microbial drug resistance it is an attractive target. To bring down this vital OMP-supported barrier to antibiotics, we must first understand how bacterial cells build it.
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Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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10
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Lee S, Housden NG, Ionescu SA, Zimmer MH, Kaminska R, Kleanthous C, Bayley H. Transmembrane Epitope Delivery by Passive Protein Threading through the Pores of the OmpF Porin Trimer. J Am Chem Soc 2020; 142:12157-12166. [PMID: 32614588 PMCID: PMC7366379 DOI: 10.1021/jacs.0c02362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Trimeric porins in the outer membrane (OM) of Gram-negative bacteria are the conduits by which nutrients and antibiotics diffuse passively into cells. The narrow gateways that porins form in the OM are also exploited by bacteriocins to translocate into cells by a poorly understood process. Here, using single-channel electrical recording in planar lipid bilayers in conjunction with protein engineering, we explicate the mechanism by which the intrinsically unstructured N-terminal translocation domain (IUTD) of the endonuclease bacteriocin ColE9 is imported passively across the Escherichia coli OM through OmpF. We show that the import is dominated by weak interactions of OmpF pores with binding epitopes within the IUTD that are orientationally biased and result in the threading of over 60 amino acids through 2 subunits of OmpF. Single-molecule kinetic analysis demonstrates that the IUTD enters from the extracellular side of OmpF and translocates to the periplasm where the polypeptide chain does an about turn in order to enter a neighboring subunit, only for some of these molecules to pop out of this second subunit before finally re-entering to form a stable complex. These intimately linked transport/binding processes generate an essentially irreversible, hook-like assembly that constrains an import activating peptide epitope between two subunits of the OmpF trimer.
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Affiliation(s)
- Sejeong Lee
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | | | - Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Matthew H Zimmer
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
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11
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Atanaskovic I, Kleanthous C. Tools and Approaches for Dissecting Protein Bacteriocin Import in Gram-Negative Bacteria. Front Microbiol 2019; 10:646. [PMID: 31001227 PMCID: PMC6455109 DOI: 10.3389/fmicb.2019.00646] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022] Open
Abstract
Bacteriocins of Gram-negative bacteria are typically multi-domain proteins that target and kill bacteria of the same or closely related species. There is increasing interest in protein bacteriocin import; from a fundamental perspective to understand how folded proteins are imported into bacteria and from an applications perspective as species-specific antibiotics to combat multidrug resistant bacteria. In order to translocate across the cell envelope and cause cell death, protein bacteriocins hijack nutrient uptake pathways. Their import is energized by parasitizing intermembrane protein complexes coupled to the proton motive force, which delivers a toxic domain into the cell. A plethora of genetic, structural, biochemical, and biophysical methods have been applied to find cell envelope components involved in bacteriocin import since their discovery almost a century ago. Here, we review the various approaches that now exist for investigating how protein bacteriocins translocate into Gram-negative bacteria and highlight areas of research that will need methodological innovations to fully understand this process. We also highlight recent studies demonstrating how bacteriocins can be used to probe organization and architecture of the Gram-negative cell envelope itself.
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Affiliation(s)
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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12
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Menikpurage IP, Barraza D, Meléndez AB, Strebe S, Mera PE. The B12 receptor BtuB alters the membrane integrity of Caulobacter crescentus. MICROBIOLOGY-SGM 2019; 165:311-323. [PMID: 30628887 DOI: 10.1099/mic.0.000753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vitamin B12 is one of the most complex biomolecules in nature. Since few organisms can synthesize B12de novo, most bacteria utilize highly sensitive and specialized transporters to scavenge B12 and its precursors. In Gram-negative bacteria, BtuB is the outer membrane TonB-dependent receptor for B12. In the fresh water bacterium Caulobacter crescentus, btuB is among the most highly expressed genes. In this study, we characterized the function of BtuB in C. crescentus and unveiled a potential new function of this receptor involved in cellular fitness. Under standard minimal or rich growth conditions, we found that supplements of vitamin B12 to cultures of C. crescentus provided no significant advantage in growth rate. Using a B12 methionine auxotroph, we showed that BtuB in C. crescentus is capable of transporting B12 at low pico-molar range. A btuB knockout strain displayed higher sensitivity to detergents and to changes in osmotic pressure compared to the wild-type. Electron micrographs of this knockout strain revealed a morphology defect. The sensitivity observed in the btuB knockout strain was not due to changes in membrane permeability or altered S-layer levels. Our results demonstrate that btuB deletion mutants exhibit increased susceptibility to membrane stressors, suggesting a potential role of this receptor in membrane homeostasis. Because we only tested BtuB's function under laboratory conditions, we cannot eliminate the possibility that BtuB also plays a key role as a B12 scavenger in C. crescentus when growing in its highly variable and nutrient-limited natural environment.
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Affiliation(s)
- Inoka P Menikpurage
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
| | - Daniela Barraza
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
| | - Ady B Meléndez
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
| | - Sierra Strebe
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
| | - Paola E Mera
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
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13
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Duché D, Houot L. Similarities and Differences between Colicin and Filamentous Phage Uptake by Bacterial Cells. EcoSal Plus 2019; 8. [PMID: 30681066 DOI: 10.1128/ecosalplus.esp-0030-2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Indexed: 06/09/2023]
Abstract
Gram-negative bacteria have evolved a complex envelope to adapt and survive in a broad range of ecological niches. This physical barrier is the first line of defense against noxious compounds and viral particles called bacteriophages. Colicins are a family of bactericidal proteins produced by and toxic to Escherichia coli and closely related bacteria. Filamentous phages have a complex structure, composed of at least five capsid proteins assembled in a long thread-shaped particle, that protects the viral DNA. Despite their difference in size and complexity, group A colicins and filamentous phages both parasitize multiprotein complexes of their sensitive host for entry. They first bind to a receptor located at the surface of the target bacteria before specifically recruiting components of the Tol system to cross the outer membrane and find their way through the periplasm. The Tol system is thought to use the proton motive force of the inner membrane to maintain outer membrane integrity during the life cycle of the cell. This review describes the sequential docking mechanisms of group A colicins and filamentous phages during their uptake by their bacterial host, with a specific focus on the translocation step, promoted by interactions with the Tol system.
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Affiliation(s)
- Denis Duché
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS, 13402 Marseille, France
| | - Laetitia Houot
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université- CNRS, 13402 Marseille, France
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14
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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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15
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Chang JW, Sato Y, Ogawa T, Arakawa T, Fukai S, Fushinobu S, Masaki H. Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell. J Biochem 2018; 164:329-339. [PMID: 29905832 DOI: 10.1093/jb/mvy056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 06/10/2018] [Indexed: 12/18/2022] Open
Abstract
Colicins are protein toxins produced by and toxic to Escherichia coli strains. Colicin D consists of an N-terminal domain (NTD), central domain (CD) and C-terminal RNase domain (CRD). The cognate immunity protein, ImmD, is co-synthesized in producer cells to block the toxic tRNase activity of the CRD. Previous studies have reported the crystal structure of CRD/ImmD complex. Colicin D hijacks the surface receptor FepA and the energy transducer TonB system using the NTD for translocation across the outer membrane of the target cells. The CD is required for endoproteolytic processing and the translocation of CRD across the inner membrane, and the membrane-associated protease FtsH and the signal peptidase LepB are exploited in this process. Although several regions of the CD have been identified in interactions with the hijacked inner membrane system or immunity protein, the structural basis of the CD is unknown. In this study, we determined the crystal structure of colicin D, containing both the CD and CRD. The full-length colicin D/ImmD heterodimer structure was built by superimposing the CD-CRD structure with the previously determined partial structures. The overall translocation process of colicin D, including the interaction between CD and LepB, is discussed.
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Affiliation(s)
- Jung-Wei Chang
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Yusuke Sato
- Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.,Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan
| | - Tetsuhiro Ogawa
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Shuya Fukai
- Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.,Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Haruhiko Masaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan
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16
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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] [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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17
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Bacterial iron acquisition mediated by outer membrane translocation and cleavage of a host protein. Proc Natl Acad Sci U S A 2018; 115:6840-6845. [PMID: 29891657 PMCID: PMC6042079 DOI: 10.1073/pnas.1800672115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The outer membrane of Gram-negative bacteria is a highly impermeable barrier to a range of toxic chemicals and is responsible for the resistance of these bacteria to important classes of antibiotics. In this work, we show that plant pathogenic Pectobacterium spp. acquire iron from the small, stable, and abundant iron-containing plant protein ferredoxin by transporting ferredoxin across the outer membrane for intracellular processing by a highly specific protease, which induces iron release. The presence of homologous uptake and processing proteins in a range of important animal and plant pathogens suggests an exploitable route through which large molecules can penetrate the outer membrane of Gram-negative bacteria. Iron is an essential micronutrient for most bacteria and is obtained from iron-chelating siderophores or directly from iron-containing host proteins. For Gram-negative bacteria, classical iron transport systems consist of an outer membrane receptor, a periplasmic binding protein, and an inner membrane ABC transporter, which work in concert to deliver iron from the cell surface to the cytoplasm. We recently showed that Pectobacterium spp. are able to acquire iron from ferredoxin, a small and stable 2Fe-2S iron sulfur cluster containing protein and identified the ferredoxin receptor, FusA, a TonB-dependent receptor that binds ferredoxin on the cell surface. The genetic context of fusA suggests an atypical iron acquisition system, lacking a periplasmic binding protein, although the mechanism through which iron is extracted from the captured ferredoxin has remained unknown. Here we show that FusC, an M16 family protease, displays a highly targeted proteolytic activity against plant ferredoxin, and that growth enhancement of Pectobacterium due to iron acquisition from ferredoxin is FusC-dependent. The periplasmic location of FusC indicates a mechanism in which ferredoxin is imported into the periplasm via FusA before cleavage by FusC, as confirmed by the uptake and accumulation of ferredoxin in the periplasm in a strain lacking fusC. The existence of homologous uptake systems in a range of pathogenic bacteria suggests that protein uptake for nutrient acquisition may be widespread in bacteria and shows that, similar to their endosymbiotic descendants mitochondria and chloroplasts, bacteria produce dedicated protein import systems.
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18
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Rassam P, Long KR, Kaminska R, Williams DJ, Papadakos G, Baumann CG, Kleanthous C. Intermembrane crosstalk drives inner-membrane protein organization in Escherichia coli. Nat Commun 2018. [PMID: 29540681 PMCID: PMC5852019 DOI: 10.1038/s41467-018-03521-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Gram-negative bacteria depend on energised protein complexes that connect the two membranes of the cell envelope. However, β-barrel outer-membrane proteins (OMPs) and α-helical inner-membrane proteins (IMPs) display quite different organisation. OMPs cluster into islands that restrict their lateral mobility, while IMPs generally diffuse throughout the cell. Here, using live cell imaging of Escherichia coli, we demonstrate that when transient, energy-dependent transmembrane connections are formed, IMPs become subjugated by the inherent organisation of OMPs and that such connections impact IMP function. We show that while establishing a translocon for import, the colicin ColE9 sequesters the IMPs of the proton motive force (PMF)-linked Tol-Pal complex into islands mirroring those of colicin-bound OMPs. Through this imposed organisation, the bacteriocin subverts the outer-membrane stabilising role of Tol-Pal, blocking its recruitment to cell division sites and slowing membrane constriction. The ordering of IMPs by OMPs via an energised inter-membrane bridge represents an emerging functional paradigm in cell envelope biology.
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Affiliation(s)
- Patrice Rassam
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,Laboratoire de Bioimagerie et Pathologie, UMR 7021, CNRS, Université de Strasbourg, Faculté de pharmacie, 74 Route du Rhin, 67401, Illkirch, France
| | - Kathleen R Long
- Department of Biology, University of York, York, YO10 5DD, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - David J Williams
- Department of Biology, University of York, York, YO10 5DD, UK.,Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Grigorios Papadakos
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,Division of Neurobiology, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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19
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Abstract
The outer membrane (OM) excludes antibiotics such as vancomycin that kill gram-positive bacteria, and so is a major contributor to multidrug resistance in gram-negative bacteria. Yet, the OM is readily bypassed by protein bacteriocins, which are toxins released by bacteria to kill their neighbors during competition for resources. Discovered over 60 y ago, it has been a mystery how these proteins cross the OM to deliver their toxic payload. We have discovered how the bacteriocin pyocin S2 (pyoS2), which degrades DNA, enters Pseudomonas aeruginosa cells. PyoS2 tricks the iron transporter FpvAI into transporting it across the OM by a process that is remarkably similar to that used by its endogenous ligand, the siderophore ferripyoverdine. Unlike their descendants, mitochondria and plastids, bacteria do not have dedicated protein import systems. However, paradoxically, import of protein bacteriocins, the mechanisms of which are poorly understood, underpins competition among pathogenic and commensal bacteria alike. Here, using X-ray crystallography, isothermal titration calorimetry, confocal fluorescence microscopy, and in vivo photoactivatable cross-linking of stalled translocation intermediates, we demonstrate how the iron transporter FpvAI in the opportunistic pathogen Pseudomonas aeruginosa is hijacked to translocate the bacteriocin pyocin S2 (pyoS2) across the outer membrane (OM). FpvAI is a TonB-dependent transporter (TBDT) that actively imports the small siderophore ferripyoverdine (Fe-Pvd) by coupling to the proton motive force (PMF) via the inner membrane (IM) protein TonB1. The crystal structure of the N-terminal domain of pyoS2 (pyoS2NTD) bound to FpvAI (Kd = 240 pM) reveals that the pyocin mimics Fe-Pvd, inducing the same conformational changes in the receptor. Mimicry leads to fluorescently labeled pyoS2NTD being imported into FpvAI-expressing P. aeruginosa cells by a process analogous to that used by bona fide TBDT ligands. PyoS2NTD induces unfolding by TonB1 of a force-labile portion of the plug domain that normally occludes the central channel of FpvAI. The pyocin is then dragged through this narrow channel following delivery of its own TonB1-binding epitope to the periplasm. Hence, energized nutrient transporters in bacteria also serve as rudimentary protein import systems, which, in the case of FpvAI, results in a protein antibiotic 60-fold bigger than the transporter’s natural substrate being translocated across the OM.
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20
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Mills A, Duong F. Lipopolysaccharides promote binding and unfolding of the antibacterial colicin E3 rRNAse domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2454-2460. [PMID: 28888366 DOI: 10.1016/j.bbamem.2017.08.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 11/17/2022]
Abstract
Nuclease colicins are antibacterial proteins produced by certain strains of E. coli to reduce competition from rival strains. These colicins are generally organized with an N-terminal transport (T)-domain, a central receptor binding (R)-domain, and a C-terminal cytotoxic nuclease domain. These colicins are always produced in complex with an inhibitory immunity protein, which dissociates prior entrance of the cytotoxic domain in the target cell. How exactly colicins traverse the cell envelope is not understood, yet this knowledge is important for the design of new antibacterial therapies. In this report, we find that the cytotoxic rRNAse domain of colicin E3, lacking both T- and R-domains, is sufficient to inhibit cell growth provided the immunity protein Im3 has been removed. Thus, while the T-domain is needed for dissociation of Im3, the rRNAse alone can associate to the cell surface without R-domain. Accordingly, we find a high affinity interaction (Kd ~1-2μM) between the rRNAse domain and lipopolysaccharides (LPS). Furthermore, we show that binding of ColE3 to LPS destabilizes the secondary structure of the toxin, which is expectedly crucial for transport through the narrow pore of the porin OmpF. The effect of LPS on binding and unfolding of ColE3 may be indicative of a broader role of LPS for transport of colicins in general.
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Affiliation(s)
- Allan Mills
- Department of Biochemistry & Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Franck Duong
- Department of Biochemistry & Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
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21
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The Colicin E1 TolC Box: Identification of a Domain Required for Colicin E1 Cytotoxicity and TolC Binding. J Bacteriol 2016; 199:JB.00412-16. [PMID: 27795317 DOI: 10.1128/jb.00412-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/17/2016] [Indexed: 11/20/2022] Open
Abstract
Colicins are protein toxins made by Escherichia coli to kill related bacteria that compete for scarce resources. All colicins must cross the target cell outer membrane in order to reach their intracellular targets. Normally, the first step in the intoxication process is the tight binding of the colicin to an outer membrane receptor protein via its central receptor-binding domain. It is shown here that for one colicin, E1, that step, although it greatly increases the efficiency of killing, is not absolutely necessary. For colicin E1, the second step, translocation, relies on the outer membrane/transperiplasmic protein TolC. The normal role of TolC in bacteria is as an essential component of a family of tripartite drug and toxin exporters, but for colicin E1, it is essential for its import. Colicin E1 and some N-terminal translocation domain peptides had been shown previously to bind in vitro to TolC and occlude channels made by TolC in planar lipid bilayer membranes. Here, a set of increasingly shorter colicin E1 translocation domain peptides was shown to bind to Escherichia coli in vivo and protect them from subsequent challenge by colicin E1. A segment of only 21 residues, the "TolC box," was thereby defined; that segment is essential for colicin E1 cytotoxicity and for binding of translocation domain peptides to TolC. IMPORTANCE The Escherichia coli outer membrane/transperiplasmic protein TolC is normally an essential component of the bacterium's tripartite drug and toxin export machinery. The protein toxin colicin E1 instead uses TolC for its import into the cells that it kills, thereby subverting its normal role. Increasingly shorter constructs of the colicin's N-terminal translocation domain were used to define an essential 21-residue segment that is required for both colicin cytotoxicity and for binding of the colicin's translocation domain to bacteria, in order to protect them from subsequent challenge by active colicin E1. Thus, an essential TolC binding sequence of colicin E1 was identified and may ultimately lead to the development of drugs to block the bacterial drug export pathway.
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22
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CdiA Effectors from Uropathogenic Escherichia coli Use Heterotrimeric Osmoporins as Receptors to Recognize Target Bacteria. PLoS Pathog 2016; 12:e1005925. [PMID: 27723824 PMCID: PMC5056734 DOI: 10.1371/journal.ppat.1005925] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/10/2016] [Indexed: 12/28/2022] Open
Abstract
Many Gram-negative bacterial pathogens express contact-dependent growth inhibition (CDI) systems that promote cell-cell interaction. CDI+ bacteria express surface CdiA effector proteins, which transfer their C-terminal toxin domains into susceptible target cells upon binding to specific receptors. CDI+ cells also produce immunity proteins that neutralize the toxin domains delivered from neighboring siblings. Here, we show that CdiAEC536 from uropathogenic Escherichia coli 536 (EC536) uses OmpC and OmpF as receptors to recognize target bacteria. E. coli mutants lacking either ompF or ompC are resistant to CDIEC536-mediated growth inhibition, and both porins are required for target-cell adhesion to inhibitors that express CdiAEC536. Experiments with single-chain OmpF fusions indicate that the CdiAEC536 receptor is heterotrimeric OmpC-OmpF. Because the OmpC and OmpF porins are under selective pressure from bacteriophages and host immune systems, their surface-exposed loops vary between E. coli isolates. OmpC polymorphism has a significant impact on CDIEC536 mediated competition, with many E. coli isolates expressing alleles that are not recognized by CdiAEC536. Analyses of recombinant OmpC chimeras suggest that extracellular loops L4 and L5 are important recognition epitopes for CdiAEC536. Loops L4 and L5 also account for much of the sequence variability between E. coli OmpC proteins, raising the possibility that CDI contributes to the selective pressure driving OmpC diversification. We find that the most efficient CdiAEC536 receptors are encoded by isolates that carry the same cdi gene cluster as E. coli 536. Thus, it appears that CdiA effectors often bind preferentially to "self" receptors, thereby promoting interactions between sibling cells. As a consequence, these effector proteins cannot recognize nor suppress the growth of many potential competitors. These findings suggest that self-recognition and kin selection are important functions of CDI. Bacterial pathogens often live in crowded communities where cells reside in close contact with one another. Many of these bacteria possess contact-dependent growth inhibition (CDI) systems, which allow cells to touch and inhibit each other using toxic CdiA proteins. CDI+ bacteria also produce immunity proteins that specifically protect the cell from the CdiA toxins of neighboring sibling cells. The CDI system from Escherichia coli EC93 was the first to be characterized and its CdiA toxin recognizes a receptor (BamA) that is identical in virtually all E. coli isolates. Here, we describe a different CDI system from uropathogenic E. coli 536, which causes urinary tract infections. In contrast to E. coli EC93, CdiA from E. coli 536 binds to receptor proteins (OmpC/OmpF) that vary widely between different E. coli isolates. Thus, uropathogenic E. coli preferentially bind and deliver toxins into sibling cells and other closely related E. coli strains. These results suggest that CDI systems distinguish between "self" and "non-self" cells. Moreover, because sibling cells are immune to CdiA-mediated growth inhibition, these findings raise the possibility that toxin exchange may be used for communication and cooperative behavior between genetically identical bacteria.
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Zakharov SD, Wang XS, Cramer WA. The Colicin E1 TolC-Binding Conformer: Pillar or Pore Function of TolC in Colicin Import? Biochemistry 2016; 55:5084-94. [PMID: 27536862 DOI: 10.1021/acs.biochem.6b00621] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The mechanism by which the drug export protein TolC is utilized for import of the cytotoxin colicin E1 across the outer membrane and periplasmic space is addressed. Studies of the initial binding of colicin E1 with TolC, occlusion of membrane-incorporated TolC ion channels, and the structure underlying the colicin-TolC complex were based on the interactions with TolC of individual colicin translocation domain (T-domain) peptides from a set of 19 that span different segments of the T-domain. These studies led to identification of a short 20-residue segment 101-120, a "TolC box", located near the center of the colicin T-domain, which is necessary for binding of colicin to TolC. Omission of this segment eliminated the ability of the T-domain to occlude TolC channels and to co-elute with TolC on a size-exclusion column. Far-ultraviolet circular dichroism spectral and thermal stability analysis of the structure of T-domain peptides implies (i) a helical hairpin conformation of the T-domain, (ii) the overlap of the TolC-binding site with a hinge of the helical hairpin, and (iii) a TolC-dependent stage of colicin import in which a central segment of the T-domain in a helical hairpin conformation binds to the TolC entry port following initial binding to the BtuB receptor. These studies provide the first structure-based information about the interaction of colicin E1 with the unique TolC protein. The model inferred for binding of the T-domain to TolC implies reservations about the traditional model for colicin import in which TolC functions to provide a channel for translocation of the colicin in an unfolded state across the bacterial outer membrane and a large part of the periplasmic space.
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Affiliation(s)
- Stanislav D Zakharov
- Department of Biological Sciences, Purdue University , Hockmeyer Building of Structural Biology, West Lafayette, Indiana 47907, United States
| | - Xin S Wang
- Department of Biological Sciences, Purdue University , Hockmeyer Building of Structural Biology, West Lafayette, Indiana 47907, United States
| | - William A Cramer
- Department of Biological Sciences, Purdue University , Hockmeyer Building of Structural Biology, West Lafayette, Indiana 47907, United States
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Bosák J, Micenková L, Doležalová M, Šmajs D. Colicins U and Y inhibit growth of Escherichia coli strains via recognition of conserved OmpA extracellular loop 1. Int J Med Microbiol 2016; 306:486-494. [PMID: 27510856 DOI: 10.1016/j.ijmm.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/28/2016] [Accepted: 07/31/2016] [Indexed: 01/04/2023] Open
Abstract
Interactions of colicins U and Y with the OmpA (Outer membrane protein A) receptor molecule were studied using site-directed mutagenesis and colicin binding assay. A systematic mutagenesis of the colicin-susceptible OmpA sequence from Escherichia coli (OmpAEC) to the colicin-resistant OmpA sequence from Serratia marcescens (OmpASM) was performed in regions corresponding to extracellular OmpA loops 1-4. Susceptibility to colicins U and Y was significantly affected by the OmpA mutation in loop 1. As with functional analysis, a decrease in binding capacity of His-tagged colicin U was found for recombinant OmpA with a mutated segment in loop 1 compared to control OmpAEC. To verify the importance of the identified amino acid residues in OmpA loop 1, we introduced loop 1 from OmpAEC into OmpASM, which resulted in the substantial increase of susceptibility to colicins U and Y. In addition, colicins U and Y were tested against a panel of 118 bacteriocin non-producing strains of four Escherichia species, including E. coli (39 strains), E. fergusonii (10 strains), E. hermannii (42 strains), and E. vulneris (27 strains). A majority (82%) of E. coli strains was susceptible to colicins U and Y. Interestingly, colicins U and Y also inhibited all of the 30 tested multidrug-resistant E. coli O25b-ST131 isolates. These findings, together with the fact that OmpA loop 1 is important for bacterial virulence and is evolutionary conserved, offer the potential of using colicins U and Y as specific anti-OmpA loop 1 directed antibacterial proteins.
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Affiliation(s)
- Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| | - Lenka Micenková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic
| | - Magda Doležalová
- Department of Environment Protection Engineering, Faculty of Technology, Tomas Bata University in Zlín, T. G. Masaryk square 275, Zlín, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic.
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25
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Structural and biophysical analysis of nuclease protein antibiotics. Biochem J 2016; 473:2799-812. [PMID: 27402794 PMCID: PMC5264503 DOI: 10.1042/bcj20160544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/07/2016] [Indexed: 01/28/2023]
Abstract
Protein antibiotics (bacteriocins) are a large and diverse family of multidomain toxins that kill specific Gram-negative bacteria during intraspecies competition for resources. Our understanding of the mechanism of import of such potent toxins has increased significantly in recent years, especially with the reporting of several structures of bacteriocin domains. Less well understood is the structural biochemistry of intact bacteriocins and how these compare across bacterial species. Here, we focus on endonuclease (DNase) bacteriocins that target the genomes of Escherichia coli and Pseudomonas aeruginosa, known as E-type colicins and S-type pyocins, respectively, bound to their specific immunity (Im) proteins. First, we report the 3.2 Å structure of the DNase colicin ColE9 in complex with its ultra-high affinity Im protein, Im9. In contrast with Im3, which when bound to the ribonuclease domain of the homologous colicin ColE3 makes contact with the translocation (T) domain of the toxin, we find that Im9 makes no such contact and only interactions with the ColE9 cytotoxic domain are observed. Second, we report small-angle X-ray scattering data for two S-type DNase pyocins, S2 and AP41, into which are fitted recently determined X-ray structures for isolated domains. We find that DNase pyocins and colicins are both highly elongated molecules, even though the order of their constituent domains differs. We discuss the implications of these architectural similarities and differences in the context of the translocation mechanism of protein antibiotics through the cell envelope of Gram-negative bacteria.
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26
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Burger VM, Nolasco DO, Stultz CM. Expanding the Range of Protein Function at the Far End of the Order-Structure Continuum. J Biol Chem 2016; 291:6706-13. [PMID: 26851282 PMCID: PMC4807258 DOI: 10.1074/jbc.r115.692590] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The traditional view of the structure-function paradigm is that a protein's function is inextricably linked to a well defined, three-dimensional structure, which is determined by the protein's primary amino acid sequence. However, it is now accepted that a number of proteins do not adopt a unique tertiary structure in solution and that some degree of disorder is required for many proteins to perform their prescribed functions. In this review, we highlight how a number of protein functions are facilitated by intrinsic disorder and introduce a new protein structure taxonomy that is based on quantifiable metrics of a protein's disorder.
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Affiliation(s)
- Virginia M Burger
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and
| | - Diego O Nolasco
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and
| | - Collin M Stultz
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and the Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138
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27
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Mora L, Moncoq K, England P, Oberto J, de Zamaroczy M. The Stable Interaction Between Signal Peptidase LepB of Escherichia coli and Nuclease Bacteriocins Promotes Toxin Entry into the Cytoplasm. J Biol Chem 2015; 290:30783-96. [PMID: 26499796 DOI: 10.1074/jbc.m115.691907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 01/13/2023] Open
Abstract
LepB is a key membrane component of the cellular secretion machinery, which releases secreted proteins into the periplasm by cleaving the inner membrane-bound leader. We showed that LepB is also an essential component of the machinery hijacked by the tRNase colicin D for its import. Here we demonstrate that this non-catalytic activity of LepB is to promote the association of the central domain of colicin D with the inner membrane before the FtsH-dependent proteolytic processing and translocation of the toxic tRNase domain into the cytoplasm. The novel structural role of LepB results in a stable interaction with colicin D, with a stoichiometry of 1:1 and a nanomolar Kd determined in vitro. LepB provides a chaperone-like function for the penetration of several nuclease-type bacteriocins into target cells. The colicin-LepB interaction is shown to require only a short peptide sequence within the central domain of these bacteriocins and to involve residues present in the short C-terminal Box E of LepB. Genomic screening identified the conserved LepB binding motif in colicin-like ORFs from 13 additional bacterial species. These findings establish a new paradigm for the functional adaptability of an essential inner-membrane enzyme.
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Affiliation(s)
- Liliana Mora
- From the Institut de Biologie Physico-Chimique, CNRS, FRE 3630 (UPR 9073), 75005 Paris, France
| | - Karine Moncoq
- Institut de Biologie Physico-Chimique, CNRS, UMR 7099 (Université Paris 7-Diderot), 75005 Paris, France
| | - Patrick England
- Institut Pasteur, PFBMI, CNRS, UMR 3528, 75015 Paris, France, and
| | - Jacques Oberto
- Institute of Integrative Cellular Biology, CEA, CNRS (Université Paris 11), 91405 Orsay, France
| | - Miklos de Zamaroczy
- From the Institut de Biologie Physico-Chimique, CNRS, FRE 3630 (UPR 9073), 75005 Paris, France,
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28
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Smallwood CR, Jordan L, Trinh V, Schuerch DW, Gala A, Hanson M, Hanson M, Shipelskiy Y, Majumdar A, Newton SMC, Klebba PE. Concerted loop motion triggers induced fit of FepA to ferric enterobactin. ACTA ACUST UNITED AC 2015; 144:71-80. [PMID: 24981231 PMCID: PMC4076525 DOI: 10.1085/jgp.201311159] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The loops of the bacterial outer membrane iron transporter FepA move at different rates to adsorb and grasp the substrate ferric enterobactin before transporting it into the periplasm. Spectroscopic analyses of fluorophore-labeled Escherichia coli FepA described dynamic actions of its surface loops during binding and transport of ferric enterobactin (FeEnt). When FeEnt bound to fluoresceinated FepA, in living cells or outer membrane fragments, quenching of fluorophore emissions reflected conformational motion of the external vestibular loops. We reacted Cys sulfhydryls in seven surface loops (L2, L3, L4, L5, L7 L8, and L11) with fluorophore maleimides. The target residues had different accessibilities, and the labeled loops themselves showed variable extents of quenching and rates of motion during ligand binding. The vestibular loops closed around FeEnt in about a second, in the order L3 > L11 > L7 > L2 > L5 > L8 > L4. This sequence suggested that the loops bind the metal complex like the fingers of two hands closing on an object, by individually adsorbing to the iron chelate. Fluorescence from L3 followed a biphasic exponential decay as FeEnt bound, but fluorescence from all the other loops followed single exponential decay processes. After binding, the restoration of fluorescence intensity (from any of the labeled loops) mirrored cellular uptake that depleted FeEnt from solution. Fluorescence microscopic images also showed FeEnt transport, and demonstrated that ferric siderophore uptake uniformly occurs throughout outer membrane, including at the poles of the cells, despite the fact that TonB, its inner membrane transport partner, was not detectable at the poles.
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Affiliation(s)
- Chuck R Smallwood
- The Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Lorne Jordan
- The Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Vy Trinh
- The Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Daniel W Schuerch
- The Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Amparo Gala
- The Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Mathew Hanson
- The Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | | | - Yan Shipelskiy
- The Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Aritri Majumdar
- The Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Salete M C Newton
- The Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
| | - Phillip E Klebba
- The Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506
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29
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Abstract
Two membranes enclose Gram-negative bacteria-an inner membrane consisting of phospholipid and an outer membrane having an asymmetric structure in which the inner leaflet contains phospholipid and the outer leaflet consists primarily of lipopolysaccharide. The impermeable nature of the outer membrane imposes a need for numerous outer membrane pores and transporters to ferry substances in and out of the cell. These outer membrane proteins have structures distinct from their inner membrane counterparts and most often function without any discernable energy source. In this chapter, we review the structures and functions of four classes of outer membrane protein: general and specific porins, specific transporters, TonB-dependent transporters, and export channels. While not an exhaustive list, these classes exemplify small-molecule transport across the outer membrane and illustrate the diversity of structures and functions found in Gram-negative bacteria.
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30
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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: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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 pathogen. Intricate regulatory mechanisms ensure that bacteria have the right complement of β-barrel outer membrane proteins (OMPs) to enable adaptation to a particular habitat. Yet no mechanism is known for replacing OMPs in the outer membrane, an issue that is further confounded by the lack of an energy source and the high stability and abundance of OMPs. Here we uncover the process underpinning OMP turnover in E. coli and show it to be passive and binary in nature, in which 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 simulations, we established the mechanism for binary OMP partitioning. OMPs clustered to form ∼0.5-μm diameter islands, where their diffusion is 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 outer membrane. 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 outer membrane of a Gram-negative bacterium is a spatially and temporally organized structure, and this organization 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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31
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Kleinschmidt JH. Folding of β-barrel membrane proteins in lipid bilayers - Unassisted and assisted folding and insertion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1927-43. [PMID: 25983306 DOI: 10.1016/j.bbamem.2015.05.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 05/06/2015] [Accepted: 05/07/2015] [Indexed: 01/08/2023]
Abstract
In cells, β-barrel membrane proteins are transported in unfolded form to an outer membrane into which they fold and insert. Model systems have been established to investigate the mechanisms of insertion and folding of these versatile proteins into detergent micelles, lipid bilayers and even synthetic amphipathic polymers. In these experiments, insertion into lipid membranes is initiated from unfolded forms that do not display residual β-sheet secondary structure. These studies therefore have allowed the investigation of membrane protein folding and insertion in great detail. Folding of β-barrel membrane proteins into lipid bilayers has been monitored from unfolded forms by dilution of chaotropic denaturants that keep the protein unfolded as well as from unfolded forms present in complexes with molecular chaperones from cells. This review is aimed to provide an overview of the principles and mechanisms observed for the folding of β-barrel transmembrane proteins into lipid bilayers, the importance of lipid-protein interactions and the function of molecular chaperones and folding assistants. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Jörg H Kleinschmidt
- Abteilung Biophysik, Institut für Biologie, FB 10, Universität Kassel and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), Heinrich-Plett-Str. 40, D-34132 Kassel, Germany.
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32
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Mora L, de Zamaroczy M. In vivo processing of DNase colicins E2 and E7 is required for their import into the cytoplasm of target cells. PLoS One 2014; 9:e96549. [PMID: 24840776 PMCID: PMC4026351 DOI: 10.1371/journal.pone.0096549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/08/2014] [Indexed: 11/19/2022] Open
Abstract
DNase colicins E2 and E7, both of which appropriate the BtuB/Tol translocation machinery to cross the outer membrane, undergo a processing step as they enter the cytoplasm. This endoproteolytic cleavage is essential for their killing action. A processed form of the same size, 18.5 kDa, which corresponds to the C-terminal catalytic domain, was detected in the cytoplasm of bacteria treated with either of the two DNase colicins. The inner-membrane protease FtsH is necessary for the processing that allows the translocation of the colicin DNase domain into the cytoplasm. The processing occurs near residue D420, at the same position as the FtsH-dependent cleavage in RNase colicins E3 and D. The cleavage site is located 30 amino acids upstream of the DNase domain. In contrast, the previously reported periplasm-dependent colicin cleavage, located at R452 in colicin E2, was shown to be generated by the outer-membrane protease OmpT and we show that this cleavage is not physiologically relevant for colicin import. Residue R452, whose mutated derivatives led to toxicity defect, was shown to have no role in colicin processing and translocation, but it plays a key role in the catalytic activity, as previously reported for other DNase colicins. Membrane associated forms of colicins E2 and E7 were detected on target cells as proteinase K resistant peptides, which include both the receptor-binding and DNase domains. A similar, but much less proteinase K-resistant form was also detected with RNase colicin E3. These colicin forms are not relevant for colicin import, but their detection on the cell surface indicates that whole nuclease-colicin molecules are found in a stable association with the outer-membrane receptor BtuB of the target cells.
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Affiliation(s)
- Liliana Mora
- Institut de Biologie Physico-Chimique, CNRS, UPR 9073, Paris, France
| | - Miklos de Zamaroczy
- Institut de Biologie Physico-Chimique, CNRS, UPR 9073, Paris, France
- * E-mail:
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33
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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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34
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Johnson CL, Ridley H, Marchetti R, Silipo A, Griffin DC, Crawford L, Bonev B, Molinaro A, Lakey JH. The antibacterial toxin colicin N binds to the inner core of lipopolysaccharide and close to its translocator protein. Mol Microbiol 2014; 92:440-52. [PMID: 24589252 PMCID: PMC4114557 DOI: 10.1111/mmi.12568] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2014] [Indexed: 12/03/2022]
Abstract
Colicins are a diverse family of large antibacterial protein toxins, secreted by and active against Escherichia coli and must cross their target cell's outer membrane barrier to kill. To achieve this, most colicins require an abundant porin (e.g. OmpF) plus a low‐copy‐number, high‐affinity, outer membrane protein receptor (e.g. BtuB). Recently, genetic screens have suggested that colicin N (ColN), which has no high‐affinity receptor, targets highly abundant lipopolysaccharide (LPS) instead. Here we reveal the details of this interaction and demonstrate that the ColN receptor‐binding domain (ColN‐R) binds to a specific region of LPS close to the membrane surface. Data from in vitro studies using calorimetry and both liquid‐ and solid‐state NMR reveal the interactions behind the in vivo requirement for a defined oligosaccharide region of LPS. Delipidated LPS (LPSΔLIPID) shows weaker binding; and thus full affinity requires the lipid component. The site of LPS binding means that ColN will preferably bind at the interface and thus position itself close to the surface of its translocon component, OmpF. ColN is, currently, unique among colicins in requiring LPS and, combined with previous data, this implies that the ColN translocon is distinct from those of other known colicins.
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Affiliation(s)
- Christopher L Johnson
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, UK
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35
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Jakes KS. Daring to be different: colicin N finds another way. Mol Microbiol 2014; 92:435-9. [PMID: 24589284 DOI: 10.1111/mmi.12569] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2014] [Indexed: 11/28/2022]
Abstract
The mechanisms by which colicins, protein toxins produced by Escherichia coli, kill other E. coli, have become much better understood in recent years. Most colicins initially bind to an outer membrane protein receptor, and then search for a separate nearby outer membrane protein translocator that serves as a pathway into target cells. Many colicins use the outer membrane porin, OmpF, as that translocator, while using a different primary receptor. Colicin N is unique among known colicins in that only OmpF had been identified as being required for uptake of the colicin and it was presumed to somehow serve as both receptor and translocator. Genetic screens also identified a number of genes required for lipopolysaccharide (LPS) synthesis as uniquely required for killing by colicin N, but not by other colicins. Johnson et al. show that the receptor-binding domain of colicin N binds to LPS, and does not require OmpF for that binding. LPS of a minimal length is required for binding, explaining the requirement for specific elements of the LPS biosynthetic pathway. For colicin N, the receptor-binding domain does not recognize a protein, but rather the most abundant component of the outer membrane itself, LPS.
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Affiliation(s)
- Karen S Jakes
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
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36
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McCaughey LC, Grinter R, Josts I, Roszak AW, Waløen KI, Cogdell RJ, Milner J, Evans T, Kelly S, Tucker NP, Byron O, Smith B, Walker D. Lectin-like bacteriocins from Pseudomonas spp. utilise D-rhamnose containing lipopolysaccharide as a cellular receptor. PLoS Pathog 2014; 10:e1003898. [PMID: 24516380 PMCID: PMC3916391 DOI: 10.1371/journal.ppat.1003898] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/10/2013] [Indexed: 11/24/2022] Open
Abstract
Lectin-like bacteriocins consist of tandem monocot mannose-binding domains and display a genus-specific killing activity. Here we show that pyocin L1, a novel member of this family from Pseudomonas aeruginosa, targets susceptible strains of this species through recognition of the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide that is predominantly a homopolymer of d-rhamnose. Structural and biophysical analyses show that recognition of CPA occurs through the C-terminal carbohydrate-binding domain of pyocin L1 and that this interaction is a prerequisite for bactericidal activity. Further to this, we show that the previously described lectin-like bacteriocin putidacin L1 shows a similar carbohydrate-binding specificity, indicating that oligosaccharides containing d-rhamnose and not d-mannose, as was previously thought, are the physiologically relevant ligands for this group of bacteriocins. The widespread inclusion of d-rhamnose in the lipopolysaccharide of members of the genus Pseudomonas explains the unusual genus-specific activity of the lectin-like bacteriocins. Due to rapidly increasing rates of antibiotic resistance observed among Gram-negative pathogens, such as Pseudomonas aeruginosa, there is an urgent requirement for novel approaches to the treatment of bacterial infections. Lectin-like bacteriocins are highly potent protein antibiotics that display an unusual ability to kill a select group of bacteria within a specific genus. In this work, we show how the lectin-like protein antibiotic, pyocin L1, can kill Pseudomonas aeruginosa with extraordinary potency through specific binding to the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide. The CPA is predominantly a homopolymer of the sugar d-rhamnose that although generally rare in nature is found frequently as a component of the lipopolysaccharide of members of the genus Pseudomonas. The targeting of d-rhamnose containing polysaccharides by pyocin L1 and a related lectin-like protein antibiotic, putidacin L1, explains the unusual genus- specific killing activity of the lectin-like bacteriocins. As we learn more about the link between changes to the microbiome and a range of chronic diseases there is a growing realisation that the ability to target specific bacterial pathogens while maintaining the normal gut flora is a desirable property for next generation antibiotics.
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Affiliation(s)
- Laura C. McCaughey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rhys Grinter
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Inokentijs Josts
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Aleksander W. Roszak
- WestCHEM, School of Chemistry, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kai I. Waløen
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard J. Cogdell
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Joel Milner
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Tom Evans
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sharon Kelly
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nicholas P. Tucker
- Strathclyde Institute for Pharmaceutical and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Brian Smith
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel Walker
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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37
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Saif Hasan S, Baniulis D, Yamashita E, Zhalnina MV, Zakharov SD, Stofleth JT, Cramer WA. Methods for studying interactions of detergents and lipids with α-helical and β-barrel integral membrane proteins. ACTA ACUST UNITED AC 2013; 74:29.7.1-29.7.30. [PMID: 24510648 DOI: 10.1002/0471140864.ps2907s74] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Methods for studying interactions of protein with lipids and detergents are described for representatives of two major classes of membrane proteins: (1) the α-helical hetero-oligomeric integral cytochrome b6 f complex of oxygenic photosynthesis from cyanobacteria, and (2) the outer membrane β-barrel proteins BtuB and OmpF from Gram-negative Escherichia coli bacteria. Details are presented on the use of detergents for purification and crystallization of the b6 f complex as well as a method for lipid exchange. The positions of detergent and lipid molecules, which define eight potential lipid-binding sites in the b6 f complex, are described. Differences in detergent strategies for isolation and crystallization of β-barrel proteins relative to those for oligomeric helical membrane proteins are discussed, and purification and assessment of protein quality by circular dichroism (CD) is presented.
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Affiliation(s)
- S Saif Hasan
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Danas Baniulis
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana.,Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Babtai, Kaunas Region, Lithuania
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Mariya V Zhalnina
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Stanislav D Zakharov
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana.,Institute of Basic Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
| | - Jason T Stofleth
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana.,Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California
| | - William A Cramer
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
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38
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FhuA interactions in a detergent-free nanodisc environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:364-71. [PMID: 24140007 DOI: 10.1016/j.bbamem.2013.09.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 11/20/2022]
Abstract
TonB-dependent membrane receptors from bacteria have been analyzed in detergent-containing solution, an environment that may influence the role of ligand in inducing downstream interactions. We report reconstitution of FhuA into a membrane mimetic: nanodiscs. In contrast to previous results in detergent, we show that binding of TonB to FhuA in nanodiscs depends strongly on ferricrocin. The stoichiometry of interaction is 1:1 and the binding constant KD is ~200nM; an equilibrium affinity that is ten-fold lower than reported in detergent. FhuA in nanodiscs also forms a high-affinity binding site for colicin M (KD ~3.5nM), while ferricrocin renders FhuA refractory to colicin binding. Together, these results demonstrate the importance of the ligand in regulating receptor interactions and the advantages of nanodiscs to study β-barrel membrane proteins in a membrane-like environment.
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39
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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] [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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40
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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] [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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41
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Translocation trumps receptor binding in colicin entry into Escherichia coli. Biochem Soc Trans 2013; 40:1443-8. [PMID: 23176496 DOI: 10.1042/bst20120207] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Of the steps involved in the killing of Escherichia coli by colicins, binding to a specific outer-membrane receptor was the best understood and earliest characterized. Receptor binding was believed to be an indispensable step in colicin intoxication, coming before the less well-understood step of translocation across the outer membrane to present the killing domain to its target. In the process of identifying the translocator for colicin Ia, I created chimaeric colicins, as well as a deletion missing the entire receptor-binding domain of colicin Ia. The normal pathway for colicin Ia killing was shown to require two copies of Cir: one that serves as the primary receptor and a second copy that serves as translocator. The novel Ia colicins retain the ability to kill E. coli, even in the absence of receptor binding, as long as they can translocate via their Cir translocator. Experiments to determine whether colicin M uses a second copy of its receptor, FhuA, as its translocator were hampered by precipitation of colicin M chimaeras in inclusion bodies. Nevertheless, I show that receptor binding can be bypassed for killing, as long as a translocation pathway is maintained for colicin M. These experiments suggest that colicin M, unlike colicin Ia, may normally use a single copy of FhuA as both its receptor and its translocator. Colicin E1 can kill in the absence of receptor binding, using translocation through TolC.
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Abstract
A Biochemical Society Focused Meeting on bacteriocins was held at the University of Nottingham on 16-18 July 2012 to mark the retirement of Professor Richard James and honour a scientific career of more than 30 years devoted to an understanding of the biology of colicins, bacteriocins produced by Escherichia coli. This meeting was the third leg of a triumvirate of symposia that included meetings at the Île de Bendor, France, in 1991 and the University of East Anglia, Norwich, U.K., in 1998, focused on bringing together leading experts in basic and applied bacteriocin research. The symposium which attracted 70 attendees consisted of 18 invited speakers and 22 selected oral communications spread over four themes: (i) Role of bacteriocins in bacterial ecology, (ii) Mode of action of bacteriocins, (ii) Mechanisms of bacteriocin import across the cell envelope, and (iv) Biotechnological and biomedical applications of bacteriocins. Speakers and poster presenters travelled from around the world, including the U.S.A., Japan, Asia and Europe, to showcase the latest developments in their scientific research.
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Bushell S, Mainprize I, Wear M, Lou H, Whitfield C, Naismith J. Wzi is an outer membrane lectin that underpins group 1 capsule assembly in Escherichia coli. Structure 2013; 21:844-53. [PMID: 23623732 PMCID: PMC3791409 DOI: 10.1016/j.str.2013.03.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/19/2013] [Accepted: 03/20/2013] [Indexed: 12/12/2022]
Abstract
Many pathogenic bacteria encase themselves in a polysaccharide capsule that provides a barrier to the physical and immunological challenges of the host. The mechanism by which the capsule assembles around the bacterial cell is unknown. Wzi, an integral outer-membrane protein from Escherichia coli, has been implicated in the formation of group 1 capsules. The 2.6 Å resolution structure of Wzi reveals an 18-stranded β-barrel fold with a novel arrangement of long extracellular loops that blocks the extracellular entrance and a helical bundle that plugs the periplasmic end. Mutagenesis shows that specific extracellular loops are required for in vivo capsule assembly. The data show that Wzi binds the K30 carbohydrate polymer and, crucially, that mutants functionally deficient in vivo show no binding to K30 polymer in vitro. We conclude that Wzi is a novel outer-membrane lectin that assists in the formation of the bacterial capsule via direct interaction with capsular polysaccharides.
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Affiliation(s)
- Simon R. Bushell
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Iain L. Mainprize
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Martin A. Wear
- School of Chemistry, King’s Buildings, University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Hubing Lou
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Chris Whitfield
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
- Corresponding author
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44
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Affiliation(s)
- Karen S. Jakes
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461;
| | - William A. Cramer
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907;
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45
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Abstract
We are investigating how protein bacteriocins import their toxic payload across the Gram-negative cell envelope, both as a means of understanding the translocation process itself and as a means of probing the organization of the cell envelope and the function of the protein machines within it. Our work focuses on the import mechanism of the group A endonuclease (DNase) colicin ColE9 into Escherichia coli, where we combine in vivo observations with structural, biochemical and biophysical approaches to dissect the molecular mechanism of colicin entry. ColE9 assembles a multiprotein ‘translocon’ complex at the E. coli outer membrane that triggers entry of the toxin across the outer membrane and the simultaneous jettisoning of its tightly bound immunity protein, Im9, in a step that is dependent on the protonmotive force. In the present paper, we focus on recent work where we have uncovered how ColE9 assembles its translocon complex, including isolation of the complex, and how this leads to subversion of a signal intrinsic to the Tol–Pal assembly within the periplasm and inner membrane. In this way, the externally located ColE9 is able to ‘connect’ to the inner membrane protonmotive force via a network of protein–protein interactions that spans the entirety of the E. coli cell envelope to drive dissociation of Im9 and initiate entry of the colicin into the cell.
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46
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Colicin A binds to a novel binding site of TolA in the Escherichia coli periplasm. Biochem Soc Trans 2012; 40:1469-74. [DOI: 10.1042/bst20120239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Colicins are protein antibiotics produced by Escherichia coli to kill closely related non-identical competing species. They have taken advantage of the promiscuity of several proteins in the cell envelope for entry into the bacterial cell. The Tol–Pal system comprises one such ensemble of periplasmic and membrane-associated interacting proteins that links the IM (inner membrane) and OM (outer membrane) and provides the cell with a structural scaffold for cell division and energy transduction. Central to the Tol–Pal system is the TolA hub protein which forms protein–protein interactions with all other members and also with extrinsic proteins such as colicins A, E1, E2–E9 and N, and the coat proteins of the Ff family of filamentous bacteriophages. In the present paper, we review the role of TolA in the translocation of colicin A through the recently determined crystal structure of the complex of TolA with a translocation domain peptide of ColA (TA53–107), we demonstrate that TA53–107 binds to TolA at a novel binding site and compare the interactions of TolA with other colicins that use the Tol–Pal system for cell entry substantiating further the role of TolA as a periplasmic hub protein.
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47
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Pathways of colicin import: utilization of BtuB, OmpF porin and the TolC drug-export protein. Biochem Soc Trans 2012; 40:1463-8. [PMID: 23176499 DOI: 10.1042/bst20120211] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pathway I. Group A nuclease colicins parasitize and bind tightly (Kd ≤ 10−9 M) to the vitamin B12 receptor on which they diffuse laterally in the OM (outer membrane) and use their long (≥100 Å; 1 Å=0.1 nm) receptor-binding domain as a ‘fishing pole’ to locate the OmpF porin channel for translocation. Crystal structures of OmpF imply that a disordered N-terminal segment of the colicin T-domain initiates insertion. Pathway II. Colicin N does not possess a ‘fishing pole’ receptor-binding domain. Instead, it uses OmpF as the Omp (outer membrane protein) for reception and translocation, processes in which LPS (lipopolysaccharide) may also serve. Keio collection experiments defined the LPS core that is used. Pathway III. Colicin E1 utilizes the drug-export protein TolC for import. CD spectra and thermal-melting analysis predict: (i) N-terminal translocation (T) and central receptor (BtuB) -binding (R) domains are predominantly α-helical; and (ii) helical coiled-coil conformation of the R-domain is similar to that of colicins E3 and Ia. Recombinant colicin peptides spanning the N-terminal translocation domain defined TolC-binding site(s). The N-terminal 40-residue segment lacks the ordered secondary structure. Peptide 41–190 is helical (78%), co-elutes with TolC and occluded TolC channels. Driven by a trans-negative potential, peptides 82–140 and 141–190 occluded TolC channels. The use of TolC for colicin E1 import implies that the interaction of this colicin with the other Tol proteins does not occur in the periplasmic space, but rather through Tol domains in the cytoplasmic membrane, thus explaining colicin E1 cytotoxicity towards a strain in which a 234 residue periplasmic TolA segment is deleted.
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48
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Hijacking cellular functions for processing and delivery of colicins E3 and D into the cytoplasm. Biochem Soc Trans 2012; 40:1486-91. [DOI: 10.1042/bst20120173] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mechanisms for importing colicins from the extracellular medium into Escherichia coli target cells implicate a complex cascade of interactions with host proteins. It is known that colicins interact with membrane receptors, and they may appropriate them structurally, but not functionally, as a scaffold on the surface of the target cell so that they can be translocated across the outer membrane. During the import into the periplasm, colicins parasitize functionally membrane porins and energy-transducers by mimicking their natural substrates or interacting partners. Such structural or functional parasitism also takes place during the late molecular events responsible for the processing and translocation of nuclease colicins across the inner membrane. Two different RNase colicins (D and E3) require an endoproteolytic cleavage, dependent on the inner membrane ATPase/protease FtsH, in order to transfer their C-terminal toxic domain into the cytoplasm. Moreover, the processing of colicin D necessitates a specific interaction with the signal peptidase LepB, but without appropriating the catalytic activity of this enzyme. A comparison of the differences in structural and functional organizations of these two colicins, as well as the pore-forming colicin B, is discussed in the present paper in connection with the sequential steps of their import mechanisms and the exploitation of the machinery of the target cell.
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49
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Patzer SI, Albrecht R, Braun V, Zeth K. Structural and mechanistic studies of pesticin, a bacterial homolog of phage lysozymes. J Biol Chem 2012; 287:23381-96. [PMID: 22593569 PMCID: PMC3390615 DOI: 10.1074/jbc.m112.362913] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yersinia pestis produces and secretes a toxin named pesticin that kills related bacteria of the same niche. Uptake of the bacteriocin is required for activity in the periplasm leading to hydrolysis of peptidoglycan. To understand the uptake mechanism and to investigate the function of pesticin, we combined crystal structures of the wild type enzyme, active site mutants, and a chimera protein with in vivo and in vitro activity assays. Wild type pesticin comprises an elongated N-terminal translocation domain, the intermediate receptor binding domain, and a C-terminal activity domain with structural analogy to lysozyme homologs. The full-length protein is toxic to bacteria when taken up to the target site via the outer or the inner membrane. Uptake studies of deletion mutants in the translocation domain demonstrate their critical size for import. To further test the plasticity of pesticin during uptake into bacterial cells, the activity domain was replaced by T4 lysozyme. Surprisingly, this replacement resulted in an active chimera protein that is not inhibited by the immunity protein Pim. Activity of pesticin and the chimera protein was blocked through introduction of disulfide bonds, which suggests unfolding as the prerequisite to gain access to the periplasm. Pesticin, a muramidase, was characterized by active site mutations demonstrating a similar but not identical residue pattern in comparison with T4 lysozyme.
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Affiliation(s)
- Silke I Patzer
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
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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] [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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