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Abstract
TonB-dependent transporters (TBDTs) are present in all gram-negative bacteria and mediate energy-dependent uptake of molecules that are too scarce or large to be taken up efficiently by outer membrane (OM) diffusion channels. This process requires energy that is derived from the proton motive force and delivered to TBDTs by the TonB-ExbBD motor complex in the inner membrane. Together with the need to preserve the OM permeability barrier, this has led to an extremely complex and fascinating transport mechanism for which the fundamentals, despite decades of research, are still unclear. In this review, we describe our current understanding of the transport mechanism of TBDTs, their potential role in the delivery of novel antibiotics, and the important contributions made by TBDT-associated (lipo)proteins.
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Affiliation(s)
- Augustinas Silale
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom; ,
| | - Bert van den Berg
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom; ,
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2
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Mayse LA, Movileanu L. Gating of β-Barrel Protein Pores, Porins, and Channels: An Old Problem with New Facets. Int J Mol Sci 2023; 24:12095. [PMID: 37569469 PMCID: PMC10418385 DOI: 10.3390/ijms241512095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
β barrels are ubiquitous proteins in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. These transmembrane proteins (TMPs) execute a wide variety of tasks. For example, they can serve as transporters, receptors, membrane-bound enzymes, as well as adhesion, structural, and signaling elements. In addition, multimeric β barrels are common structural scaffolds among many pore-forming toxins. Significant progress has been made in understanding the functional, structural, biochemical, and biophysical features of these robust and versatile proteins. One frequently encountered fundamental trait of all β barrels is their voltage-dependent gating. This process consists of reversible or permanent conformational transitions between a large-conductance, highly permeable open state and a low-conductance, solute-restrictive closed state. Several intrinsic molecular mechanisms and environmental factors modulate this universal property of β barrels. This review article outlines the typical signatures of voltage-dependent gating. Moreover, we discuss recent developments leading to a better qualitative understanding of the closure dynamics of these TMPs.
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Affiliation(s)
- Lauren A. Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244, USA;
- Department of Biomedical and Chemical Engineering, Syracuse University, 223 Link Hall, Syracuse, NY 13244, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244, USA;
- Department of Biomedical and Chemical Engineering, Syracuse University, 223 Link Hall, Syracuse, NY 13244, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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3
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Riback JA, Bowman MA, Zmyslowski AM, Knoverek CR, Jumper JM, Hinshaw JR, Kaye EB, Freed KF, Clark PL, Sosnick TR. Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water. Science 2017; 358:238-241. [PMID: 29026044 PMCID: PMC5959285 DOI: 10.1126/science.aan5774] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/07/2017] [Indexed: 01/02/2023]
Abstract
A substantial fraction of the proteome is intrinsically disordered, and even well-folded proteins adopt non-native geometries during synthesis, folding, transport, and turnover. Characterization of intrinsically disordered proteins (IDPs) is challenging, in part because of a lack of accurate physical models and the difficulty of interpreting experimental results. We have developed a general method to extract the dimensions and solvent quality (self-interactions) of IDPs from a single small-angle x-ray scattering measurement. We applied this procedure to a variety of IDPs and found that even IDPs with low net charge and high hydrophobicity remain highly expanded in water, contrary to the general expectation that protein-like sequences collapse in water. Our results suggest that the unfolded state of most foldable sequences is expanded; we conjecture that this property was selected by evolution to minimize misfolding and aggregation.
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Affiliation(s)
- Joshua A Riback
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Micayla A Bowman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Adam M Zmyslowski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Catherine R Knoverek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - John M Jumper
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry and James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - James R Hinshaw
- Department of Chemistry and James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Emily B Kaye
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Karl F Freed
- Department of Chemistry and James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
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Thakur AK, Larimi MG, Gooden K, Movileanu L. Aberrantly Large Single-Channel Conductance of Polyhistidine Arm-Containing Protein Nanopores. Biochemistry 2017; 56:4895-4905. [PMID: 28812882 DOI: 10.1021/acs.biochem.7b00577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There have been only a few studies reporting on the impact of polyhistidine affinity tags on the structure, function, and dynamics of proteins. Because of the relatively short size of the tags, they are often thought to have little or no effect on the conformation or activity of a protein. Here, using membrane protein design and single-molecule electrophysiology, we determined that the presence of a hexahistidine arm at the N-terminus of a truncated FhuA-based protein nanopore, leaving the C-terminus untagged, produces an unusual increase in the unitary conductance to ∼8 nS in 1 M KCl. To the best of our knowledge, this is the largest single-channel conductance ever recorded with a monomeric β-barrel outer membrane protein. The hexahistidine arm was captured by an anti-polyhistidine tag monoclonal antibody added to the side of the channel-forming protein addition, but not to the opposite side, documenting that this truncated FhuA-based protein nanopore inserts into a planar lipid bilayer with a preferred orientation. This finding is in agreement with the protein insertion in vivo, in which the large loops face the extracellular side of the membrane. The aberrantly large single-channel conductance, likely induced by a greater cross-sectional area of the pore lumen, along with the vectorial insertion into a lipid membrane, will have profound implications for further developments of engineered protein nanopores.
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Affiliation(s)
- Avinash Kumar Thakur
- Department of Physics, Syracuse University , 201 Physics Building, Syracuse, New York 13244-1130, United States.,Structural Biology, Biochemistry, and Biophysics Program, Syracuse University , 111 College Place, Syracuse, New York 13244-4100, United States
| | - Motahareh Ghahari Larimi
- Department of Physics, Syracuse University , 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Kristin Gooden
- Department of Physics and Astronomy, University of Missouri , 223 Physics Building, Columbia, Missouri 65211-7010, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University , 201 Physics Building, Syracuse, New York 13244-1130, United States.,Structural Biology, Biochemistry, and Biophysics Program, Syracuse University , 111 College Place, Syracuse, New York 13244-4100, United States.,Department of Biomedical and Chemical Engineering, Syracuse University , 329 Link Hall, Syracuse, New York 13244, United States
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Abstract
Iron is an essential micronutrient for both microbes and humans alike. For well over half a century we have known that this element, in particular, plays a pivotal role in health and disease and, most especially, in shaping host-pathogen interactions. Intracellular iron concentrations serve as a critical signal in regulating the expression not only of high-affinity iron acquisition systems in bacteria, but also of toxins and other noted virulence factors produced by some major human pathogens. While we now are aware of many strategies that the host has devised to sequester iron from invading microbes, there are as many if not more sophisticated mechanisms by which successful pathogens overcome nutritional immunity imposed by the host. This review discusses some of the essential components of iron sequestration and scavenging mechanisms of the host, as well as representative Gram-negative and Gram-positive pathogens, and highlights recent advances in the field. Last, we address how the iron acquisition strategies of pathogenic bacteria may be exploited for the development of novel prophylactics or antimicrobials.
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Going Outside the TonB Box: Identification of Novel FepA-TonB Interactions In Vivo. J Bacteriol 2017; 199:JB.00649-16. [PMID: 28264993 DOI: 10.1128/jb.00649-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/15/2017] [Indexed: 01/30/2023] Open
Abstract
In Gram-negative bacteria, the cytoplasmic membrane protein TonB transmits energy derived from proton motive force to energize transport of important nutrients through TonB-dependent transporters in the outer membrane. Each transporter consists of a beta barrel domain and a lumen-occluding cork domain containing an essential sequence called the TonB box. To date, the only identified site of transporter-TonB interaction is between the TonB box and residues ∼158 to 162 of TonB. While the mechanism of ligand transport is a mystery, a current model based on site-directed spin labeling and molecular dynamics simulations is that, following ligand binding, the otherwise-sequestered TonB box extends into the periplasm for recognition by TonB, which mediates transport by pulling or twisting the cork. In this study, we tested that hypothesis with the outer membrane transporter FepA using in vivo photo-cross-linking to explore interactions of its TonB box and determine whether additional FepA-TonB interaction sites exist. We found numerous specific sites of FepA interaction with TonB on the periplasmic face of the FepA cork in addition to the TonB box. Two residues, T32 and A33, might constitute a ligand-sensitive conformational switch. The facts that some interactions were enhanced in the absence of ligand and that other interactions did not require the TonB box argued against the current model and suggested that the transport process is more complex than originally conceived, with subtleties that might provide a mechanism for discrimination among ligand-loaded transporters. These results constitute the first study on the dynamics of TonB-gated transporter interaction with TonB in vivoIMPORTANCE The TonB system of Gram-negative bacteria has a noncanonical active transport mechanism involving signal transduction and proteins integral to both membranes. To achieve transport, the cytoplasmic membrane protein TonB physically contacts outer membrane transporters such as FepA. Only one contact between TonB and outer membrane transporters has been identified to date: the TonB box at the transporter amino terminus. The TonB box has low information content, raising the question of how TonB can discriminate among multiple different TonB-dependent transporters present in the bacterium if it is the only means of contact. Here we identified several additional sites through which FepA contacts TonB in vivo, including two neighboring residues that may explain how FepA signals to TonB that ligand has bound.
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Hickman SJ, Cooper REM, Bellucci L, Paci E, Brockwell DJ. Gating of TonB-dependent transporters by substrate-specific forced remodelling. Nat Commun 2017; 8:14804. [PMID: 28429713 PMCID: PMC5413942 DOI: 10.1038/ncomms14804] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/31/2017] [Indexed: 12/21/2022] Open
Abstract
Membrane proteins play vital roles in inside-out and outside-in signal transduction by responding to inputs that include mechanical stimuli. Mechanical gating may be mediated by the membrane or by protein(s) but evidence for the latter is scarce. Here we use force spectroscopy, protein engineering and bacterial growth assays to investigate the effects of force on complexes formed between TonB and TonB-dependent transporters (TBDT) from Gram-negative bacteria. We confirm the feasibility of protein-only mediated mechanical gating by demonstrating that the interaction between TonB and BtuB (a TBDT) is sufficiently strong under force to create a channel through the TBDT. In addition, by comparing the dimensions of the force-induced channel in BtuB and a second TBDT (FhuA), we show that the mechanical properties of the interaction are perfectly tuned to their function by inducing formation of a channel whose dimensions are tailored to the ligand.
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Affiliation(s)
- Samuel J Hickman
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Rachael E M Cooper
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Luca Bellucci
- NEST, Istituto Nanoscienze-CNR, Piazza San Silvestro, 12-56127 Pisa, Italy
| | - Emanuele Paci
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David J Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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Abstract
The rotational surveillance and energy transfer (ROSET) model of TonB action suggests a mechanism by which the electrochemical proton gradient across the Gram-negative bacterial inner membrane (IM) promotes the transport of iron through ligand-gated porins (LGP) in the outer membrane (OM). TonB associates with the IM by an N-terminal hydrophobic helix that forms a complex with ExbBD. It also contains a central extended length of rigid polypeptide that spans the periplasm and a dimeric C-terminal-ββαβ-domain (CTD) with LysM motifs that binds the peptidoglycan (PG) layer beneath the OM bilayer. The TonB CTD forms a dimer with affinity for both PG- and TonB-independent OM proteins (e.g., OmpA), localizing it near the periplasmic interface of the OM bilayer. Porins and other OM proteins associate with PG, and this general affinity allows the TonB CTD dimer to survey the periplasmic surface of the OM bilayer. Energized rotational motion of the TonB N terminus in the fluid IM bilayer promotes the lateral movement of the TonB-ExbBD complex in the IM and of the TonB CTD dimer across the inner surface of the OM. When it encounters an accessible TonB box of a (ligand-bound) LGP, the monomeric form of the CTD binds and recruits it into a 4-stranded β-sheet. Because the CTD is rotating, this binding reaction transfers kinetic energy, created by the electrochemical proton gradient across the IM, through the periplasm to the OM protein. The equilibration of the TonB C terminus between the dimeric and monomeric forms that engage in different binding reactions allows the identification of iron-loaded LGP and then the internalization of iron through their trans-outer membrane β-barrels. Hence, the ROSET model postulates a mechanism for the transfer of energy from the IM to the OM, triggering iron uptake.
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Grinter R, Josts I, Zeth K, Roszak AW, McCaughey LC, Cogdell RJ, Milner JJ, Kelly SM, Byron O, Walker D. Structure of the atypical bacteriocin pectocin M2 implies a novel mechanism of protein uptake. Mol Microbiol 2014; 93:234-46. [PMID: 24865810 PMCID: PMC4671253 DOI: 10.1111/mmi.12655] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2014] [Indexed: 01/08/2023]
Abstract
The colicin-like bacteriocins are potent protein antibiotics that have evolved to efficiently cross the outer membrane of Gram-negative bacteria by parasitizing nutrient uptake systems. We have structurally characterized the colicin M-like bacteriocin, pectocin M2, which is active against strains of Pectobacterium spp. This unusual bacteriocin lacks the intrinsically unstructured translocation domain that usually mediates translocation of these bacteriocins across the outer membrane, containing only a single globular ferredoxin domain connected to its cytotoxic domain by a flexible α-helix, which allows it to adopt two distinct conformations in solution. The ferredoxin domain of pectocin M2 is homologous to plant ferredoxins and allows pectocin M2 to parasitize a system utilized by Pectobacterium to obtain iron during infection of plants. Furthermore, we identify a novel ferredoxin-containing bacteriocin pectocin P, which possesses a cytotoxic domain homologous to lysozyme, illustrating that the ferredoxin domain acts as a generic delivery module for cytotoxic domains in Pectobacterium.
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Affiliation(s)
- Rhys Grinter
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8QQ, UK
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11
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Chiaruttini N, Letellier L, Viasnoff V. A novel method to couple electrophysiological measurements and fluorescence imaging of suspended lipid membranes: the example of T5 bacteriophage DNA ejection. PLoS One 2013; 8:e84376. [PMID: 24376806 PMCID: PMC3871697 DOI: 10.1371/journal.pone.0084376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/22/2013] [Indexed: 12/21/2022] Open
Abstract
We present an innovative method to couple electrophysiological measurements with fluorescence imaging of functionalized suspended bilayers. Our method combines several advantages: it is well suited to study transmembrane proteins that are difficult to incorporate in suspended bilayers, it allows single molecule resolution both in terms of electrophysiological measurements and fluorescence imaging, and it enables mechanical stimulations of the membrane. The approach comprises of two steps: first the reconstitution of membrane proteins in giant unilamellar vesicles; then the formation of a suspended bilayer spanning a 5 to 15 micron-wide aperture that can be visualized by high NA microscope objectives. We exemplified how the technique can be used to detect in real time the translocation of T5 DNA across the bilayer during its ejection from the bacteriophage capsid.
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Affiliation(s)
- Nicolas Chiaruttini
- ESPCI Paristech, CNRS, Paris, France
- Aurélien Roux Lab, Biochemistry Department, University of Geneva, Geneva, Switzerland
| | - Lucienne Letellier
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud-11, CNRS, Orsay, France
| | - Virgile Viasnoff
- ESPCI Paristech, CNRS, Paris, France
- Aurélien Roux Lab, Biochemistry Department, University of Geneva, Geneva, Switzerland
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud-11, CNRS, Orsay, France
- MechanoBiology Institute of Singapore, Singapore, Singapore
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Breyton C, Flayhan A, Gabel F, Lethier M, Durand G, Boulanger P, Chami M, Ebel C. Assessing the conformational changes of pb5, the receptor-binding protein of phage T5, upon binding to its Escherichia coli receptor FhuA. J Biol Chem 2013; 288:30763-30772. [PMID: 24014030 DOI: 10.1074/jbc.m113.501536] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Within tailed bacteriophages, interaction of the receptor-binding protein (RBP) with the target cell triggers viral DNA ejection into the host cytoplasm. In the case of phage T5, the RBP pb5 and the receptor FhuA, an outer membrane protein of Escherichia coli, have been identified. Here, we use small angle neutron scattering and electron microscopy to investigate the FhuA-pb5 complex. Specific deuteration of one of the partners allows the complete masking in small angle neutron scattering of the surfactant and unlabeled proteins when the complex is solubilized in the fluorinated surfactant F6-DigluM. Thus, individual structures within a membrane protein complex can be described. The solution structure of FhuA agrees with its crystal structure; that of pb5 shows an elongated shape. Neither displays significant conformational changes upon interaction. The mechanism of signal transduction within phage T5 thus appears different from that of phages binding cell wall saccharides, for which structural information is available.
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Affiliation(s)
- Cécile Breyton
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France,; CNRS, UMR5075, IBS, F-38027 Grenoble, France,; the Commissariat à l'Energie Atomique, DSV, IBS, F-38027 Grenoble, France,.
| | - Ali Flayhan
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France,; CNRS, UMR5075, IBS, F-38027 Grenoble, France,; the Commissariat à l'Energie Atomique, DSV, IBS, F-38027 Grenoble, France
| | - Frank Gabel
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France,; CNRS, UMR5075, IBS, F-38027 Grenoble, France,; the Commissariat à l'Energie Atomique, DSV, IBS, F-38027 Grenoble, France
| | - Mathilde Lethier
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France,; CNRS, UMR5075, IBS, F-38027 Grenoble, France,; the Commissariat à l'Energie Atomique, DSV, IBS, F-38027 Grenoble, France
| | - Grégory Durand
- the Université d'Avignon, Equipe Chimie Bioorganique et Systèmes Amphiphiles, F-84029 Avignon, France,; the Institut des Biomolécules Max Mousseron, UMR 5247, F-34093 Montpellier, France
| | - Pascale Boulanger
- the Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, UMR CNRS 8619, F-91405 Orsay, France, and
| | - Mohamed Chami
- the Center for Cellular Imaging and NanoAnalytics, Biozentrum, University Basel, CH-4058 Basel, Switzerland
| | - Christine Ebel
- From the Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France,; CNRS, UMR5075, IBS, F-38027 Grenoble, France,; the Commissariat à l'Energie Atomique, DSV, IBS, F-38027 Grenoble, France
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