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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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Lin X, Zmyslowski AM, Gagnon IA, Nakamoto RK, Sosnick TR. Development of in vivo HDX-MS with applications to a TonB-dependent transporter and other proteins. Protein Sci 2022; 31:e4402. [PMID: 36040258 PMCID: PMC9382693 DOI: 10.1002/pro.4402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful tool that monitors protein dynamics in solution. However, the reversible nature of HDX labels has largely limited the application to in vitro systems. Here, we describe a protocol for measuring HDX-MS in living Escherichia coli cells applied to BtuB, a TonB-dependent transporter found in outer membranes (OMs). BtuB is a convenient and biologically interesting system for testing in vivo HDX-MS due to its controllable HDX behavior and large structural rearrangements that occur during the B12 transport cycle. Our previous HDX-MS study in native OMs provided evidence for B12 binding and breaking of a salt bridge termed the Ionic Lock, an event that leads to the unfolding of the amino terminus. Although purified OMs provide a more native-like environment than reconstituted systems, disruption of the cell envelope during lysis perturbs the linkage between BtuB and the TonB complex that drives B12 transport. The in vivo HDX response of BtuB's plug domain (BtuBp) to B12 binding corroborates our previous in vitro findings that B12 alone is sufficient to break the Ionic Lock. In addition, we still find no evidence of B12 binding-induced unfolding in other regions of BtuBp that could enable B12 passage. Our protocol was successful in reporting on the HDX of several endogenous E. coli proteins measured in the same measurement. Our success in performing HDX in live cells opens the possibility for future HDX-MS studies in a native cellular environment. IMPORTANCE: We present a protocol for performing in vivo HDX-MS, focusing on BtuB, a protein whose native membrane environment is believed to be mechanistically important for B12 transport. The in vivo HDX-MS data corroborate the conclusions from our previous in vitro HDX-MS study of the allostery initiated by B12 binding. Our success with BtuB and other proteins opens the possibility for performing additional HDX-MS studies in a native cellular environment.
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Affiliation(s)
- Xiaoxuan Lin
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Adam M. Zmyslowski
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
- Present address:
Evozyne LLCChicagoIllinoisUSA
| | - Isabelle A. Gagnon
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Robert K. Nakamoto
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Tobin R. Sosnick
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
- Prizker School for Molecular EngineeringThe University of ChicagoChicagoIllinoisUSA
- Institute for Biophysical DynamicsThe University of ChicagoChicagoIllinoisUSA
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Zmyslowski AM, Baxa MC, Gagnon IA, Sosnick TR. HDX-MS performed on BtuB in E. coli outer membranes delineates the luminal domain's allostery and unfolding upon B12 and TonB binding. Proc Natl Acad Sci U S A 2022; 119:e2119436119. [PMID: 35549554 PMCID: PMC9171809 DOI: 10.1073/pnas.2119436119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 04/09/2022] [Indexed: 11/18/2022] Open
Abstract
To import large metabolites across the outer membrane of gram-negative bacteria, TonB-dependent transporters (TBDTs) undergo significant conformational change. After substrate binding in BtuB, the Escherichia coli vitamin B12 TBDT, TonB binds and couples BtuB to the inner-membrane proton motive force that powers transport [N. Noinaj, M. Guillier, T. J. Barnard, S. K. Buchanan, Annu. Rev. Microbiol. 64, 43–60 (2010)]. However, the role of TonB in rearranging the plug domain of BtuB to form a putative pore remains enigmatic. Some studies focus on force-mediated unfolding [S. J. Hickman, R. E. M. Cooper, L. Bellucci, E. Paci, D. J. Brockwell, Nat. Commun. 8, 14804 (2017)], while others propose force-independent pore formation by TonB binding [T. D. Nilaweera, D. A. Nyenhuis, D. S. Cafiso, eLife 10, e68548 (2021)], leading to breakage of a salt bridge termed the “Ionic Lock.” Our hydrogen–deuterium exchange/mass spectrometry (HDX-MS) measurements in E. coli outer membranes find that the region surrounding the Ionic Lock, far from the B12 site, is fully destabilized upon substrate binding. A comparison of the exchange between the B12-bound and the B12+TonB–bound complexes indicates that B12 binding is sufficient to unfold the Ionic Lock region, with the subsequent binding of a TonB fragment having much weaker effects. TonB binding accelerates exchange in the third substrate-binding loop, but pore formation does not obviously occur in this or any region. This study provides a detailed structural and energetic description of the early stages of B12 passage that provides support both for and against current models of the transport process.
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Affiliation(s)
- Adam M. Zmyslowski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Michael C. Baxa
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Isabelle A. Gagnon
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
| | - Tobin R. Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637
- Prizker School for Molecular Engineering, The University of Chicago, Chicago, IL 60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637
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Nilaweera TD, Nyenhuis DA, Cafiso DS. Structural intermediates observed only in intact Escherichia coli indicate a mechanism for TonB-dependent transport. eLife 2021; 10:68548. [PMID: 34251336 PMCID: PMC8341980 DOI: 10.7554/elife.68548] [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: 03/18/2021] [Accepted: 07/11/2021] [Indexed: 12/17/2022] Open
Abstract
Outer membrane TonB-dependent transporters facilitate the uptake of trace nutrients and carbohydrates in Gram-negative bacteria and are essential for pathogenic bacteria and the health of the microbiome. Despite this, their mechanism of transport is still unknown. Here, pulse electron paramagnetic resonance (EPR) measurements were made in intact cells on the Escherichia coli vitamin B12 transporter, BtuB. Substrate binding was found to alter the C-terminal region of the core and shift an extracellular substrate binding loop 2 nm toward the periplasm; moreover, this structural transition is regulated by an ionic lock that is broken upon binding of the inner membrane protein TonB. Significantly, this structural transition is not observed when BtuB is reconstituted into phospholipid bilayers. These measurements suggest an alternative to existing models of transport, and they demonstrate the importance of studying outer membrane proteins in their native environment.
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Affiliation(s)
- Thushani D Nilaweera
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, United States
| | - David A Nyenhuis
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, United States
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, United States
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Pieńko T, Czarnecki J, Równicki M, Wojciechowska M, Wierzba AJ, Gryko D, Bartosik D, Trylska J. Vitamin B 12-peptide nucleic acids use the BtuB receptor to pass through the Escherichia coli outer membrane. Biophys J 2021; 120:725-737. [PMID: 33453274 DOI: 10.1016/j.bpj.2021.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
Short modified oligonucleotides that bind in a sequence-specific way to messenger RNA essential for bacterial growth could be useful to fight bacterial infections. One such promising oligonucleotide is peptide nucleic acid (PNA), a synthetic DNA analog with a peptide-like backbone. However, the limitation precluding the use of oligonucleotides, including PNA, is that bacteria do not import them from the environment. We have shown that vitamin B12, which most bacteria need to take up for growth, delivers PNAs to Escherichia coli cells when covalently linked with PNAs. Vitamin B12 enters E. coli via a TonB-dependent transport system and is recognized by the outer-membrane vitamin B12-specific BtuB receptor. We engineered the E. coli ΔbtuB mutant and found that transport of the vitamin B12-PNA conjugate requires BtuB. Thus, the conjugate follows the same route through the outer membrane as taken by free vitamin B12. From enhanced sampling all-atom molecular dynamics simulations, we determined the mechanism of conjugate permeation through BtuB. BtuB is a β-barrel occluded by its luminal domain. The potential of mean force shows that conjugate passage is unidirectional and its movement into the BtuB β-barrel is energetically favorable upon luminal domain unfolding. Inside BtuB, PNA extends making its permeation mechanically feasible. BtuB extracellular loops are actively involved in transport through an induced-fit mechanism. We prove that the vitamin B12 transport system can be hijacked to enable PNA delivery to E. coli cells.
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Affiliation(s)
- Tomasz Pieńko
- Centre of New Technologies, University of Warsaw, Warsaw, Poland; Department of Drug Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, Warsaw, Poland.
| | - Jakub Czarnecki
- Faculty of Biology, University of Warsaw, Warsaw, Poland; Bacterial Genome Plasticity, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Marcin Równicki
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | | | - Dorota Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.
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Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli. PLoS Comput Biol 2020; 16:e1008024. [PMID: 32609716 PMCID: PMC7360065 DOI: 10.1371/journal.pcbi.1008024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/14/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
Vitamin B12 (or cobalamin) is an enzymatic cofactor essential both for mammals and bacteria. However, cobalamin can be synthesized only by few microorganisms so most bacteria need to take it up from the environment through the TonB-dependent transport system. The first stage of cobalamin import to E. coli cells occurs through the outer-membrane receptor called BtuB. Vitamin B12 binds with high affinity to the extracellular side of the BtuB protein. BtuB forms a β-barrel with inner luminal domain and extracellular loops. To mechanically allow for cobalamin passage, the luminal domain needs to partially unfold with the help of the inner-membrane TonB protein. However, the mechanism of cobalamin permeation is unknown. Using all-atom molecular dynamics, we simulated the transport of cobalamin through the BtuB receptor embedded in an asymmetric and heterogeneous E. coli outer-membrane. To enhance conformational sampling of the BtuB loops, we developed the Gaussian force-simulated annealing method (GF-SA) and coupled it with umbrella sampling. We found that cobalamin needs to rotate in order to permeate through BtuB. We showed that the mobility of BtuB extracellular loops is crucial for cobalamin binding and transport and resembles an induced-fit mechanism. Loop mobility depends not only on the position of cobalamin but also on the extension of luminal domain. We provided atomistic details of cobalamin transport through the BtuB receptor showing the essential role of the mobility of BtuB extracellular loops. A similar TonB-dependent transport system is used also by many other compounds, such as haem and siderophores, and importantly, can be hijacked by natural antibiotics. Our work could have implications for future delivery of antibiotics to bacteria using this transport system.
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Nilaweera TD, Nyenhuis DA, Nakamoto RK, Cafiso DS. Disulfide Chaperone Knockouts Enable In Vivo Double Spin Labeling of an Outer Membrane Transporter. Biophys J 2019; 117:1476-1484. [PMID: 31582182 DOI: 10.1016/j.bpj.2019.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/28/2019] [Accepted: 09/06/2019] [Indexed: 10/26/2022] Open
Abstract
Recent advances in the application of electron paramagnetic resonance spectroscopy have demonstrated that it is possible to obtain structural information on bacterial outer membrane (OM) proteins in intact cells from extracellularly labeled cysteines. However, in the Escherichia coli OM B12 transport protein, BtuB, the double labeling of many cysteine pairs is not possible in a wild-type K12-derived E. coli strain. It has also not yet been possible to selectively label single or paired cysteines that face the periplasmic space. Here, we demonstrate that the inability to produce reactive cysteine residues in pairs is a result of the disulfide bond formation system, which functions to oxidize pairs of free-cysteine residues. Mutant strains that are dsbA or dsbB null facilitate labeling pairs of cysteines. Moreover, we demonstrate that the double labeling of sites on the periplasmic-facing surface of BtuB is possible using a dsbA null strain. BtuB is found to exhibit different structures and structural changes in the cell than it does in isolated OMs or reconstituted systems, and the ability to label and perform electron paramagnetic resonance in cells is expected to be applicable to a range of other bacterial OM proteins.
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Affiliation(s)
- Thushani D Nilaweera
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - David A Nyenhuis
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Robert K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, Virginia.
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Jiménez RHF, Freed DM, Cafiso DS. Lipid and membrane mimetic environments modulate spin label side chain configuration in the outer membrane protein A. J Phys Chem B 2011; 115:14822-30. [PMID: 22034842 DOI: 10.1021/jp207420d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present work, the factors that determine EPR line shapes from spin labels at the protein-hydrocarbon interface of a β-barrel membrane protein are examined. The EPR spectra from hydrocarbon facing sites in the outer membrane protein A (OmpA) are highly dependent upon the detergent or lipid into which OmpA is reconstituted. In general, line shapes at these sites are correlated with the solvent accessibility in the supporting amphiphile. A notable exception is CHAPS, which yields rigid limit EPR line shapes for labels at every position along a transmembrane β-strand in OmpA. EPR line shapes from the surface of OmpA are not strongly influenced by steric interference with neighboring side chains, but are modulated by solutes that should interact with hydrophobic surfaces. These results suggest that differences in EPR spectra in different supporting environments are not the result of differences in protein dynamics but are a result of different configurations or rotameric states that are assumed by the label. This conclusion is supported by distance measurements across the OmpA β-barrel, which indicate that labels yielding more motionally restricted line shapes interact more closely with the protein surface. These results have implications for the use of spin-label-derived distance constraints in protein structure determination and demonstrate that spin labels on membrane proteins provide a highly sensitive probe for the environment surrounding a membrane protein.
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Affiliation(s)
- Ricardo H Flores Jiménez
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904-4319, United States
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Freed DM, Horanyi PS, Wiener MC, Cafiso DS. Conformational exchange in a membrane transport protein is altered in protein crystals. Biophys J 2010; 99:1604-10. [PMID: 20816073 DOI: 10.1016/j.bpj.2010.06.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 06/07/2010] [Accepted: 06/14/2010] [Indexed: 11/24/2022] Open
Abstract
Successful macromolecular crystallography requires solution conditions that may alter the conformational sampling of a macromolecule. Here, site-directed spin labeling is used to examine a conformational equilibrium within BtuB, the Escherichia coli outer membrane transporter for vitamin B(12). Electron paramagnetic resonance (EPR) spectra from a spin label placed within the N-terminal energy coupling motif (Ton box) of BtuB indicate that this segment is in equilibrium between folded and unfolded forms. In bilayers, substrate binding shifts this equilibrium toward the unfolded form; however, EPR spectra from this same spin-labeled mutant indicate that this unfolding transition is blocked in protein crystals. Moreover, crystal structures of this spin-labeled mutant are consistent with the EPR result. When the free energy difference between substates is estimated from the EPR spectra, the crystal environment is found to alter this energy by 3 kcal/mol when compared to the bilayer state. Approximately half of this energy change is due to solutes or osmolytes in the crystallization buffer, and the remainder is contributed by the crystal lattice. These data provide a quantitative measure of how a conformational equilibrium in BtuB is modified in the crystal environment, and suggest that more-compact, less-hydrated substates will be favored in protein crystals.
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Affiliation(s)
- Daniel M Freed
- Departments of Chemistry, University of Virginia, Charlottesville, Virginia, USA
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Gumbart J, Wiener MC, Tajkhorshid E. Coupling of calcium and substrate binding through loop alignment in the outer-membrane transporter BtuB. J Mol Biol 2009; 393:1129-42. [PMID: 19747487 DOI: 10.1016/j.jmb.2009.09.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 11/29/2022]
Abstract
In Gram-negative bacteria, TonB-dependent outer-membrane transporters bind large, scarce organometallic substrates with high affinity preceding active transport. The cobalamin transporter BtuB requires the additional binding of two Ca(2+) ions before substrate binding can occur, but the underlying molecular mechanism is unknown. Using the crystallographic structures available for different bound states of BtuB, we have carried out extended molecular dynamics simulations of multiple functional states of BtuB to address the role of Ca(2+) in substrate recruitment. We find that Ca(2+) binding both stabilizes and repositions key extracellular loops of BtuB, optimizing interactions with the substrate. Interestingly, replacement by Mg(2+) abolishes this effect, in accordance with experiments. Using a set of new force-field parameters developed for cyanocobalamin, we also simulated the substrate-bound form of BtuB, where we observed interactions not seen in the crystal structure between the substrate and loops previously found to be important for binding and transport. Based on our results, we suggest that the large size of cobalamin compared to other TonB-dependent transporter substrates explains the requirement of Ca(2+) binding for high-affinity substrate recruitment in BtuB.
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Affiliation(s)
- James Gumbart
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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