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Knejski PP, Erramilli SK, Kossiakoff AA. Chaperone-assisted cryo-EM structure of P. aeruginosa PhuR reveals molecular basis for heme binding. Structure 2024; 32:411-423.e6. [PMID: 38325368 PMCID: PMC10997469 DOI: 10.1016/j.str.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/14/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
Pathogenic bacteria, such as Pseudomonas aeruginosa, depend on scavenging heme for the acquisition of iron, an essential nutrient. The TonB-dependent transporter (TBDT) PhuR is the major heme uptake protein in P. aeruginosa clinical isolates. However, a comprehensive understanding of heme recognition and TBDT transport mechanisms, especially PhuR, remains limited. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) and a phage display-generated synthetic antibody (sAB) as a fiducial marker to enable the determination of a high-resolution (2.5 Å) structure of PhuR with a bound heme. Notably, the structure reveals iron coordination by Y529 on a conserved extracellular loop, shedding light on the role of tyrosine in heme binding. Biochemical assays and negative-stain EM demonstrated that the sAB specifically targets the heme-bound state of PhuR. These findings provide insights into PhuR's heme binding and offer a template for developing conformation-specific sABs against outer membrane proteins (OMPs) for structure-function investigations.
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Affiliation(s)
- Paweł P Knejski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
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Will V, Gasser V, Kuhn L, Fritsch S, Heinrichs DE, Schalk IJ. Siderophore specificities of the Pseudomonas aeruginosa TonB-dependent transporters ChtA and ActA. FEBS Lett 2023; 597:2963-2974. [PMID: 37758521 DOI: 10.1002/1873-3468.14740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
Abstract
Iron is an essential nutrient for the survival and virulence of Pseudomonas aeruginosa. The pathogen expresses at least 15 different iron-uptake pathways, the majority involving small iron chelators called siderophores. P. aeruginosa produces two siderophores, but can also use many produced by other microorganisms. This implies that the bacterium expresses appropriate TonB-dependent transporters (TBDTs) at the outer membrane to import the ferric form of each of the siderophores used. Here, we show that the two α-carboxylate-type siderophores rhizoferrin-Fe and staphyloferrin A-Fe are transported into P. aeruginosa cells by the TBDT ActA. Among the mixed α-carboxylate/hydroxamate-type siderophores, we found aerobactin-Fe to be transported by ChtA and schizokinen-Fe and arthrobactin-Fe by ChtA and another unidentified TBDT. Our findings enhance the understanding of the adaptability of P. aeruginosa and hold significant implications for developing novel strategies to combat antibiotic resistance.
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Affiliation(s)
- Virginie Will
- CNRS, University of Strasbourg, UMR7242, ESBS, Strasbourg, France
- University of Strasbourg, UMR7242, ESBS, Strasbourg, France
| | - Véronique Gasser
- CNRS, University of Strasbourg, UMR7242, ESBS, Strasbourg, France
- University of Strasbourg, UMR7242, ESBS, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Proteomique Strasbourg - Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS FR1589, Strasbourg Cedex, France
| | - Sarah Fritsch
- CNRS, University of Strasbourg, UMR7242, ESBS, Strasbourg, France
- University of Strasbourg, UMR7242, ESBS, Strasbourg, France
| | - David E Heinrichs
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Isabelle J Schalk
- CNRS, University of Strasbourg, UMR7242, ESBS, Strasbourg, France
- University of Strasbourg, UMR7242, ESBS, Strasbourg, France
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Knejski PP, Erramilli SK, Kossiakoff AA. Chaperone-assisted cryo-EM structure of P. aeruginosa PhuR reveals molecular basis for heme uptake. bioRxiv 2023:2023.08.01.551527. [PMID: 37577460 PMCID: PMC10418163 DOI: 10.1101/2023.08.01.551527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Pathogenic bacteria, such as Pseudomonas aeruginosa, depend on scavenging heme for the acquisition of iron, an essential nutrient. The TonB-dependent transporter (TBDT) PhuR is the major heme uptake protein in P. aeruginosa clinical isolates. However, a comprehensive understanding of heme recognition and TBDT transport mechanisms, especially PhuR, remains limited. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) and a phage display-generated synthetic antibody (sAB) as a fiducial marker to enable the determination of a high-resolution (2.5 Å) structure of PhuR with a bound heme. Notably, the structure reveals iron coordination by Y529 on a conserved extracellular loop, shedding light on the role of tyrosine in heme binding. Biochemical assays and negative-stain EM demonstrated that the sAB specifically targets the heme-bound state of PhuR. These findings provide insights into PhuR's heme binding and offer a template for developing conformation-specific sABs against outer membrane proteins (OMPs) for structure-function investigations.
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Affiliation(s)
- Paweł P. Knejski
- Deparment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
- Present address: Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Satchal K. Erramilli
- Deparment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Anthony A. Kossiakoff
- Deparment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
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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: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Liang J, Xu J, Zhao W, Wang J, Chen K, Li Y, Tian Y. Benzo[a]pyrene might be transported by a TonB-dependent transporter in Novosphingobium pentaromativorans US6-1. J Hazard Mater 2021; 404:124037. [PMID: 33059256 DOI: 10.1016/j.jhazmat.2020.124037] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Sphingomonads are well known for their ability to efficiently degrade polycyclic aromatic hydrocarbons (PAHs), but little is known about the mechanism of PAH uptake and transport across the cell membrane. RNA sequencing analysis of a sphingomonad, Novosphingobium pentaromativorans US6-1 showed that 38 TonB-dependent transporter (TBDT) genes were significantly upregulated under 5-ring PAH-benzo[a]pyrene (BaP) stress. In order to reveal whether TBDTs are involved in uptake and transport BaP in US6-1, the key TBDT genes were deleted to generate mutants. The results showed that the growth status of these mutants was not different from that of the wild-type strains, but the PAH degradation ability decreased, especially for the mutant strain Δtbdt-11, which did not encode the tbdt-11 gene. Meanwhile, the cell surface hydrophobicity (CSH) of Δtbdt-11 was found to be significantly lower than that of the wild-type strain under BaP stress. Furthermore, the transcriptional activity of genes encoding PAH degradative enzymes was found to be greatly reduced in Δtbdt-11. Confocal microscopy observations showed that US6-1 could transport BaP across the outer membrane, but this transport capacity was significantly reduced in Δtbdt-11 and wild-type US6-1 treated with PMF uncoupler, further confirming that the tbdt-11 gene was associated with PAH active transport.
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Affiliation(s)
- Jiaqing Liang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiantao Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Weijun Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiaofeng Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Kai Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yuqian Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
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Pollet RM, Martin LM, Koropatkin NM. TonB-dependent transporters in the Bacteroidetes: Unique domain structures and potential functions. Mol Microbiol 2021; 115:490-501. [PMID: 33448497 DOI: 10.1111/mmi.14683] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/26/2022]
Abstract
The human gut microbiota endows the host with a wealth of metabolic functions central to health, one of which is the degradation and fermentation of complex carbohydrates. The Bacteroidetes are one of the dominant bacterial phyla of this community and possess an expanded capacity for glycan utilization. This is mediated via the coordinated expression of discrete polysaccharide utilization loci (PUL) that invariantly encode a TonB-dependent transporter (SusC) that works with a glycan-capturing lipoprotein (SusD). More broadly within Gram-negative bacteria, TonB-dependent transporters (TBDTs) are deployed for the uptake of not only sugars, but also more often for essential nutrients such as iron and vitamins. Here, we provide a comprehensive look at the repertoire of TBDTs found in the model gut symbiont Bacteroides thetaiotaomicron and the range of predicted functional domains associated with these transporters and SusD proteins for the uptake of both glycans and other nutrients. This atlas of the B. thetaiotaomicron TBDTs reveals that there are at least three distinct subtypes of these transporters encoded within its genome that are presumably regulated in different ways to tune nutrient uptake.
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Affiliation(s)
| | - Lauryn M Martin
- Department of Biology, Alcorn State University, Alcorn, MS, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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