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Senoo A, Hoshino M, Shiomi T, Nakakido M, Nagatoishi S, Kuroda D, Nakagawa I, Tame JRH, Caaveiro JMM, Tsumoto K. Structural basis for the recognition of human hemoglobin by the heme-acquisition protein Shr from Streptococcus pyogenes. Sci Rep 2024; 14:5374. [PMID: 38438508 PMCID: PMC10912661 DOI: 10.1038/s41598-024-55734-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/27/2024] [Indexed: 03/06/2024] Open
Abstract
In Gram-positive bacteria, sophisticated machineries to acquire the heme group of hemoglobin (Hb) have evolved to extract the precious iron atom contained in it. In the human pathogen Streptococcus pyogenes, the Shr protein is a key component of this machinery. Herein we present the crystal structure of hemoglobin-interacting domain 2 (HID2) of Shr bound to Hb. HID2 interacts with both, the protein and heme portions of Hb, explaining the specificity of HID2 for the heme-bound form of Hb, but not its heme-depleted form. Further mutational analysis shows little tolerance of HID2 to interfacial mutations, suggesting that its interaction surface with Hb could be a suitable candidate to develop efficient inhibitors abrogating the binding of Shr to Hb.
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Affiliation(s)
- Akinobu Senoo
- Laboratory of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka City, 812-8582, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masato Hoshino
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Toshiki Shiomi
- Laboratory of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka City, 812-8582, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoru Nagatoishi
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Daisuke Kuroda
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Jose M M Caaveiro
- Laboratory of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka City, 812-8582, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
- The Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8629, Japan.
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2
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Macdonald R, Mahoney BJ, Soule J, Goring AK, Ford J, Loo JA, Cascio D, Clubb RT. The Shr receptor from Streptococcus pyogenes uses a cap and release mechanism to acquire heme-iron from human hemoglobin. Proc Natl Acad Sci U S A 2023; 120:e2211939120. [PMID: 36693107 PMCID: PMC9945957 DOI: 10.1073/pnas.2211939120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/19/2022] [Indexed: 01/25/2023] Open
Abstract
Streptococcus pyogenes (group A Streptococcus) is a clinically important microbial pathogen that requires iron in order to proliferate. During infections, S. pyogenes uses the surface displayed Shr receptor to capture human hemoglobin (Hb) and acquires its iron-laden heme molecules. Through a poorly understood mechanism, Shr engages Hb via two structurally unique N-terminal Hb-interacting domains (HID1 and HID2) which facilitate heme transfer to proximal NEAr Transporter (NEAT) domains. Based on the results of X-ray crystallography, small angle X-ray scattering, NMR spectroscopy, native mass spectrometry, and heme transfer experiments, we propose that Shr utilizes a "cap and release" mechanism to gather heme from Hb. In the mechanism, Shr uses the HID1 and HID2 modules to preferentially recognize only heme-loaded forms of Hb by contacting the edges of its protoporphyrin rings. Heme transfer is enabled by significant receptor dynamics within the Shr-Hb complex which function to transiently uncap HID1 from the heme bound to Hb's β subunit, enabling the gated release of its relatively weakly bound heme molecule and subsequent capture by Shr's NEAT domains. These dynamics may maximize the efficiency of heme scavenging by S. pyogenes, enabling it to preferentially recognize and remove heme from only heme-loaded forms of Hb that contain iron.
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Affiliation(s)
- Ramsay Macdonald
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Brendan J. Mahoney
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Jess Soule
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Andrew K. Goring
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Jordan Ford
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
| | - Duilio Cascio
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
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3
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Clayton J, Ellis-Guardiola K, Mahoney BJ, Soule J, Clubb RT, Wereszczynski J. Directed inter-domain motions enable the IsdH Staphylococcus aureus receptor to rapidly extract heme from human hemoglobin. J Mol Biol 2022; 434:167623. [DOI: 10.1016/j.jmb.2022.167623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/07/2022] [Accepted: 05/01/2022] [Indexed: 11/29/2022]
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4
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Valenciano-Bellido S, Caaveiro JMM, Morante K, Sushko T, Nakakido M, Nagatoishi S, Tsumoto K. Structure and role of the linker domain of the iron surface-determinant protein IsdH in heme transportation in Staphylococcus aureus. J Biol Chem 2022; 298:101995. [PMID: 35500652 PMCID: PMC9163592 DOI: 10.1016/j.jbc.2022.101995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus is a major cause of deadly nosocomial infections, a severe problem fueled by the steady increase of resistant bacteria. The iron surface determinant (Isd) system is a family of proteins that acquire nutritional iron from the host organism, helping the bacterium to proliferate during infection, and therefore represents a promising antibacterial target. In particular, the surface protein IsdH captures hemoglobin (Hb) and acquires the heme moiety containing the iron atom. Structurally, IsdH comprises three distinctive NEAr-iron Transporter (NEAT) domains connected by linker domains. The objective of this study was to characterize the linker region between NEAT2 and NEAT3 from various biophysical viewpoints and thereby advance our understanding of its role in the molecular mechanism of heme extraction. We demonstrate the linker region contributes to the stability of the bound protein, likely influencing the flexibility and orientation of the NEAT3 domain in its interaction with Hb, but only exerts a modest contribution to the affinity of IsdH for heme. Based on these data, we suggest that the flexible nature of the linker facilitates the precise positioning of NEAT3 to acquire heme. In addition, we also found that residues His45 and His89 of Hb located in the heme transfer route toward IsdH do not play a critical role in the transfer rate-determining step. In conclusion, this study clarifies key elements of the mechanism of heme extraction of human Hb by IsdH, providing key insights into the Isd system and other protein systems containing NEAT domains.
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Affiliation(s)
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
| | - Koldo Morante
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tatyana Sushko
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan; Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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5
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De Bei O, Marchetti M, Ronda L, Gianquinto E, Lazzarato L, Chirgadze DY, Hardwick SW, Cooper LR, Spyrakis F, Luisi BF, Campanini B, Bettati S. Cryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction. Proc Natl Acad Sci U S A 2022; 119:e2116708119. [PMID: 35357971 PMCID: PMC9168843 DOI: 10.1073/pnas.2116708119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/11/2022] [Indexed: 12/02/2022] Open
Abstract
Iron surface determinant B (IsdB) is a hemoglobin (Hb) receptor essential for hemic iron acquisition by Staphylococcus aureus. Heme transfer to IsdB is possible from oxidized Hb (metHb), but inefficient from Hb either bound to oxygen (oxyHb) or bound to carbon monoxide (HbCO), and encompasses a sequence of structural events that are currently poorly understood. By single-particle cryo-electron microscopy, we determined the structure of two IsdB:Hb complexes, representing key species along the heme extraction pathway. The IsdB:HbCO structure, at 2.9-Å resolution, provides a snapshot of the preextraction complex. In this early stage of IsdB:Hb interaction, the hemophore binds to the β-subunits of the Hb tetramer, exploiting a folding-upon-binding mechanism that is likely triggered by a cis/trans isomerization of Pro173. Binding of IsdB to α-subunits occurs upon dissociation of the Hb tetramer into α/β dimers. The structure of the IsdB:metHb complex reveals the final step of the extraction process, where heme transfer to IsdB is completed. The stability of the complex, both before and after heme transfer from Hb to IsdB, is influenced by isomerization of Pro173. These results greatly enhance current understanding of structural and dynamic aspects of the heme extraction mechanism by IsdB and provide insight into the interactions that stabilize the complex before the heme transfer event. This information will support future efforts to identify inhibitors of heme acquisition by S. aureus by interfering with IsdB:Hb complex formation.
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Affiliation(s)
- Omar De Bei
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
| | - Marialaura Marchetti
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Medicine and Surgery, University of Parma, Parma 43126, Italy
| | - Luca Ronda
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Medicine and Surgery, University of Parma, Parma 43126, Italy
- Institute of Biophysics, National Research Council, Pisa 56124, Italy
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin 10125, Italy
| | - Loretta Lazzarato
- Department of Drug Science and Technology, University of Turin, Turin 10125, Italy
| | - Dimitri Y. Chirgadze
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Steven W. Hardwick
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Lee R. Cooper
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin 10125, Italy
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Barbara Campanini
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Food and Drug, University of Parma, Parma 43124, Italy
| | - Stefano Bettati
- Interdepartmental Center Biopharmanet-TEC, University of Parma, Parma 43124, Italy
- Department of Medicine and Surgery, University of Parma, Parma 43126, Italy
- Institute of Biophysics, National Research Council, Pisa 56124, Italy
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6
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Ellis-Guardiola K, Mahoney BJ, Clubb RT. NEAr Transporter (NEAT) Domains: Unique Surface Displayed Heme Chaperones That Enable Gram-Positive Bacteria to Capture Heme-Iron From Hemoglobin. Front Microbiol 2021; 11:607679. [PMID: 33488548 PMCID: PMC7815599 DOI: 10.3389/fmicb.2020.607679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/03/2020] [Indexed: 11/13/2022] Open
Abstract
Iron is an important micronutrient that is required by bacteria to proliferate and to cause disease. Many bacterial pathogens forage iron from human hemoglobin (Hb) during infections, which contains this metal within heme (iron-protoporphyrin IX). Several clinically important pathogenic species within the Firmicutes phylum scavenge heme using surface-displayed or secreted NEAr Transporter (NEAT) domains. In this review, we discuss how these versatile proteins function in the Staphylococcus aureus Iron-regulated surface determinant system that scavenges heme-iron from Hb. S. aureus NEAT domains function as either Hb receptors or as heme-binding chaperones. In vitro studies have shown that heme-binding NEAT domains can rapidly exchange heme amongst one another via transiently forming transfer complexes, leading to the interesting hypothesis that they may form a protein-wire within the peptidoglycan layer through which heme flows from the microbial surface to the membrane. In Hb receptors, recent studies have revealed how dedicated heme- and Hb-binding NEAT domains function synergistically to extract Hb's heme molecules, and how receptor binding to the Hb-haptoglobin complex may block its clearance by macrophages, prolonging microbial access to Hb's iron. The functions of NEAT domains in other Gram-positive bacteria are also reviewed.
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Affiliation(s)
- Ken Ellis-Guardiola
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Brendan J. Mahoney
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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7
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di Masi A, De Simone G, Ciaccio C, D'Orso S, Coletta M, Ascenzi P. Haptoglobin: From hemoglobin scavenging to human health. Mol Aspects Med 2020; 73:100851. [PMID: 32660714 DOI: 10.1016/j.mam.2020.100851] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
Haptoglobin (Hp) belongs to the family of acute-phase plasma proteins and represents the most important plasma detoxifier of hemoglobin (Hb). The basic Hp molecule is a tetrameric protein built by two α/β dimers. Each Hp α/β dimer is encoded by a single gene and is synthesized as a single polypeptide. Following post-translational protease-dependent cleavage of the Hp polypeptide, the α and β chains are linked by disulfide bridge(s) to generate the mature Hp protein. As human Hp gene is characterized by two common Hp1 and Hp2 alleles, three major genotypes can result (i.e., Hp1-1, Hp2-1, and Hp2-2). Hp regulates Hb clearance from circulation by the macrophage-specific receptor CD163, thus preventing Hb-mediated severe consequences for health. Indeed, the antioxidant and Hb binding properties of Hp as well as its ability to stimulate cells of the monocyte/macrophage lineage and to modulate the helper T-cell type 1 and type 2 balance significantly associate with a variety of pathogenic disorders (e.g., infectious diseases, diabetes, cardiovascular diseases, and cancer). Alternative functions of the variants Hp1 and Hp2 have been reported, particularly in the susceptibility and protection against infectious (e.g., pulmonary tuberculosis, HIV, and malaria) and non-infectious (e.g., diabetes, cardiovascular diseases and obesity) diseases. Both high and low levels of Hp are indicative of clinical conditions: Hp plasma levels increase during infections, inflammation, and various malignant diseases, and decrease during malnutrition, hemolysis, hepatic disease, allergic reactions, and seizure disorders. Of note, the Hp:Hb complexes display heme-based reactivity; in fact, they bind several ferrous and ferric ligands, including O2, CO, and NO, and display (pseudo-)enzymatic properties (e.g., NO and peroxynitrite detoxification). Here, genetic, biochemical, biomedical, and biotechnological aspects of Hp are reviewed.
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Affiliation(s)
- Alessandra di Masi
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | - Giovanna De Simone
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133, Roma, Italy; Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Via Celso Ulpiani 27, I-70126, Bari, Italy
| | - Silvia D'Orso
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133, Roma, Italy; Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Via Celso Ulpiani 27, I-70126, Bari, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146, Roma, Italy.
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8
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The Staphylococcus aureus IsdH Receptor Forms a Dynamic Complex with Human Hemoglobin that Triggers Heme Release via Two Distinct Hot Spots. J Mol Biol 2019; 432:1064-1082. [PMID: 31881209 DOI: 10.1016/j.jmb.2019.12.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/22/2019] [Accepted: 12/12/2019] [Indexed: 02/02/2023]
Abstract
Iron is an essential nutrient that is actively acquired by bacterial pathogens during infections. Clinically important Staphylococcus aureus obtains iron by extracting heme from hemoglobin (Hb) using the closely related IsdB and IsdH surface receptors. In IsdH, extraction is mediated by a conserved tridomain unit that contains its second (N2) and third (N3) NEAT domains joined by a helical linker, called IsdHN2N3. Leveraging the crystal structure of the IsdHN2N3:Hb complex, we have probed the mechanism of heme capture using NMR, stopped-flow transfer kinetics measurements, and molecular dynamics (MD) simulations. NMR studies of the 220 kDa IsdHN2N3:Hb complex reveal that it is dynamic, with persistent interdomain motions enabling the linker and N3 domains in the receptor to transiently engage Hb to remove its heme. An alanine mutagenesis analysis reveals that two receptor subsites positioned ~20 Å apart trigger heme release by contacting Hb's F-helix. These subsites are located within the N3 and linker domains and appear to play distinct roles in stabilizing the heme transfer transition state. Linker domain contacts primarily function to destabilize Hb-heme interactions, thereby lowering ΔH‡, while contacts from the N3 subsite play a similar destabilizing role, but also form a bridge through which heme moves from Hb to the receptor. Interestingly, MD simulations suggest that within the transiently forming interface, both the F-helix and receptor bridge are in motion, dynamically sampling conformations that are suitable for heme transfer. Thus, IsdH triggers heme release from Hb via a flexible, low-affinity interface that forms fleetingly in solution.
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9
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Gianquinto E, Moscetti I, De Bei O, Campanini B, Marchetti M, Luque FJ, Cannistraro S, Ronda L, Bizzarri AR, Spyrakis F, Bettati S. Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: a kinetic and mechanistic insight. Sci Rep 2019; 9:18629. [PMID: 31819099 PMCID: PMC6901573 DOI: 10.1038/s41598-019-54970-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/21/2019] [Indexed: 12/21/2022] Open
Abstract
Among multidrug-resistant bacteria, methicillin-resistant Staphylococcus aureus is emerging as one of the most threatening pathogens. S. aureus exploits different mechanisms for its iron supply, but the preferred one is acquisition of organic iron through the expression of hemoglobin (Hb) receptors. One of these, IsdB, belonging to the Isd (Iron-Regulated Surface Determinant) system, was shown to be essential for bacterial growth and virulence. Therefore, interaction of IsdB with Hb represents a promising target for the rational design of a new class of antibacterial molecules. However, despite recent investigations, many structural and mechanistic details of complex formation and heme extraction process are still elusive. By combining site-directed mutagenesis, absorption spectroscopy, surface plasmon resonance and molecular dynamics simulations, we tackled most of the so far unanswered questions: (i) the exact complex stoichiometry, (ii) the microscopic kinetic rates of complex formation, (iii) the IsdB selectivity for binding to, and extracting heme from, α and β subunits of Hb, iv) the role of specific amino acid residues and structural regions in driving complex formation and heme transfer, and (v) the structural/dynamic effect played by the hemophore on Hb.
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Affiliation(s)
- Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy
| | - Ilaria Moscetti
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Omar De Bei
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, Parma, 43124, Italy.,Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy
| | - Marialaura Marchetti
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy.,Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Santa Coloma de Gramenet, 08921, Spain
| | - Salvatore Cannistraro
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Luca Ronda
- Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy.,Department of Medicine and Surgery, University of Parma, Parma, 43126, Italy.,Institute of Biophysics, National Research Council, Pisa, 56124, Italy
| | - Anna Rita Bizzarri
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy.
| | - Stefano Bettati
- Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy. .,Department of Medicine and Surgery, University of Parma, Parma, 43126, Italy. .,Institute of Biophysics, National Research Council, Pisa, 56124, Italy.
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10
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Mikkelsen JH, Runager K, Andersen CBF. The human protein haptoglobin inhibits IsdH-mediated heme-sequestering by Staphylococcus aureus. J Biol Chem 2019; 295:1781-1791. [PMID: 31819010 DOI: 10.1074/jbc.ra119.011612] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/26/2019] [Indexed: 12/29/2022] Open
Abstract
Iron is an essential nutrient for all living organisms. To acquire iron, many pathogens have developed elaborate systems to steal it from their hosts. The iron acquisition system in the opportunistic pathogen Staphylococcus aureus comprises nine proteins, called iron-regulated surface determinants (Isds). The Isd components enable S. aureus to extract heme from hemoglobin (Hb), transport it into the bacterial cytoplasm, and ultimately release iron from the porphyrin ring. IsdB and IsdH act as hemoglobin receptors and are known to actively extract heme from extracellular Hb. To limit microbial pathogenicity during infection, host organisms attempt to restrict the availability of nutrient metals at the host-pathogen interface. The human acute phase protein haptoglobin (Hp) protects the host from oxidative damage by clearing hemoglobin that has leaked from red blood cells and also restricts the availability of extracellular Hb-bound iron to invading pathogens. To investigate whether Hp serves an additional role in nutritional immunity through a direct inhibition of IsdH-mediated iron acquisition, here we measured heme extraction from the Hp-Hb complex by UV-visible spectroscopy and determined the crystal structure of the Hp-Hb-IsdH complex at 2.9 Å resolution. We found that Hp strongly inhibits IsdH-mediated heme extraction and that Hp binding prevents local unfolding of the Hb heme pocket, leaving IsdH unable to wrest the heme from Hb. Furthermore, we noted that the Hp-Hb binding appears to trap IsdH in an initial state before heme transfer. Our findings provide insights into Hp-mediated IsdH inhibition and the dynamics of IsdH-mediated heme extraction.
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Affiliation(s)
- Jakob H Mikkelsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Kasper Runager
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
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11
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Macdonald R, Mahoney BJ, Ellis-Guardiola K, Maresso A, Clubb RT. NMR experiments redefine the hemoglobin binding properties of bacterial NEAr-iron Transporter domains. Protein Sci 2019; 28:1513-1523. [PMID: 31120610 DOI: 10.1002/pro.3662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/14/2019] [Indexed: 01/02/2023]
Abstract
Iron is a versatile metal cofactor that is used in a wide range of essential cellular processes. During infections, many bacterial pathogens acquire iron from human hemoglobin (Hb), which contains the majority of the body's total iron content in the form of heme (iron protoporphyrin IX). Clinically important Gram-positive bacterial pathogens scavenge heme using an array of secreted and cell-wall-associated receptors that contain NEAr-iron Transporter (NEAT) domains. Experimentally defining the Hb binding properties of NEAT domains has been challenging, limiting our understanding of their function in heme uptake. Here we show that solution-state NMR spectroscopy is a powerful tool to define the Hb binding properties of NEAT domains. The utility of this method is demonstrated using the NEAT domains from Bacillus anthracis and Listeria monocytogenes. Our results are compatible with the existence of at least two types of NEAT domains that are capable of interacting with either Hb or heme. These binding properties can be predicted from their primary sequences, with Hb- and heme-binding NEAT domains being distinguished by the presence of (F/Y)YH(Y/F) and S/YXXXY motifs, respectively. The results of this work should enable the functions of a wide range of NEAT domain containing proteins in pathogenic bacteria to be reliably predicted.
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Affiliation(s)
- Ramsay Macdonald
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, 90095.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, 90095
| | - Brendan J Mahoney
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, 90095.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, 90095
| | - Ken Ellis-Guardiola
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, 90095.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, 90095
| | - Anthony Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, 77030
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, 90095.,UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, 90095.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, 90095
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12
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Using the hemoglobin-binding Staphylococcus aureus protein IsdH to enable plasma analysis of hemolyzed blood samples. ACTA ACUST UNITED AC 2019; 57:1690-1698. [DOI: 10.1515/cclm-2019-0381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/26/2019] [Indexed: 11/15/2022]
Abstract
Abstract
Background
Intravascular hemolysis and in vitro hemolysis are prevalent contributors to failed blood sample analysis in the routine hospital laboratory. Interferences by hemoglobin in spectrophotometric and certain enzyme activity assays is the major causative factor.
Methods
By exploiting the hemoglobin-binding properties of the iron-regulated surface determinant H (IsdH) protein from Staphylococcus aureus we have developed a new method to instantly remove hemoglobin and hemoglobin-haptoglobin complexes from plasma in vitro thereby enabling the measurement of hemoglobin-sensitive analytes in hemolyzed plasma. In the present study we used an engineered IsdH mutant form conjugated to Sepharose for the efficient removal of plasma hemoglobin in concentrations up to 15 mg/mL. The high abundance of haptoglobin, which forms a tight complex with hemoglobin in plasma, did not affect the hemoglobin removal by IsdH Sepharose.
Results
Applying the method on plasma samples that beforehand were spiked with blood hemolysate re-enabled measurement of the hemolysis sensitive parameters: alkaline phosphatase, conjugated bilirubin, iron, ferritin, γ-glutamyltransferase, total thyroxine and troponin T. IsdH Sepharose-mediated hemoglobin removal also enabled measurement of hemolysis sensitive parameters in hemolyzed samples from anonymized patients.
Conclusions
In conclusion, IsdH Sepharose is a simple cost-effective pretreatment of hemolyzed samples correcting and enabling the measurement of several important hemoglobin-sensitive parameters in a way compatible with standard procedures in routine laboratories.
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13
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Conroy BS, Grigg JC, Kolesnikov M, Morales LD, Murphy MEP. Staphylococcus aureus heme and siderophore-iron acquisition pathways. Biometals 2019; 32:409-424. [PMID: 30911924 DOI: 10.1007/s10534-019-00188-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/18/2019] [Indexed: 11/24/2022]
Abstract
Staphylococcus aureus is a versatile opportunistic human pathogen. Infection by this bacterium requires uptake of iron from the human host, but iron is highly restricted in this environment. Staphylococcus aureus iron sufficiency is achieved primarily through uptake of heme and high-affinity iron chelators, known as siderophores. Two siderophores (staphyloferrins) are produced and secreted by S. aureus into the extracellular environment to capture iron. Staphylococcus aureus expresses specific uptake systems for staphyloferrins and more general uptake systems for siderophores produced by other microorganisms. The S. aureus heme uptake system uses highly-specific cell surface receptors to extract heme from hemoglobin and hemoglobin-haptoglobin complexes for transport into the cytoplasm where it is degraded to liberate iron. Initially thought to be independent systems, recent findings indicate that these iron uptake pathways intersect. IruO is a reductase that releases iron from heme and some ferric-siderophores. Moreover, multifunctional SbnI produces a precursor for staphyloferrin B biosynthesis, and also binds heme to regulate expression of the staphyloferrin B biosynthesis pathway. Intersection of the S. aureus iron uptake pathways is hypothesized to be important for rapid adaptation to available iron sources. Components of the heme and siderophore uptake systems are currently being targeted in the development of therapeutics against S. aureus.
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Affiliation(s)
- Brigid S Conroy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, Canada
| | - Jason C Grigg
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, Canada
| | - Maxim Kolesnikov
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, Canada
| | - L Daniela Morales
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, V6T 1Z3, Canada.
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14
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Macdonald R, Cascio D, Collazo MJ, Phillips M, Clubb RT. The Streptococcus pyogenes Shr protein captures human hemoglobin using two structurally unique binding domains. J Biol Chem 2018; 293:18365-18377. [PMID: 30301765 DOI: 10.1074/jbc.ra118.005261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/03/2018] [Indexed: 12/19/2022] Open
Abstract
In order to proliferate and mount an infection, many bacterial pathogens need to acquire iron from their host. The most abundant iron source in the body is the oxygen transporter hemoglobin (Hb). Streptococcus pyogenes, a potentially lethal human pathogen, uses the Shr protein to capture Hb on the cell surface. Shr is an important virulence factor, yet the mechanism by which it captures Hb and acquires its heme is not well-understood. Here, we show using NMR and biochemical methods that Shr binds Hb using two related modules that were previously defined as domains of unknown function (DUF1533). These hemoglobin-interacting domains (HIDs), called HID1 and HID2, are autonomously folded and independently bind Hb. The 1.5 Å resolution crystal structure of HID2 revealed that it is a structurally unique Hb-binding domain. Mutagenesis studies revealed a conserved tyrosine in both HIDs that is essential for Hb binding. Our biochemical studies indicate that HID2 binds Hb with higher affinity than HID1 and that the Hb tetramer is engaged by two Shr receptors. NMR studies reveal the presence of a third autonomously folded domain between HID2 and a heme-binding NEAT1 domain, suggesting that this linker domain may position NEAT1 near Hb for heme capture.
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Affiliation(s)
- Ramsay Macdonald
- From the Department of Chemistry and Biochemistry,; UCLA-DOE Institute of Genomics and Proteomics and
| | | | | | | | - Robert T Clubb
- From the Department of Chemistry and Biochemistry,; UCLA-DOE Institute of Genomics and Proteomics and; Molecular Biology Institute, UCLA, Los Angeles, California 90095.
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15
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Mozzi A, Forni D, Clerici M, Cagliani R, Sironi M. The Diversity of Mammalian Hemoproteins and Microbial Heme Scavengers Is Shaped by an Arms Race for Iron Piracy. Front Immunol 2018; 9:2086. [PMID: 30271410 PMCID: PMC6142043 DOI: 10.3389/fimmu.2018.02086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/23/2018] [Indexed: 11/13/2022] Open
Abstract
Iron is an essential micronutrient for most living species. In mammals, hemoglobin (Hb) stores more than two thirds of the body's iron content. In the bloodstream, haptoglobin (Hp) and hemopexin (Hpx) sequester free Hb or heme. Pathogenic microorganisms usually acquire iron from their hosts and have evolved complex systems of iron piracy to circumvent nutritional immunity. Herein, we performed an evolutionary analysis of genes coding for mammalian heme-binding proteins and heme-scavengers in pathogen species. The underlying hypothesis is that these molecules are engaged in a molecular arms race. We show that positive selection drove the evolution of mammalian Hb and Hpx. Positively selected sites in Hb are located at the interaction surface with Neisseria meningitidis heme scavenger HpuA and with Staphylococcus aureus iron-regulated surface determinant B (IsdB). In turn, positively selected sites in HpuA and IsdB are located in the flexible protein regions that contact Hb. A residue in Hb (S45H) was also selected on the Caprinae branch. This site stabilizes the interaction with Trypanosoma brucei hemoglobin-haptoglobin (HbHp) receptor (TbHpHbR), a molecule that also mediates trypanosome lytic factor (TLF) entry. In TbHpHbR, positive selection drove the evolution of a variant (L210S) which allows evasion from TLF but reduces affinity for HbHp. Finally, selected sites in Hpx are located at the interaction surface with the Haemophilus influenzae hemophore HxuA, which in turn displays fast evolving sites at the Hpx-binding interface. These results shed light into host-pathogens conflicts and establish the importance of nutritional immunity as an evolutionary force.
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Affiliation(s)
- Alessandra Mozzi
- Scientific Institute, IRCCS E. Medea, Bioinformatics, Lecco, Italy
| | - Diego Forni
- Scientific Institute, IRCCS E. Medea, Bioinformatics, Lecco, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Rachele Cagliani
- Scientific Institute, IRCCS E. Medea, Bioinformatics, Lecco, Italy
| | - Manuela Sironi
- Scientific Institute, IRCCS E. Medea, Bioinformatics, Lecco, Italy
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16
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Sjodt M, Macdonald R, Marshall JD, Clayton J, Olson JS, Phillips M, Gell DA, Wereszczynski J, Clubb RT. Energetics underlying hemin extraction from human hemoglobin by Staphylococcus aureus. J Biol Chem 2018. [PMID: 29540481 DOI: 10.1074/jbc.ra117.000803] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Staphylococcus aureus is a leading cause of life-threatening infections in the United States. It actively acquires the essential nutrient iron from human hemoglobin (Hb) using the iron-regulated surface-determinant (Isd) system. This process is initiated when the closely related bacterial IsdB and IsdH receptors bind to Hb and extract its hemin through a conserved tri-domain unit that contains two NEAr iron Transporter (NEAT) domains that are connected by a helical linker domain. Previously, we demonstrated that the tri-domain unit within IsdH (IsdHN2N3) triggers hemin release by distorting Hb's F-helix. Here, we report that IsdHN2N3 promotes hemin release from both the α- and β-subunits. Using a receptor mutant that only binds to the α-subunit of Hb and a stopped-flow transfer assay, we determined the energetics and micro-rate constants of hemin extraction from tetrameric Hb. We found that at 37 °C, the receptor accelerates hemin release from Hb up to 13,400-fold, with an activation enthalpy of 19.5 ± 1.1 kcal/mol. We propose that hemin removal requires the rate-limiting hydrolytic cleavage of the axial HisF8 Nϵ-Fe3+ bond, which, based on molecular dynamics simulations, may be facilitated by receptor-induced bond hydration. Isothermal titration calorimetry experiments revealed that two distinct IsdHN2N3·Hb protein·protein interfaces promote hemin release. A high-affinity receptor·Hb(A-helix) interface contributed ∼95% of the total binding standard free energy, enabling much weaker receptor interactions with Hb's F-helix that distort its hemin pocket and cause unfavorable changes in the binding enthalpy. We present a model indicating that receptor-introduced structural distortions and increased solvation underlie the IsdH-mediated hemin extraction mechanism.
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Affiliation(s)
- Megan Sjodt
- From the Department of Chemistry and Biochemistry.,UCLA-DOE Institute of Genomics and Proteomics, and
| | - Ramsay Macdonald
- From the Department of Chemistry and Biochemistry.,UCLA-DOE Institute of Genomics and Proteomics, and
| | | | - Joseph Clayton
- the Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616
| | - John S Olson
- the Department of BioSciences, Rice University, Houston, Texas 77251, and
| | | | - David A Gell
- the School of Medicine, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Jeff Wereszczynski
- the Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Robert T Clubb
- From the Department of Chemistry and Biochemistry, .,UCLA-DOE Institute of Genomics and Proteomics, and.,Molecular Biology Institute, UCLA, Los Angeles, California 90095
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17
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Misra N, Wines TF, Knopp CL, McGuire MA, Tinker JK. Expression, immunogenicity and variation of iron-regulated surface protein A from bovine isolates of Staphylococcus aureus. FEMS Microbiol Lett 2017; 364:3739792. [PMID: 28430959 DOI: 10.1093/femsle/fnx082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 04/18/2017] [Indexed: 01/24/2023] Open
Abstract
Staphylococcus aureus iron-regulated surface protein A (IsdA) is a fibrinogen and fibronectin adhesin that also contributes to iron sequestration and resistance to innate immunity. IsdA is conserved in human isolates and has been investigated as a human vaccine candidate. Here we report the expression of isdA, the efficacy of anti-IsdA responses and the existence of IsdA sequence variants from bovine Staphylococcus. Clinical staphylococci were obtained from US dairy farms and assayed by PCR for the presence and expression of isdA. isdA-positive species from bovines included S. aureus, S. haemolyticus and S. chromogenes. Immunoassays on bovine milk and serum confirmed the induction and opsonophagocytic activity of anti-IsdA humoral responses. The variable region of isdA was sequenced and protein alignments predicted the presence of two main variants consistent with those from human S. aureus. Mouse antibodies against one IsdA variant reduced staphylococcal binding to fibronectin in vitro in an isotype-dependent manner. Purified IsdA variants bound distinctly to fibronectin and fibrinogen. Our findings demonstrate that variability within the C-terminus of this adhesin affects immune reactivity and binding specificity, but are consistent with the significance of IsdA in bovine disease and relevant for vaccine development.
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Affiliation(s)
- Neha Misra
- Biomolecular Ph.D. Program, Boise State University, Boise, ID 83725, USA
| | - Tyler F Wines
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Colton L Knopp
- Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Mark A McGuire
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID 83844, USA
| | - Juliette K Tinker
- Biomolecular Ph.D. Program, Boise State University, Boise, ID 83725, USA.,Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
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18
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Bowden CFM, Chan ACK, Li EJW, Arrieta AL, Eltis LD, Murphy MEP. Structure-function analyses reveal key features in Staphylococcus aureus IsdB-associated unfolding of the heme-binding pocket of human hemoglobin. J Biol Chem 2017; 293:177-190. [PMID: 29109153 DOI: 10.1074/jbc.m117.806562] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/19/2017] [Indexed: 11/06/2022] Open
Abstract
IsdB is a receptor on the surface of the bacterial pathogen Staphylococcus aureus that extracts heme from hemoglobin (Hb) to enable growth on Hb as a sole iron source. IsdB is critically important both for in vitro growth on Hb and in infection models and is also highly up-regulated in blood, serum, and tissue infection models, indicating a key role of this receptor in bacterial virulence. However, structural information for IsdB is limited. We present here a crystal structure of a complex between human Hb and IsdB. In this complex, the α subunits of Hb are refolded with the heme displaced to the interface with IsdB. We also observe that atypical residues of Hb, His58 and His89 of αHb, coordinate to the heme iron, which is poised for transfer into the heme-binding pocket of IsdB. Moreover, the porphyrin ring interacts with IsdB residues Tyr440 and Tyr444 Previously, Tyr440 was observed to coordinate heme iron in an IsdB·heme complex structure. A Y440F/Y444F IsdB variant we produced was defective in heme transfer yet formed a stable complex with Hb (Kd = 6 ± 2 μm) in solution with spectroscopic features of the bis-His species observed in the crystal structure. Haptoglobin binds to a distinct site on Hb to inhibit heme transfer to IsdB and growth of S. aureus, and a ternary complex of IsdB·Hb·Hp was observed. We propose a model for IsdB heme transfer from Hb that involves unfolding of Hb and heme iron ligand exchange.
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Affiliation(s)
- Catherine F M Bowden
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Emily J W Li
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Angelé L Arrieta
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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19
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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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20
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Andersen CBF, Stødkilde K, Sæderup KL, Kuhlee A, Raunser S, Graversen JH, Moestrup SK. Haptoglobin. Antioxid Redox Signal 2017; 26:814-831. [PMID: 27650279 DOI: 10.1089/ars.2016.6793] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Haptoglobin (Hp) is an abundant human plasma protein that tightly captures hemoglobin (Hb) during hemolysis. The Hb-Hp complex formation reduces the oxidative properties of heme/Hb and promotes recognition by the macrophage scavenger receptor CD163. This leads to Hb-Hp breakdown and heme catabolism by heme oxygenase and biliverdin reductase. Gene duplications of a part of or the entire Hp gene in the primate evolution have led to variant Hp gene products that collectively may be designated "the haptoglobins (Hps)" as they all bind Hb. These variant products include the human-specific multimeric Hp phenotypes in individuals, which are hetero- or homozygous for an Hp2 gene allele. The Hp-related protein (Hpr) is another Hp duplication product in humans and other primates. Alternative functions of the variant Hps are indicated by numerous reports on association between Hp phenotypes and disease as well as the elucidation of a specific role of Hpr in the innate immune defense. Recent Advances: Recent functional and structural information on Hp and receptor systems for Hb removal now provides insight on how Hp carries out essential functions such as the Hb detoxification/removal, and how Hpr, by acting as an Hp-lookalike, can sneak a lethal toxin into trypanosome parasites that cause mammalian sleeping sickness. Critical Issues and Future Directions: The new structural insight may facilitate ongoing attempts of developing Hp derivatives for prevention of Hb toxicity in hemolytic diseases such as sickle cell disease and other hemoglobinopathies. Furthermore, the new structural knowledge may help identifying yet unknown functions based on other disease-relevant biological interactions involving Hps. Antioxid. Redox Signal. 26, 814-831.
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Affiliation(s)
| | | | - Kirstine Lindhardt Sæderup
- 2 Cancer and Inflammation, Department of Molecular Medicine, University of Southern Denmark , Odense C, Denmark
| | - Anne Kuhlee
- 3 Department of Structural Biochemistry, Max-Planck Institute of Molecular Physiology , Dortmund, Germany
| | - Stefan Raunser
- 3 Department of Structural Biochemistry, Max-Planck Institute of Molecular Physiology , Dortmund, Germany
| | - Jonas H Graversen
- 2 Cancer and Inflammation, Department of Molecular Medicine, University of Southern Denmark , Odense C, Denmark
| | - Søren Kragh Moestrup
- 1 Department of Biomedicine, University of Aarhus , Aarhus C, Denmark .,2 Cancer and Inflammation, Department of Molecular Medicine, University of Southern Denmark , Odense C, Denmark .,4 Department of Clinical Biochemistry and Pharmacology, Odense University Hospital , Odense C, Denmark
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21
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Abstract
Iron is essential for the survival of most bacteria but presents a significant challenge given its limited bioavailability. Furthermore, the toxicity of iron combined with the need to maintain physiological iron levels within a narrow concentration range requires sophisticated systems to sense, regulate, and transport iron. Most bacteria have evolved mechanisms to chelate and transport ferric iron (Fe3+) via siderophore receptor systems, and pathogenic bacteria have further lowered this barrier by employing mechanisms to utilize the host's hemoproteins. Once internalized, heme is cleaved by both oxidative and nonoxidative mechanisms to release iron. Heme, itself a lipophilic and toxic molecule, presents a significant challenge for transport into the cell. As such, pathogenic bacteria have evolved sophisticated cell surface signaling and transport systems to obtain heme from the host. In this review, we summarize the structure and function of the heme-sensing and transport systems of pathogenic bacteria and the potential of these systems as antimicrobial targets.
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Affiliation(s)
- Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201;
| | - Angela Wilks
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201;
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22
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Diverse structural approaches to haem appropriation by pathogenic bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:422-433. [PMID: 28130069 DOI: 10.1016/j.bbapap.2017.01.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/16/2017] [Accepted: 01/23/2017] [Indexed: 11/24/2022]
Abstract
The critical need for iron presents a challenge for pathogenic bacteria that must survive in an environment bereft of accessible iron due to a natural low bioavailability and their host's nutritional immunity. Appropriating haem, either direct from host haemoproteins or by secreting haem-scavenging haemophores, is one way pathogenic bacteria can overcome this challenge. After capturing their target, haem appropriation systems must remove haem from a high-affinity binding site (on the host haemoprotein or bacterial haemophore) and transfer it to a binding site of lower affinity on a bacterial receptor. Structural information is now available to show how, using a combination of induced structural changes and steric clashes, bacteria are able to extract haem from haemophores, haemopexin and haemoglobin. This review focuses on structural descriptions of these bacterial haem acquisition systems, summarising how they bind haem and their target haemoproteins with particularly emphasis on the mechanism of haem extraction.
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23
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Sakipov S, Rafikova O, Kurnikova MG, Rafikov R. Molecular mechanisms of bio-catalysis of heme extraction from hemoglobin. Redox Biol 2017; 11:516-523. [PMID: 28088643 PMCID: PMC5237811 DOI: 10.1016/j.redox.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 11/19/2022] Open
Abstract
Red blood cell hemolysis in sickle cell disease (SCD) releases free hemoglobin. Extracellular hemoglobin and its degradation products, free heme and iron, are highly toxic due to oxidative stress induction and decrease in nitric oxide availability. We propose an approach that helps to eliminate extracellular hemoglobin toxicity in SCD by employing a bacterial protein system that evolved to extract heme from extracellular hemoglobin. NEAr heme Transporter (NEAT) domains from iron-regulated surface determinant proteins from Staphylococcus aureus specifically bind free heme as well as facilitate its extraction from hemoglobin. We demonstrate that a purified NEAT domain fused with human haptoglobin β-chain is able to remove heme from hemoglobin and reduce heme content and peroxidase activity of hemoglobin. We further use molecular dynamics (MD) simulations to resolve molecular pathway of heme transfer from hemoglobin to NEAT, and to elucidate molecular mechanism of such heme transferring process. Our study is the first of its kind, in which simulations are employed to characterize the process of heme leaving hemoglobin and subsequent rebinding with a NEAT domain. Our MD results highlight important amino acid residues that facilitate heme transfer and will guide further studies for the selection of best NEAT candidate to attenuate free hemoglobin toxicity.
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Affiliation(s)
- Serzhan Sakipov
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Olga Rafikova
- Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Maria G Kurnikova
- Chemistry Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Ruslan Rafikov
- Department of Medicine, University of Arizona, Tucson, AZ, USA.
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24
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Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire. Nat Commun 2016; 7:13376. [PMID: 27857134 PMCID: PMC5120205 DOI: 10.1038/ncomms13376] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 09/28/2016] [Indexed: 11/08/2022] Open
Abstract
Staphylococcus aureus is both an important pathogen and a human commensal. To explore this ambivalent relationship between host and microbe, we analysed the memory humoral response against IsdB, a protein involved in iron acquisition, in four healthy donors. Here we show that in all donors a heavily biased use of two immunoglobulin heavy chain germlines generated high affinity (pM) antibodies that neutralize the two IsdB NEAT domains, IGHV4-39 for NEAT1 and IGHV1-69 for NEAT2. In contrast to the typical antibody/antigen interactions, the binding is primarily driven by the germline-encoded hydrophobic CDRH-2 motifs of IGHV1-69 and IGHV4-39, with a binding mechanism nearly identical for each antibody derived from different donors. Our results suggest that IGHV1-69 and IGHV4-39, while part of the adaptive immune system, may have evolved under selection pressure to encode a binding motif innately capable of recognizing and neutralizing a structurally conserved protein domain involved in pathogen iron acquisition.
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25
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Sæderup KL, Stødkilde K, Graversen JH, Dickson CF, Etzerodt A, Hansen SWK, Fago A, Gell D, Andersen CBF, Moestrup SK. The Staphylococcus aureus Protein IsdH Inhibits Host Hemoglobin Scavenging to Promote Heme Acquisition by the Pathogen. J Biol Chem 2016; 291:23989-23998. [PMID: 27681593 DOI: 10.1074/jbc.m116.755934] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/25/2016] [Indexed: 12/30/2022] Open
Abstract
Hemolysis is a complication in septic infections with Staphylococcus aureus, which utilizes the released Hb as an iron source. S. aureus can acquire heme in vitro from hemoglobin (Hb) by a heme-sequestering mechanism that involves proteins from the S. aureus iron-regulated surface determinant (Isd) system. However, the host has its own mechanism to recapture the free Hb via haptoglobin (Hp) binding and uptake of Hb-Hp by the CD163 receptor in macrophages. It has so far remained unclear how the Isd system competes with this host iron recycling system in situ to obtain the important nutrient. By binding and uptake studies, we now show that the IsdH protein, which serves as an Hb receptor in the Isd system, directly interferes with the CD163-mediated clearance by binding the Hb-Hp complex and inhibiting CD163 recognition. Analysis of truncated IsdH variants including one or more of three near iron transporter domains, IsdHN1, IsdHN2, and IsdHN3, revealed that Hb binding of IsdHN1 and IsdHN2 accounted for the high affinity for Hb-Hp complexes. The third near iron transporter domain, IsdHN3, exhibited redox-dependent heme extraction, when Hb in the Hb-Hp complex was in the oxidized met form but not in the reduced oxy form. IsdB, the other S. aureus Hb receptor, failed to extract heme from Hb-Hp, and it was a poor competitor for Hb-Hp binding to CD163. This indicates that Hb recognition by IsdH, but not by IsdB, sterically inhibits the receptor recognition of Hb-Hp. This function of IsdH may have an overall stimulatory effect on S. aureus heme acquisition and growth.
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Affiliation(s)
| | | | | | - Claire F Dickson
- the School of Medicine, University of Tasmania, Hobart, Tasmania 7005, Australia, and
| | | | | | - Angela Fago
- Zoophysiology Section, Department of Bioscience, Aarhus University, DK-8000 Aarhus, Denmark
| | - David Gell
- the School of Medicine, University of Tasmania, Hobart, Tasmania 7005, Australia, and
| | | | - Søren Kragh Moestrup
- From the Department of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark, .,the Department of Biomedicine and.,the Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense, Denmark
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Structural basis for haem piracy from host haemopexin by Haemophilus influenzae. Nat Commun 2016; 7:11590. [PMID: 27188378 PMCID: PMC4873976 DOI: 10.1038/ncomms11590] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 04/11/2016] [Indexed: 02/07/2023] Open
Abstract
Haemophilus influenzae is an obligate human commensal/pathogen that requires haem for survival and can acquire it from several host haemoproteins, including haemopexin. The haem transport system from haem-haemopexin consists of HxuC, a haem receptor, and the two-partner-secretion system HxuB/HxuA. HxuA, which is exposed at the cell surface, is strictly required for haem acquisition from haemopexin. HxuA forms complexes with haem-haemopexin, leading to haem release and its capture by HxuC. The key question is how HxuA liberates haem from haemopexin. Here, we solve crystal structures of HxuA alone, and HxuA in complex with the N-terminal domain of haemopexin. A rational basis for the release of haem from haem-haemopexin is derived from both in vivo and in vitro studies. HxuA acts as a wedge that destabilizes the two-domains structure of haemopexin with a mobile loop on HxuA that favours haem ejection by redirecting key residues in the haem-binding pocket of haemopexin. Haemophilus influenzae requires haem, and acquires it from host haemoproteins including haemopexin. Here, the authors examine the haem transport system consisting of HxuA, HxuB and HxuC via the structures of HxuA in complex with haemopexin.
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Rapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD Simulations. PLoS One 2015; 10:e0145125. [PMID: 26658942 PMCID: PMC4684392 DOI: 10.1371/journal.pone.0145125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 11/29/2015] [Indexed: 11/19/2022] Open
Abstract
In vertebrates, most iron is present as heme or is chelated by proteins. Thus, Gram-positive pathogens such as Staphylococcus aureus have evolved an iron-regulated surface determinant (Isd) system that transports heme across thick cell walls into the cytoplasm. Recent studies have demonstrated that heme is rapidly transferred between the NEAr Transporter (NEAT) domains of the Isd system, despite its high affinity toward each domain, suggesting the presence of an intermediate NEAT•heme•NEAT complex. In the present study, we performed short restrained molecular dynamics (MD) simulations to dock the acceptor NEAT domain to the donor NEAT•heme complex and obtained models where the two NEAT domains were arranged with two-fold pseudo symmetry around the heme molecule. After turning off the restraints, complex structures were stably maintained during subsequent unrestrained MD simulations, except for the hydrogen bond between the propionate group of the heme molecule and the donor NEAT domain, potentially facilitating the transition of heme from the donor to the acceptor. Subsequent structural optimization using the quantum mechanics/molecular mechanics (QM/MM) method showed that two tyrosine residues, one from each NEAT domain, were simultaneously coordinated to the ferric heme iron in the intermediate complex only if they were deprotonated. Based on these results, we propose a reaction scheme for heme transfer between NEAT domains.
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28
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Dickson CF, Jacques DA, Clubb RT, Guss JM, Gell DA. The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native α-globin haem pocket. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1295-306. [PMID: 26057669 PMCID: PMC8518021 DOI: 10.1107/s1399004715005817] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/23/2015] [Indexed: 12/13/2022]
Abstract
Staphylococcus aureus is a common and serious cause of infection in humans. The bacterium expresses a cell-surface receptor that binds to, and strips haem from, human haemoglobin (Hb). The binding interface has previously been identified; however, the structural changes that promote haem release from haemoglobin were unknown. Here, the structure of the receptor-Hb complex is reported at 2.6 Å resolution, which reveals a conformational change in the α-globin F helix that disrupts the haem-pocket structure and alters the Hb quaternary interactions. These features suggest potential mechanisms by which the S. aureus Hb receptor induces haem release from Hb.
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29
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Hannauer M, Arifin AJ, Heinrichs DE. Involvement of reductases IruO and NtrA in iron acquisition byStaphylococcus aureus. Mol Microbiol 2015; 96:1192-210. [DOI: 10.1111/mmi.13000] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Mélissa Hannauer
- Department of Microbiology and Immunology; University of Western Ontario; London ON Canada N6A 5C1
| | - Andrew J. Arifin
- Department of Microbiology and Immunology; University of Western Ontario; London ON Canada N6A 5C1
| | - David E. Heinrichs
- Department of Microbiology and Immunology; University of Western Ontario; London ON Canada N6A 5C1
- Centre for Human Immunology; University of Western Ontario; London ON Canada N6A 5C1
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30
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Sheldon JR, Heinrichs DE. Recent developments in understanding the iron acquisition strategies of gram positive pathogens. FEMS Microbiol Rev 2015; 39:592-630. [DOI: 10.1093/femsre/fuv009] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 12/26/2022] Open
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31
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Sjodt M, Macdonald R, Spirig T, Chan AH, Dickson CF, Fabian M, Olson JS, Gell DA, Clubb RT. The PRE-Derived NMR Model of the 38.8-kDa Tri-Domain IsdH Protein from Staphylococcus aureus Suggests That It Adaptively Recognizes Human Hemoglobin. J Mol Biol 2015; 428:1107-1129. [PMID: 25687963 DOI: 10.1016/j.jmb.2015.02.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 01/31/2015] [Accepted: 02/07/2015] [Indexed: 01/11/2023]
Abstract
Staphylococcus aureus is a medically important bacterial pathogen that, during infections, acquires iron from human hemoglobin (Hb). It uses two closely related iron-regulated surface determinant (Isd) proteins to capture and extract the oxidized form of heme (hemin) from Hb, IsdH and IsdB. Both receptors rapidly extract hemin using a conserved tri-domain unit consisting of two NEAT (near iron transporter) domains connected by a helical linker domain. To gain insight into the mechanism of extraction, we used NMR to investigate the structure and dynamics of the 38.8-kDa tri-domain IsdH protein (IsdH(N2N3), A326-D660 with a Y642A mutation that prevents hemin binding). The structure was modeled using long-range paramagnetic relaxation enhancement (PRE) distance restraints, dihedral angle, small-angle X-ray scattering, residual dipolar coupling and inter-domain NOE nuclear Overhauser effect data. The receptor adopts an extended conformation wherein the linker and N3 domains pack against each other via a hydrophobic interface. In contrast, the N2 domain contacts the linker domain via a hydrophilic interface and, based on NMR relaxation data, undergoes inter-domain motions enabling it to reorient with respect to the body of the protein. Ensemble calculations were used to estimate the range of N2 domain positions compatible with the PRE data. A comparison of the Hb-free and Hb-bound forms reveals that Hb binding alters the positioning of the N2 domain. We propose that binding occurs through a combination of conformational selection and induced-fit mechanisms that may promote hemin release from Hb by altering the position of its F helix.
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Affiliation(s)
- Megan Sjodt
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Ramsay Macdonald
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Thomas Spirig
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Albert H Chan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Claire F Dickson
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Marian Fabian
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, USA
| | - John S Olson
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, USA
| | - David A Gell
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095, USA.
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32
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Ascenzi P, di Masi A, Leboffe L, Frangipani E, Nardini M, Verde C, Visca P. Structural Biology of Bacterial Haemophores. Adv Microb Physiol 2015; 67:127-76. [PMID: 26616517 DOI: 10.1016/bs.ampbs.2015.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Iron plays a key role in a wide range of metabolic and signalling functions representing an essential nutrient for almost all forms of life. However, the ferric form is hardly soluble, whereas the ferrous form is highly toxic. Thus, in biological fluids, most of the iron is sequestered in iron- or haem-binding proteins and the level of free iron is low, making haem and iron acquisition a challenge for pathogenic bacteria during infections. Although toxic to the host, free haem is a major and readily available source of iron for several pathogenic microorganisms. Both Gram-positive and Gram-negative bacteria have developed several strategies to acquire free haem-Fe and protein-bound haem-Fe. Haemophores are a class of secreted and cell surface-exposed proteins promoting free-haem uptake, haem extraction from host haem proteins, and haem presentation to specific outer-membrane receptors that internalize the metal-porphyrins. Here, structural biology of bacterial haemophores is reviewed focusing on haem acquisition, haem internalization, and haem-degrading systems.
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Affiliation(s)
- Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Roma, Italy; Istituto di Bioscienze e BioRisorse, Consiglio Nazionale delle Ricerche, Napoli, Italy.
| | | | - Loris Leboffe
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy
| | | | - Marco Nardini
- Dipartimento di Bioscienze, Università di Milano, Milano, Italy
| | - Cinzia Verde
- Istituto di Bioscienze e BioRisorse, Consiglio Nazionale delle Ricerche, Napoli, Italy; Dipartimento di Scienze, Università Roma Tre, Roma, Italy
| | - Paolo Visca
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy
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33
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Malmirchegini GR, Sjodt M, Shnitkind S, Sawaya MR, Rosinski J, Newton SM, Klebba PE, Clubb RT. Novel mechanism of hemin capture by Hbp2, the hemoglobin-binding hemophore from Listeria monocytogenes. J Biol Chem 2014; 289:34886-99. [PMID: 25315777 DOI: 10.1074/jbc.m114.583013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Iron is an essential nutrient that is required for the growth of the bacterial pathogen Listeria monocytogenes. In cell cultures, this microbe secretes hemin/hemoglobin-binding protein 2 (Hbp2; Lmo2185) protein, which has been proposed to function as a hemophore that scavenges heme from the environment. Based on its primary sequence, Hbp2 contains three NEAr transporter (NEAT) domains of unknown function. Here we show that each of these domains mediates high affinity binding to ferric heme (hemin) and that its N- and C-terminal domains interact with hemoglobin (Hb). The results of hemin transfer experiments are consistent with Hbp2 functioning as an Hb-binding hemophore that delivers hemin to other Hbp2 proteins that are attached to the cell wall. Surprisingly, our work reveals that the central NEAT domain in Hbp2 binds hemin even though its primary sequence lacks a highly conserved YXXXY motif that is used by all other previously characterized NEAT domains to coordinate iron in the hemin molecule. To elucidate the mechanism of hemin binding by Hbp2, we determined crystal structures of its central NEAT domain (Hbp2(N2); residues 183-303) in its free and hemin-bound states. The structures reveal an unprecedented mechanism of hemin binding in which Hbp2(N2) undergoes a major conformational rearrangement that facilitates metal coordination by a non-canonical tyrosine residue. These studies highlight previously unrecognized plasticity in the hemin binding mechanism of NEAT domains and provide insight into how L. monocytogenes captures heme iron.
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Affiliation(s)
- G Reza Malmirchegini
- From the Department of Chemistry and Biochemistry and the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - Megan Sjodt
- From the Department of Chemistry and Biochemistry and the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - Sergey Shnitkind
- From the Department of Chemistry and Biochemistry and the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - Michael R Sawaya
- From the Department of Chemistry and Biochemistry and the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and Howard Hughes Medical Institute and
| | - Justin Rosinski
- From the Department of Chemistry and Biochemistry and the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
| | - Salete M Newton
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66502
| | - Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66502
| | - Robert T Clubb
- From the Department of Chemistry and Biochemistry and the UCLA-Department of Energy Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095 and
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34
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Non-heme-binding domains and segments of the Staphylococcus aureus IsdB protein critically contribute to the kinetics and equilibrium of heme acquisition from methemoglobin. PLoS One 2014; 9:e100744. [PMID: 24959723 PMCID: PMC4069089 DOI: 10.1371/journal.pone.0100744] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/28/2014] [Indexed: 11/19/2022] Open
Abstract
The hemoglobin receptor IsdB rapidly acquires heme from methemoglobin (metHb) in the heme acquisition pathway of Staphylococcus aureus. IsdB consists of N-terminal segment (NS), NEAT1 (N1), middle (MD), and heme binding NEAT2 (N2) domains, and C-terminal segment (CS). This study aims to elucidate the roles of these domains or segments in the metHb/IsdB reaction. Deletion of CS does not alter the kinetics and equilibrium of the reaction. Sequential deletions of NS and N1 in NS-N1-MD-N2 progressively reduce heme transfer rates and change the kinetic pattern from one to two phases, but have no effect on the equilibrium of the heme transfer reaction, whereas further deletion of MD reduces the percentage of transferred metHb heme. MD-N2 has higher affinity for heme than N2. MD in trans reduces rates of heme dissociation from holo-N2 and increases the percentage of metHb heme captured by N2 by 4.5 fold. NS-N1-MD and N2, but not NS-N1, MD, and N2, reconstitute the rapid metHb/IsdB reaction. NS-N1-MD-NIsdC, a fusion protein of NS-N1-MD and the NEAT domain of IsdC, slowly acquires heme from metHb by itself but together with N2 results in rapid heme loss from metHb. Thus, NS-N1 and MD domains specifically and critically contribute to the kinetics and equilibrium of the metHb/IsdB reaction, respectively. These findings support a mechanism of direct heme acquisition by IsdB in which MD enhances the affinity of N2 for heme to thermodynamically drive heme transfer from metHb to IsdB and in which NS is required for the rapid and single phase kinetics of the metHb/IsdB reaction.
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35
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Fonner BA, Tripet BP, Eilers BJ, Stanisich J, Sullivan-Springhetti RK, Moore R, Liu M, Lei B, Copié V. Solution structure and molecular determinants of hemoglobin binding of the first NEAT domain of IsdB in Staphylococcus aureus. Biochemistry 2014; 53:3922-33. [PMID: 24871270 PMCID: PMC4072347 DOI: 10.1021/bi5005188] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
The
human pathogen Staphylococcus aureus acquires heme iron from hemoglobin (Hb) via the action of a series
of iron-regulated surface determinant (Isd) proteins. The cell wall
anchored IsdB protein is recognized as the predominant Hb receptor,
and is comprised of two NEAr transporter (NEAT) domains that act in
concert to bind, extract, and transfer heme from Hb to downstream
Isd proteins. Structural details of the NEAT 2 domain of IsdB have
been investigated, but the molecular coordination between NEAT 2 and
NEAT 1 to extract heme from hemoglobin has yet to be characterized.
To obtain a more complete understanding of IsdB structure and function,
we have solved the 3D solution structure of the NEAT 1 domain of IsdB
(IsdBN1) spanning residues 125–272 of the full-length
protein by NMR. The structure reveals a canonical NEAT domain fold
and has particular structural similarity to the NEAT 1 and NEAT 2
domains of IsdH, which also interact with Hb. IsdBN1 is
also comprised of a short N-terminal helix, which has not been previously
observed in other NEAT domain structures. Interestingly, the Hb binding
region (loop 2 of IsdBN1) is disordered in solution. Analysis
of Hb binding demonstrates that IsdBN1 can bind metHb weakly
and the affinity of this interaction is further increased by the presence
of IsdB linker domain. IsdBN1 loop 2 variants reveal that
phenylalanine 164 (F164) of IsdB is necessary for Hb binding and rapid
heme transfer from metHb to IsdB. Together, these findings provide
a structural role for IsdBN1 in enhancing the rate of extraction
of metHb heme by the IsdB NEAT 2 domain.
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Affiliation(s)
- Brittany A Fonner
- Department of Chemistry and Biochemistry, Montana State University , 103 Chemistry and Biochemistry Building, PO Box 173400, Bozeman, Montana 59717-3400, United States
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36
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Bowden CFM, Verstraete MM, Eltis LD, Murphy MEP. Hemoglobin binding and catalytic heme extraction by IsdB near iron transporter domains. Biochemistry 2014; 53:2286-94. [PMID: 24645787 DOI: 10.1021/bi500230f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Isd (iron-regulated surface determinant) system is a multiprotein transporter that allows bacterium Staphylococcus aureus to take up iron from hemoglobin (Hb) during human infection. In this system, IsdB is a cell wall-anchored surface protein that contains two near iron transporter (NEAT) domains, one of which binds heme. IsdB rapidly extracts heme from Hb and transfers it to IsdA for relay into the bacterial cell. Using a series of recombinant IsdB constructs that included at least one NEAT domain, we demonstrated that both domains are required to bind Hb with high affinity (KD = 0.42 ± 0.05 μM) and to extract heme from Hb. Moreover, IsdB extracted heme only from oxidized metHb, although it also bound oxyHb and the Hb-CO complex. In a reconstituted model of the biological heme relay pathway, IsdB catalyzed the transfer of heme from metHb to IsdA with a Km for metHb of 0.75 ± 0.07 μN and a kcat of 0.22 ± 0.01 s(-1). The latter is consistent with the transfer of heme from metHb to IsdB being the rate-limiting step. With both NEAT domains and the linker region present in a single contiguous polypeptide, high-affinity Hb binding was achieved, rapid heme uptake was observed, and multiple turnovers of heme extraction from metHb and transfer to IsdA were conducted, representing all known Hb-heme uptake functions of the full-length IsdB protein.
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Affiliation(s)
- Catherine F M Bowden
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia , Vancouver, BC, Canada V6T 1Z3
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