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Gómez-Garzón C, Payne SM. Divide and conquer: genetics, mechanism, and evolution of the ferrous iron transporter Feo in Helicobacter pylori. Front Microbiol 2023; 14:1219359. [PMID: 37469426 PMCID: PMC10353542 DOI: 10.3389/fmicb.2023.1219359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/14/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction Feo is the most widespread and conserved system for ferrous iron uptake in bacteria, and it is important for virulence in several gastrointestinal pathogens. However, its mechanism remains poorly understood. Hitherto, most studies regarding the Feo system were focused on Gammaproteobacterial models, which possess three feo genes (feoA, B, and C) clustered in an operon. We found that the human pathogen Helicobacter pylori possesses a unique arrangement of the feo genes, in which only feoA and feoB are present and encoded in distant loci. In this study, we examined the functional significance of this arrangement. Methods Requirement and regulation of the individual H. pylori feo genes were assessed through in vivo assays and gene expression profiling. The evolutionary history of feo was inferred via phylogenetic reconstruction, and AlphaFold was used for predicting the FeoA-FeoB interaction. Results and Discussion Both feoA and feoB are required for Feo function, and feoB is likely subjected to tight regulation in response to iron and nickel by Fur and NikR, respectively. Also, we established that feoA is encoded in an operon that emerged in the common ancestor of most, but not all, helicobacters, and this resulted in feoA transcription being controlled by two independent promoters. The H. pylori Feo system offers a new model to understand ferrous iron transport in bacterial pathogens.
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Affiliation(s)
- Camilo Gómez-Garzón
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Shelley M. Payne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
- John Ring LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, TX, United States
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Feng M, Namanja-Magliano H, Rajagopalan S, Mishra T, Ducati RG, Hirsch BM, Kelly L, Szymczak W, Fajardo JE, Sidoli S, Fiser A, Jacobs WR, Schramm VL. MAT Gain of Activity Mutation in Helicobacter pylori Is Associated with Resistance to MTAN Transition State Analogues. ACS Infect Dis 2023; 9:966-978. [PMID: 36920074 DOI: 10.1021/acsinfecdis.2c00644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Helicobacter pylori is found in the gut lining of more than half of the world's population, causes gastric ulcers, and contributes to stomach cancers. Menaquinone synthesis in H. pylori relies on the rare futalosine pathway, where H. pylori 5'-methylthioadenosine nucleosidase (MTAN) is proposed to play an essential role. Transition state analogues of MTAN, including BuT-DADMe-ImmA (BTDIA) and MeT-DADMe-ImmA (MTDIA), exhibit bacteriostatic action against numerous diverse clinical isolates of H. pylori with minimum inhibitory concentrations (MIC's) of <2 ng/mL. Three H. pylori BTDIA-resistant clones were selected under increasing BTDIA pressure. Whole genome sequencing showed no mutations in MTAN. Instead, resistant clones had mutations in metK, methionine adenosyltransferase (MAT), feoA, a regulator of the iron transport system, and flhF, a flagellar synthesis regulator. The mutation in metK causes expression of a MAT with increased catalytic activity, leading to elevated cellular S-adenosylmethionine. Metabolite analysis and the mutations associated with resistance suggest multiple inputs associated with BTDIA resistance. Human gut microbiome exposed to MTDIA revealed no growth inhibition under aerobic or anaerobic conditions. Transition state analogues of H. pylori MTAN have potential as agents for treating H. pylori infection without disruption of the human gut microbiome or inducing resistance in the MTAN target.
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Affiliation(s)
- Mu Feng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Hilda Namanja-Magliano
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Saranathan Rajagopalan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Tanmay Mishra
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Rodrigo G Ducati
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Brett M Hirsch
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Libusha Kelly
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States.,Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Wendy Szymczak
- Department of Pathology, Montefiore-Einstein Medical Center, Bronx, New York 10467, United States
| | - Jorge Eduardo Fajardo
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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Byer AS, Pei X, Patterson MG, Ando N. Small-angle X-ray scattering studies of enzymes. Curr Opin Chem Biol 2023; 72:102232. [PMID: 36462455 PMCID: PMC9992928 DOI: 10.1016/j.cbpa.2022.102232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/14/2022] [Accepted: 10/22/2022] [Indexed: 12/02/2022]
Abstract
Enzyme function requires conformational changes to achieve substrate binding, domain rearrangements, and interactions with partner proteins, but these movements are difficult to observe. Small-angle X-ray scattering (SAXS) is a versatile structural technique that can probe such conformational changes under solution conditions that are physiologically relevant. Although it is generally considered a low-resolution structural technique, when used to study conformational changes as a function of time, ligand binding, or protein interactions, SAXS can provide rich insight into enzyme behavior, including subtle domain movements. In this perspective, we highlight recent uses of SAXS to probe structural enzyme changes upon ligand and partner-protein binding and discuss tools for signal deconvolution of complex protein solutions.
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Affiliation(s)
- Amanda S Byer
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Xiaokun Pei
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael G Patterson
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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Chun H, Kurasawa JH, Olivares P, Marakasova ES, Shestopal SA, Hassink GU, Karnaukhova E, Migliorini M, Obi JO, Smith AK, Wintrode PL, Durai P, Park K, Deredge D, Strickland DK, Sarafanov AG. Characterization of interaction between blood coagulation factor VIII and LRP1 suggests dynamic binding by alternating complex contacts. J Thromb Haemost 2022; 20:2255-2269. [PMID: 35810466 PMCID: PMC9804390 DOI: 10.1111/jth.15817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/15/2022] [Accepted: 07/01/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Deficiency in blood coagulation factor VIII (FVIII) results in life-threating bleeding (hemophilia A) treated by infusions of FVIII concentrates. To improve disease treatment, FVIII has been modified to increase its plasma half-life, which requires understanding mechanisms of FVIII catabolism. An important catabolic actor is hepatic low density lipoprotein receptor-related protein 1 (LRP1), which also regulates many other clinically significant processes. Previous studies showed complexity of FVIII site for binding LRP1. OBJECTIVES To characterize binding sites between FVIII and LRP1 and suggest a model of the interaction. METHODS A series of recombinant ligand-binding complement-type repeat (CR) fragments of LRP1 including mutated variants was generated in a baculovirus system and tested for FVIII interaction using surface plasmon resonance, tissue culture model, hydrogen-deuterium exchange mass spectrometry, and in silico. RESULTS Multiple CR doublets within LRP1 clusters II and IV were identified as alternative FVIII-binding sites. These interactions follow the canonical binding mode providing major binding energy, and additional weak interactions are contributed by adjacent CR domains. A representative CR doublet was shown to have multiple contact sites on FVIII. CONCLUSIONS FVIII and LRP1 interact via formation of multiple complex contacts involving both canonical and non-canonical binding combinations. We propose that FVIII-LRP1 interaction occurs via switching such alternative binding combinations in a dynamic mode, and that this mechanism is relevant to other ligand interactions of the low-density lipoprotein receptor family members including LRP1.
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Affiliation(s)
- Haarin Chun
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
| | - James H. Kurasawa
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
- Present address:
Biologics Engineering, R&D, AstraZeneca, GaithersburgMarylandUSA
| | - Philip Olivares
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
| | - Ekaterina S. Marakasova
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
- Present address:
(1) Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver SpringMarylandUSA
- Present address:
George Mason University, School of Systems Biology, FairfaxVirginiaUSA
| | - Svetlana A. Shestopal
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
| | - Gabriela U. Hassink
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
- Present address:
GSK‐Rockville Center for Vaccines Research, RockvilleMarylandUSA
| | - Elena Karnaukhova
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
| | - Mary Migliorini
- Center for Vascular and Inflammatory DiseasesDepartments of Surgery and PhysiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Juliet O. Obi
- Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreMarylandUSA
| | - Ally K. Smith
- Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreMarylandUSA
| | - Patrick L. Wintrode
- Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreMarylandUSA
| | - Prasannavenkatesh Durai
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungRepublic of Korea
| | - Keunwan Park
- Natural Product Informatics Research CenterKorea Institute of Science and TechnologyGangneungRepublic of Korea
| | - Daniel Deredge
- Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreMarylandUSA
| | - Dudley K. Strickland
- Center for Vascular and Inflammatory DiseasesDepartments of Surgery and PhysiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Andrey G. Sarafanov
- Center for Biologics Evaluation and ResearchU.S. Food and Drug AdministrationSilver SpringMarylandUSA
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Sestok AE, O'Sullivan SM, Smith AT. A general protocol for the expression and purification of the intact transmembrane transporter FeoB. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183973. [PMID: 35636558 PMCID: PMC9203943 DOI: 10.1016/j.bbamem.2022.183973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 04/27/2023]
Abstract
Ferrous iron (Fe2+) transport is an essential process that supports the growth, intracellular survival, and virulence of several drug-resistant pathogens, and the ferrous iron transport (Feo) system is the most important and widespread protein complex that mediates Fe2+ transport in these organisms. The Feo system canonically comprises three proteins (FeoA/B/C). FeoA and FeoC are both small, accessory proteins localized to the cytoplasm, and their roles in the Fe2+ transport process have been of great debate. FeoB is the only wholly-conserved component of the Feo system and serves as the inner membrane-embedded Fe2+ transporter with a soluble G-protein-like N-terminal domain. In vivo studies have underscored the importance of Feo during infection, emphasizing the need to better understand Feo-mediated Fe2+ uptake, although a paucity of research exists on intact FeoB. To surmount this problem, we designed an overproduction and purification system that can be applied generally to a suite of intact FeoBs from several organisms. Importantly, we noted that FeoB is extremely sensitive to excess salt while in the membrane of a recombinant host, and we designed a workflow to circumvent this issue. We also demonstrated effective protein extraction from the lipid bilayer through small-scale solubilization studies. We then applied this approach to the large-scale purifications of Escherichia coli and Pseudomonas aeruginosa FeoBs to high purity and homogeneity. Lastly, we show that our protocol can be generally applied to various FeoB proteins. Thus, this workflow allows for isolation of suitable quantities of FeoB for future biochemical and biophysical characterization.
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Affiliation(s)
- Alex E Sestok
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Sean M O'Sullivan
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA.
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Brown JB, Lee MA, Smith AT. The structure of Vibrio cholerae FeoC reveals conservation of the helix-turn-helix motif but not the cluster-binding domain. J Biol Inorg Chem 2022; 27:485-495. [PMID: 35796835 PMCID: PMC9398973 DOI: 10.1007/s00775-022-01945-4] [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: 02/28/2022] [Accepted: 06/04/2022] [Indexed: 11/26/2022]
Abstract
Most pathogenic bacteria require ferrous iron (Fe2+) in order to sustain infection within hosts. The ferrous iron transport (Feo) system is the most highly conserved prokaryotic transporter of Fe2+, but its mechanism remains to be fully characterized. Most Feo systems are composed of two proteins: FeoA, a soluble SH3-like accessory protein, and FeoB, a membrane protein that translocates Fe2+ across a lipid bilayer. Some bacterial feo operons encode FeoC, a third soluble, winged-helix protein that remains enigmatic in function. We previously demonstrated that selected FeoC proteins bind O2-sensitive [4Fe-4S] clusters via Cys residues, leading to the proposal that some FeoCs could sense O2 to regulate Fe2+ transport. However, not all FeoCs conserve these Cys residues, and FeoC from the causative agent of cholera (Vibrio cholerae) notably lacks any Cys residues, precluding cluster binding. In this work, we determined the NMR structure of VcFeoC, which is monomeric and conserves the helix-turn-helix domain seen in other FeoCs. In contrast, however, the structure of VcFeoC reveals a truncated winged β-sheet in which the cluster-binding domain is notably absent. Using homology modeling, we predicted the structure of VcNFeoB and used docking to identify an interaction site with VcFeoC, which is confirmed by NMR spectroscopy. These findings provide the first atomic-level structure of VcFeoC and contribute to a better understanding of its role vis-à-vis FeoB.
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Affiliation(s)
- Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Mark A Lee
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA.
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