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Yazzie MT, Reitz ZL, Schmid R, Petras D, Aron AT. Native metabolomics for mass spectrometry-based siderophore discovery. Methods Enzymol 2024; 702:317-352. [PMID: 39155117 DOI: 10.1016/bs.mie.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Microorganisms, plants, and animals alike have specialized acquisition pathways for obtaining metals, with microorganisms and plants biosynthesizing and secreting small molecule natural products called siderophores and metallophores with high affinities and specificities for iron or other non-iron metals, respectively. This chapter details a novel approach to discovering metal-binding molecules, including siderophores and metallophores, from complex samples ranging from microbial supernatants to biological tissue to environmental samples. This approach, called Native Metabolomics, is a mass spectrometry method in which pH adjustment and metal infusion post-liquid chromatography are interfaced with ion identity molecular networking (IIMN). This rule-based data analysis workflow that enables the identification of metal-binding species based on defined mass (m/z) offsets with the same chromatographic profiles and retention times. Ion identity molecular networking connects compounds that are structurally similar by their fragmentation pattern and species that are ion adducts of the same compound by chromatographic shape correlations. This approach has previously revealed new insights into metal binding metabolites, including that yersiniabactin can act as a biological zincophore (in addition to its known role as a siderophore), that the recently elucidated lepotchelin natural products are cyanobacterial metallophores, and that antioxidants in traditional medicine bind iron. Native metabolomics can be conducted on any liquid chromatography-mass spectrometry system to explore the binding of any metal or multiple metals simultaneously, underscoring the potential for this method to become an essential strategy for elucidating biological metal-binding molecules.
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Affiliation(s)
- Marquis T Yazzie
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, United States
| | - Zachary L Reitz
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, United States
| | - Robin Schmid
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Daniel Petras
- Department of Biochemistry, University of California Riverside, Riverside, CA, United States; Interfaculty of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, United States.
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Gomes AFR, Almeida MC, Sousa E, Resende DISP. Siderophores and metallophores: Metal complexation weapons to fight environmental pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:173044. [PMID: 38723971 DOI: 10.1016/j.scitotenv.2024.173044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/14/2024]
Abstract
Siderophores are small molecules of organic nature, released by bacteria to chelate iron from the surrounding environment and subsequently incorporate it into the cytoplasm. In addition to iron, these secondary metabolites can complex with a wide variety of metals, which is why they are commonly studied in the environment. Heavy metals can be very toxic when present in large amounts on the planet, affecting public health and all living organisms. The pollution caused by these toxic metals is increasing, and therefore it is urgent to find practical, sustainable, and economical solutions for remediation. One of the strategies is siderophore-assisted bioremediation, an innovative and advantageous alternative for various environmental applications. This research highlights the various uses of siderophores and metallophores in the environment, underscoring their significance to ecosystems. The study delves into the utilization of siderophores and metallophores in both marine and terrestrial settings (e.g. bioremediation, biocontrol of pathogens, and plant growth promotion), such as bioremediation, biocontrol of pathogens, and plant growth promotion, providing context for the different instances outlined in the existing literature and highlighting their relevance in each field. The study delves into the structures and types of siderophores focusing on their singular characteristics for each application and methodologies used. Focusing on recent developments over the last two decades, the opportunities and challenges associated with siderophores and metallophores applications in the environment were mapped to arm researchers in the fight against environmental pollution.
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Affiliation(s)
- Ana F R Gomes
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
| | - Mariana C Almeida
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Emília Sousa
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
| | - Diana I S P Resende
- LQOF - Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, FFUP - Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.
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Gomes AF, Sousa E, Resende DISP. A Practical Toolkit for the Detection, Isolation, Quantification, and Characterization of Siderophores and Metallophores in Microorganisms. ACS OMEGA 2024; 9:26863-26877. [PMID: 38947835 PMCID: PMC11209696 DOI: 10.1021/acsomega.4c03042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 07/02/2024]
Abstract
Siderophores are well-recognized low-molecular-weight compounds produced by numerous microorganisms to acquire iron from the surrounding environments. These secondary metabolites can form complexes with other metals besides iron, forming soluble metallophores; because of that, they are widely investigated in either the medicinal or environmental field. One of the bottlenecks of siderophore research is related to the identification of new siderophores from microbial sources. Herein we have compiled a comprehensive range of standard and updated methodologies that have been developed over the past few years to provide a comprehensive toolbox in this area to current researchers.
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Affiliation(s)
- Ana F.
R. Gomes
- LQOF
- Laboratório de Química Orgânica e Farmacêutica,
Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
- CIIMAR-
Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
| | - Emília Sousa
- LQOF
- Laboratório de Química Orgânica e Farmacêutica,
Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
- CIIMAR-
Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
| | - Diana I. S. P. Resende
- LQOF
- Laboratório de Química Orgânica e Farmacêutica,
Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
- CIIMAR-
Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal
- ICBAS
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
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Zou Z, Robinson JI, Steinberg LK, Henderson JP. Uropathogenic Escherichia coli wield enterobactin-derived catabolites as siderophores. J Biol Chem 2024; 300:105554. [PMID: 38072063 PMCID: PMC10788543 DOI: 10.1016/j.jbc.2023.105554] [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: 07/28/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) secrete multiple siderophore types to scavenge extracellular iron(III) ions during clinical urinary tract infections, despite the metabolic costs of biosynthesis. Here, we find the siderophore enterobactin (Ent) and its related products to be prominent components of the iron-responsive extracellular metabolome of a model UPEC strain. Using defined Ent biosynthesis and import mutants, we identify lower molecular weight dimeric exometabolites as products of incomplete siderophore catabolism, rather than prematurely released biosynthetic intermediates. In E. coli, iron acquisition from iron(III)-Ent complexes requires intracellular esterases that hydrolyze the siderophore. Although UPEC are equipped to consume the products of completely hydrolyzed Ent, we find that Ent and its derivatives may be incompletely hydrolyzed to yield products with retained siderophore activity. These results are consistent with catabolic inefficiency as means to obtain more than one iron ion per siderophore molecule. This is compatible with an evolved UPEC strategy to maximize the nutritional returns from metabolic investments in siderophore biosynthesis.
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Affiliation(s)
- Zongsen Zou
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - John I Robinson
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Lindsey K Steinberg
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Jeffrey P Henderson
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA.
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Zou Z, Robinson JI, Steinberg LK, Henderson JP. Uropathogenic Escherichia coli wield enterobactin-derived catabolites as siderophores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550588. [PMID: 37546885 PMCID: PMC10402112 DOI: 10.1101/2023.07.25.550588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Uropathogenic E. coli (UPEC) secrete multiple siderophore types to scavenge extracellular iron(III) ions during clinical urinary tract infections, despite the metabolic costs of biosynthesis. Here we find the siderophore enterobactin and its related products to be prominent components of the iron-responsive extracellular metabolome of a model UPEC strain. Using defined enterobactin biosynthesis and import mutants, we identify lower molecular weight, dimeric exometabolites as products of incomplete siderophore catabolism, rather than prematurely released biosynthetic intermediates. In E. coli, iron acquisition from iron(III)-enterobactin complexes requires intracellular esterases that hydrolyze the siderophore. Although UPEC are equipped to consume the products of completely hydrolyzed enterobactin, we find that enterobactin and its derivatives may be incompletely hydrolyzed to yield products with retained siderophore activity. These results are consistent with catabolic inefficiency as means to obtain more than one iron ion per siderophore molecule. This is compatible with an evolved UPEC strategy to maximize the nutritional returns from metabolic investments in siderophore biosynthesis.
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Affiliation(s)
- Zongsen Zou
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John I. Robinson
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lindsey K. Steinberg
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey P. Henderson
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
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Philipp Egbers H, Zurhelle C, Boris Koch P, Harder T, Tebben J. Selective purification of catecholate, hydroxamate and α–hydroxycarboxylate siderophores with Titanium Dioxide Affinity Chromatography. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.122639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Yin SJ, Wang X, Jiang H, Lu M, Yang FQ. Preparation of yolk-shell structure NH 2-MIL-125 magnetic nanoparticles for the selective extraction of nucleotides. Mikrochim Acta 2021; 188:419. [PMID: 34782919 DOI: 10.1007/s00604-021-05071-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/16/2021] [Indexed: 12/01/2022]
Abstract
Yolk-shell structure magnetic metal-organic framework nanoparticles were prepared via post solvothermal method and employed as a magnetic solid-phase extraction adsorbent for selective pre-concentration of 5'-ribonucleotides by π stacking interaction, hydrogen bonding, and the strong interaction between titanium ions (Ti4+) and phosphate group. The properties of the materials were confirmed by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, X-ray photoelectron spectrometry, vibrating sample magnetometer, infrared spectroscopy, thermogravimetric analysis, and Brunauer-Emmett-Teller analysis. The main parameters affecting the adsorption-desorption process, including adsorbent amount, incubation time, incubation temperature, sample pH, shaking speed, elution solution, and elution time, were systematically optimized. Finally, 1.0 mg of adsorbent mixed with 1.0 mL sample solution (10.0 mmol⋅L-1 NaCl, pH 3.0) and shaken at 135 rpm for 5 min at 40 °C, washed with 1.0 mL Na3PO4-NH3∙H2O under vortex for 5 min were selected as optimized adsorption-desorption conditions. The binding performance of adsorbent towards five nucleotides was evaluated by static adsorption experiments. The data are well-fitted to the Langmuir isotherm model and the maximum adsorption capacity is 27.8 mg g-1 for adenosine 5'-monophosphate. The limit of detection of the method is 19.44-38.41 ng mL-1. Under the optimal conditions, the adsorbent was successfully applied to magnetic solid-phase extraction and high performance liquid chromatography determination of five nucleotides in octopus, chicken, fish, and pork samples.
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Affiliation(s)
- Shi-Jun Yin
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Xu Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Hui Jiang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Min Lu
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Feng-Qing Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, People's Republic of China.
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