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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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Weishaupt AK, Lamann K, Tallarek E, Pezacki AT, Matier CD, Schwerdtle T, Aschner M, Chang CJ, Stürzenbaum SR, Bornhorst J. Dysfunction in atox-1 and ceruloplasmin alters labile Cu levels and consequently Cu homeostasis in C. elegans. Front Mol Biosci 2024; 11:1354627. [PMID: 38389896 PMCID: PMC10882093 DOI: 10.3389/fmolb.2024.1354627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Copper (Cu) is an essential trace element, however an excess is toxic due to its redox properties. Cu homeostasis therefore needs to be tightly regulated via cellular transporters, storage proteins and exporters. An imbalance in Cu homeostasis has been associated with neurodegenerative disorders such as Wilson's disease, but also Alzheimer's or Parkinson's disease. In our current study, we explored the utility of using Caenorhabditis elegans (C. elegans) as a model of Cu dyshomeostasis. The application of excess Cu dosing and the use of mutants lacking the intracellular Cu chaperone atox-1 and major Cu storage protein ceruloplasmin facilitated the assessment of Cu status, functional markers including total Cu levels, labile Cu levels, Cu distribution and the gene expression of homeostasis-related genes. Our data revealed a decrease in total Cu uptake but an increase in labile Cu levels due to genetic dysfunction, as well as altered gene expression levels of Cu homeostasis-associated genes. In addition, the data uncovered the role ceruloplasmin and atox-1 play in the worm's Cu homeostasis. This study provides insights into suitable functional Cu markers and Cu homeostasis in C. elegans, with a focus on labile Cu levels, a promising marker of Cu dysregulation during disease progression.
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Affiliation(s)
- Ann-Kathrin Weishaupt
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany
| | | | | | - Aidan T Pezacki
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Carson D Matier
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Tanja Schwerdtle
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Christopher J Chang
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Stephen R Stürzenbaum
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Julia Bornhorst
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany
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Dell’Anno F, Vitale GA, Buonocore C, Vitale L, Palma Esposito F, Coppola D, Della Sala G, Tedesco P, de Pascale D. Novel Insights on Pyoverdine: From Biosynthesis to Biotechnological Application. Int J Mol Sci 2022; 23:ijms231911507. [PMID: 36232800 PMCID: PMC9569983 DOI: 10.3390/ijms231911507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Pyoverdines (PVDs) are a class of siderophores produced mostly by members of the genus Pseudomonas. Their primary function is to accumulate, mobilize, and transport iron necessary for cell metabolism. Moreover, PVDs also play a crucial role in microbes’ survival by mediating biofilm formation and virulence. In this review, we reorganize the information produced in recent years regarding PVDs biosynthesis and pathogenic mechanisms, since PVDs are extremely valuable compounds. Additionally, we summarize the therapeutic applications deriving from the PVDs’ use and focus on their role as therapeutic target themselves. We assess the current biotechnological applications of different sectors and evaluate the state-of-the-art technology relating to the use of synthetic biology tools for pathway engineering. Finally, we review the most recent methods and techniques capable of identifying such molecules in complex matrices for drug-discovery purposes.
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Aron AT, Petras D, Schmid R, Gauglitz JM, Büttel I, Antelo L, Zhi H, Nuccio SP, Saak CC, Malarney KP, Thines E, Dutton RJ, Aluwihare LI, Raffatellu M, Dorrestein PC. Native mass spectrometry-based metabolomics identifies metal-binding compounds. Nat Chem 2022; 14:100-109. [PMID: 34795435 PMCID: PMC8959065 DOI: 10.1038/s41557-021-00803-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 08/27/2021] [Indexed: 11/09/2022]
Abstract
Although metals are essential for the molecular machineries of life, systematic methods for discovering metal-small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization-mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecular networking, a rule-based data analysis workflow. This method enabled the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion species with the same chromatographic profiles. As this native electrospray metabolomics approach is suited to the use of any liquid chromatography-mass spectrometry system to explore the binding of any metal, this method has the potential to become an essential strategy for elucidating metal-binding molecules in biology.
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Affiliation(s)
- Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, Germany
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, La Jolla, CA, USA
| | - Isabell Büttel
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Luis Antelo
- Institute of Biotechnology and Drug Research (IBWF gGmbH), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hui Zhi
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Sean-Paul Nuccio
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Christina C Saak
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kien P Malarney
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Eckhard Thines
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Biotechnology and Drug Research (IBWF gGmbH), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Rachel J Dutton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Lihini I Aluwihare
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Chiba University-University of California San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
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Espósito BP, Martins AC, de Carvalho RRV, Aschner M. High throughput fluorimetric assessment of iron traffic and chelation in iron-overloaded Caenorhabditis elegans. Biometals 2020; 33:255-267. [PMID: 32979113 DOI: 10.1007/s10534-020-00250-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/16/2020] [Indexed: 01/31/2023]
Abstract
The nematode Caenorhabditis elegans (C. elegans) is a convenient tool to evaluate iron metabolism as it shares great orthology with human proteins involved in iron transport, in addition to being transparent and readily available. In this work, we describe how wild-type (N2) C. elegans nematodes in the first larval stage can be loaded with acetomethoxycalcein (CAL-AM) and study it as a whole-organism model for both iron speciation and chelator permeability of the labile iron pool (LIP). This model may be relevant for high throughput assessment of molecules intended for chelation therapy of iron overload diseases.
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Affiliation(s)
- Breno Pannia Espósito
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil.
| | - Airton Cunha Martins
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
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