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Wood PL. Metabolic and Lipid Biomarkers for Pathogenic Algae, Fungi, Cyanobacteria, Mycobacteria, Gram-Positive Bacteria, and Gram-Negative Bacteria. Metabolites 2024; 14:378. [PMID: 39057701 PMCID: PMC11278827 DOI: 10.3390/metabo14070378] [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: 06/12/2024] [Revised: 06/27/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
The utilization of metabolomics and lipidomics analytical platforms in the study of pathogenic microbes is slowly expanding. These research approaches will significantly contribute to the establishment of microbial metabolite and lipid databases of significant value to all researchers in microbiology. In this review, we present a high-level overview of some examples of biomarkers that can be used to detect the presence of microbes, monitor the expansion/decline of a microbe population, and add to our understanding of microbe biofilms and pathogenicity. In addition, increased knowledge of the metabolic functions of pathogenic microbes can contribute to our understanding of microbes that are utilized in diverse industrial applications. Our review focuses on lipids, secondary metabolites, and non-ribosomal peptides that can be monitored using electrospray ionization high-resolution mass spectrometry (ESI-HRMS).
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Affiliation(s)
- Paul L Wood
- Metabolomics Unit, College of Veterinary Medicine, Lincoln Memorial University, 6965 Cumberland Gap Parkway, Harrogate, TN 37752, USA
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2
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Hsu FF. Multiple stage linear ion-trap mass spectrometry toward characterization of native bacterial lipids-a critical review. Biochimie 2023; 215:88-99. [PMID: 37567358 DOI: 10.1016/j.biochi.2023.08.009] [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] [Received: 04/15/2023] [Revised: 05/25/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Great strides in the field of lipidomics driven by advances in mass spectrometry techniques in the last decade have moved lipid analysis to a new level and significantly improved our understanding of lipid biochemistry. Multiple stage mass spectrometry (MSn) with high resolution mass spectrometry (HRMS) that allows sequential isolation, fragmentation, and recognition of ion structures, is a powerful tool for characterization of complex and diversified lipid in bacterial cells, in which lipids are often critical for cell aggregation and dissociation, and play important biological roles. In addition to common phospholipids, many bacteria contain unique lipids that are specific to the bacterium genus and even to the bacterium species. In this review, application of linear ion-trap (LIT) MSn in the structural characterization of native bacterial lipids including (1) novel lipids consisting of many isomeric structures, (2) lipids with unique functional groups and modification, (3) complex sphingolipids, peptidolipids, and lipocyclopeptides from various bacteria are presented. LIT MSn approach affords realization of the mechanisms underlying the fragmentation processes, resulting in identification of complex lipid structures that would be very difficult to define using other analytical methods.
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Affiliation(s)
- Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Box 8127, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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3
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Wamer N, Morse CN, Gadient JN, Dodson TA, Carlson EA, Prestwich EG. Comparison of Small Biomolecule Ionization and Fragmentation in Pseudomonas aeruginosa Using Common MALDI Matrices. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:355-365. [PMID: 36696681 PMCID: PMC9983012 DOI: 10.1021/jasms.2c00157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/05/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Different bacterial cell surface associated biomolecules can be analyzed by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and coupled with collision induced dissociation (CID) for identification. Pseudomonas aeruginosa is an opportunistic, Gram-negative bacterium that causes acute or chronic biofilm infections. Cells of P. aeruginosa communicate through a system of signaling biomolecules known as quorum sensing (QS). The QS system can result in the production of biosurfactant rhamnolipids known to associate and alter the cellular membrane. MALDI-TOF utilizes a variety of matrices that can interact differently with biomolecules for selective ionization. We examined six common matrices to determine the optimal matrix specific to different molecule classes in P. aeruginosa associated with cell surfaces. Three major molecule classes (quinolones, rhamnolipids, and phospholipids) were observed to ionize selectively with the different matrices tested. Sodiated and protonated adducts differed between matrices utilized in our study. Isobaric ions were identified as different molecule classes depending on the matrix used. We highlight the role of matrix selection in MALDI-TOF identification of molecules within a complex biological mixture.
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Affiliation(s)
- Nathan
C. Wamer
- Department
of Medicinal and Biological Chemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Chase N. Morse
- Department
of Medicinal and Biological Chemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Jennifer N. Gadient
- The
College of Natural Sciences and Mathematics, NSM Instrumentation Center, University of Toledo, Toledo, Ohio 43606, United States
| | - Taylor A. Dodson
- Department
of Medicinal and Biological Chemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Eric A. Carlson
- Department
of Medicinal and Biological Chemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Erin G. Prestwich
- Department
of Medicinal and Biological Chemistry, University
of Toledo, Toledo, Ohio 43606, United States
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4
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Cebolla VL, Jarne C, Vela J, Garriga R, Membrado L, Galbán J. Scanning densitometry and mass spectrometry for HPTLC analysis of lipids: The last 10 years. J LIQ CHROMATOGR R T 2021. [DOI: 10.1080/10826076.2020.1866600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Carmen Jarne
- Instituto de Carboquímica, ICB-CSIC, Zaragoza, Spain
| | - Jesús Vela
- Departamento de Química Analítica, EINA, Universidad de Zaragoza, Zaragoza, Spain
| | - Rosa Garriga
- Departamento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Luis Membrado
- Instituto de Carboquímica, ICB-CSIC, Zaragoza, Spain
| | - Javier Galbán
- Departamento de Química Analítica, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
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Deschamps E, Schaumann A, Schmitz-Afonso I, Afonso C, Dé E, Loutelier-Bourhis C, Alexandre S. Membrane phospholipid composition of Pseudomonas aeruginosa grown in a cystic fibrosis mucus-mimicking medium. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183482. [PMID: 33002450 DOI: 10.1016/j.bbamem.2020.183482] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa is a bacterium able to induce serious pulmonary infections in cystic fibrosis (CF) patients. This bacterium is very often antibiotic resistant, partly because of its membrane impermeability, which is linked to the membrane lipid composition. This work aims to study the membrane phospholipids of P. aeruginosa grown in CF sputum-like media. METHODS Three media were used: Mueller Hilton broth (MHB), synthetic cystic fibrosis medium (SCFM) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) complemented SCFM (SCFM-PC). Lipids were extracted and LC-MS/MS analyses were performed. Growth curves, atomic force microscopy images and minimal inhibitory concentration determination were performed in order to compare the growth and potentially link lipid modifications to antibiotic resistance. RESULTS Semi-quantification showed phospholipid quantity variation depending on the growth medium. Phosphatidylcholines were detected in traces in SCFM. MS/MS experiments showed an increase of phospholipids derived from DOPC in SCFM-PC. We observed no influence of the medium on the bacterial growth and a minor influence on the bacterial shape. MIC values were generally higher in SCFM and SCFM-PC than in MHB. CONCLUSIONS We defined a CF sputum-like media which can be used for the membrane lipid extraction of P. aeruginosa. We also showed that the growth medium does have an influence on its membrane lipid composition and antibiotic resistance, especially for SCFM-PC in which P. aeruginosa uses DOPC, in order to make its own membrane. GENERAL SIGNIFICANCE Our results show that considerable caution must be taken when choosing a medium for lipid identification and antibiotic testing -especially for phospholipids-enriched media.
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Affiliation(s)
- Estelle Deschamps
- Normandie Univ, PBS, UMR 6270 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, CURIB, Bvd De Broglie, 76821 Mont-Saint-Aignan, Cedex, France; Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnière, 76821 Mont-Saint-Aignan, Cedex, France
| | - Annick Schaumann
- Normandie Univ, PBS, UMR 6270 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, CURIB, Bvd De Broglie, 76821 Mont-Saint-Aignan, Cedex, France
| | - Isabelle Schmitz-Afonso
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnière, 76821 Mont-Saint-Aignan, Cedex, France
| | - Carlos Afonso
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnière, 76821 Mont-Saint-Aignan, Cedex, France
| | - Emmanuelle Dé
- Normandie Univ, PBS, UMR 6270 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, CURIB, Bvd De Broglie, 76821 Mont-Saint-Aignan, Cedex, France
| | - Corinne Loutelier-Bourhis
- Normandie Univ, COBRA, UMR 6014 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, IRCOF, 1 rue Tesnière, 76821 Mont-Saint-Aignan, Cedex, France
| | - Stéphane Alexandre
- Normandie Univ, PBS, UMR 6270 and FR 3038, Université de Rouen, INSA de Rouen, CNRS, CURIB, Bvd De Broglie, 76821 Mont-Saint-Aignan, Cedex, France.
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6
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Sherma J, Rabel F. Review of advances in planar chromatography-mass spectrometry published in the period 2015–2019. J LIQ CHROMATOGR R T 2020. [DOI: 10.1080/10826076.2020.1725561] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Joseph Sherma
- Department of Chemistry, Lafayette College, Easton, PA, USA
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7
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von Gerichten J, Lamprecht D, Opálka L, Soulard D, Marsching C, Pilz R, Sencio V, Herzer S, Galy B, Nordström V, Hopf C, Gröne HJ, Trottein F, Sandhoff R. Bacterial immunogenic α-galactosylceramide identified in the murine large intestine: dependency on diet and inflammation. J Lipid Res 2019; 60:1892-1904. [PMID: 31484693 DOI: 10.1194/jlr.ra119000236] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/22/2019] [Indexed: 12/22/2022] Open
Abstract
The glycosphingolipid, α-galactosylceramide (αGalCer), when presented by CD1d on antigen-presenting cells, efficiently activates invariant natural killer T (iNKT) cells. Thereby, it modulates immune responses against tumors, microbial and viral infections, and autoimmune diseases. Recently, the production of αGalCer by Bacteroidetes from the human gut microbiome was elucidated. Using hydrophilic interaction chromatography coupled to MS2, we screened murine intestinal tracts to identify and quantify αGalCers, and we investigated the αGalCer response to different dietary and physiologic conditions. In both the cecum and the colon of mice, we found 1-15 pmol of αGalCer per milligram of protein; in contrast, mice lacking microbiota (germ-free mice) and fed identical diet did not harbor αGalCer. The identified αGalCer contained a β(R)-hydroxylated hexadecanoyl chain N-linked to C18-sphinganine, which differed from what has been reported with Bacteroides fragilis Unlike β-anomeric structures, but similar to αGalCers from B. fragilis, the synthetic form of the murine αGalCer induced iNKT cell activation in vitro. Last, we observed a decrease in αGalCer production in mice exposed to conditions that alter the composition of the gut microbiota, including Western type diet, colitis, and influenza A virus infection. Collectively, this study suggests that αGalCer is produced by commensals in the mouse intestine and reveals that stressful conditions causing dysbiosis alter its synthesis. The consequences of this altered production on iNKT cell-mediated local and systemic immune responses are worthy of future studies.
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Affiliation(s)
- Johanna von Gerichten
- Lipid Pathobiochemistry Group, Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Dominic Lamprecht
- Lipid Pathobiochemistry Group, Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
| | - Lukáš Opálka
- Lipid Pathobiochemistry Group, Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany.,Skin Barrier Research Group, Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Daphnée Soulard
- Centre d'Infection et d'Immunité de Lille, Inserm U1019, CNRS UMR 8204, University of Lille, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Christian Marsching
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Robert Pilz
- Lipid Pathobiochemistry Group, Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Valentin Sencio
- Centre d'Infection et d'Immunité de Lille, Inserm U1019, CNRS UMR 8204, University of Lille, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Silke Herzer
- Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
| | - Bruno Galy
- Division of Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Viola Nordström
- Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Hermann-Josef Gröne
- Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany.,Institute of Pharmacology, University of Marburg, Marburg, Germany
| | - François Trottein
- Centre d'Infection et d'Immunité de Lille, Inserm U1019, CNRS UMR 8204, University of Lille, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Roger Sandhoff
- Lipid Pathobiochemistry Group, Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
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8
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Gutiérrez-Gómez U, Servín-González L, Soberón-Chávez G. Role of β-oxidation and de novo fatty acid synthesis in the production of rhamnolipids and polyhydroxyalkanoates by Pseudomonas aeruginosa. Appl Microbiol Biotechnol 2019; 103:3753-3760. [PMID: 30919102 DOI: 10.1007/s00253-019-09734-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/02/2019] [Indexed: 10/27/2022]
Abstract
Pseudomonas aeruginosa are ubiquitous γ-proteobacteria capable of producing the biosurfactant rhamnolipids (RL) and the polymer polyhydroxyalkanoate (PHA). RL are glycolipids with high biotechnological potential, whereas PHA is used for the production of biodegradable plastics. It has been proposed that the β-oxidation pathway provides intermediates for RL biosynthesis, even when using a non-fatty acid carbon source for growth, while an intermediate of de novo fatty acid biosynthesis (FASII) pathway [(R)-3-hydroxyacyl-ACP] is used for PHA biosynthesis. The aim of this work is to study the inter-relationship of the RL and PHA biosynthetic pathways in a culture medium with a non-fatty acid carbon source, focusing on the role of FASII and β-oxidation in supplying the substrates for the first step in RL and PHA synthesis, carried out by the RhlA and PhaG enzymes, respectively. The PHA synthases (PhaC1 and PhaC2) are only able to use CoA-linked 3-hydroxy acids and the PhaG enzyme catalyzes the conversion of (R)-3-hydroxyacyl-ACP to (R)-3-hydroxyacyl-CoA, the substrate of PhaC1 and PhaC2. RhlA in turn catalyzes the synthesis of the RL precursor 3-(3-hydroxyalkanoyloxy) alkanoic acids (HAA) by the dimerization of two 3-hydroxyalkanoic acid molecules (that have been shown to be also (R)-3-hydroxyacyl-ACP). In this work, we show that RhlA can produce both RL and PHA precursors (presumably CoA-linked HAA), that the blockage of carbon flux through β-oxidation pathway does not decrease RL titer, and that the enoyl-CoA hydratase RhlY and enoyl-CoA hydratase/isomerase RhlZ produce the main fatty acids precursor of RL using as substrate also a FASII intermediate (presumably (S)-3-hydroxyacyl-CoA).
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Affiliation(s)
- Uriel Gutiérrez-Gómez
- Programa de Producción de Biomoléculas de Interés Biomédico en Bacterias y Hongos. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, C. P. 04510, CDMX, Mexico
| | - Luis Servín-González
- Programa de Producción de Biomoléculas de Interés Biomédico en Bacterias y Hongos. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, C. P. 04510, CDMX, Mexico
| | - Gloria Soberón-Chávez
- Programa de Producción de Biomoléculas de Interés Biomédico en Bacterias y Hongos. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, C. P. 04510, CDMX, Mexico.
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