1
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“Omic” Approaches to Bacteria and Antibiotic Resistance Identification. Int J Mol Sci 2022; 23:ijms23179601. [PMID: 36077000 PMCID: PMC9455953 DOI: 10.3390/ijms23179601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022] Open
Abstract
The quick and accurate identification of microorganisms and the study of resistance to antibiotics is crucial in the economic and industrial fields along with medicine. One of the fastest-growing identification methods is the spectrometric approach consisting in the matrix-assisted laser ionization/desorption using a time-of-flight analyzer (MALDI-TOF MS), which has many advantages over conventional methods for the determination of microorganisms presented. Thanks to the use of a multiomic approach in the MALDI-TOF MS analysis, it is possible to obtain a broad spectrum of data allowing the identification of microorganisms, understanding their interactions and the analysis of antibiotic resistance mechanisms. In addition, the literature data indicate the possibility of a significant reduction in the time of the sample preparation and analysis time, which will enable a faster initiation of the treatment of patients. However, it is still necessary to improve the process of identifying and supplementing the existing databases along with creating new ones. This review summarizes the use of “-omics” approaches in the MALDI TOF MS analysis, including in bacterial identification and antibiotic resistance mechanisms analysis.
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2
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Pizzato J, Tang W, Bernabeu S, Bonnin RA, Bille E, Farfour E, Guillard T, Barraud O, Cattoir V, Plouzeau C, Corvec S, Shahrezaei V, Dortet L, Larrouy-Maumus G. Discrimination of Escherichia coli, Shigella flexneri, and Shigella sonnei using lipid profiling by MALDI-TOF mass spectrometry paired with machine learning. Microbiologyopen 2022; 11:e1313. [PMID: 36004556 PMCID: PMC9405496 DOI: 10.1002/mbo3.1313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/03/2022] [Indexed: 11/15/2022] Open
Abstract
Matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry (MALDI‐TOF MS) has become a staple in clinical microbiology laboratories. Protein‐profiling of bacteria using this technique has accelerated the identification of pathogens in diagnostic workflows. Recently, lipid profiling has emerged as a way to complement bacterial identification where protein‐based methods fail to provide accurate results. This study aimed to address the challenge of rapid discrimination between Escherichia coli and Shigella spp. using MALDI‐TOF MS in the negative ion mode for lipid profiling coupled with machine learning. Both E. coli and Shigella species are closely related; they share high sequence homology, reported for 16S rRNA gene sequence similarities between E. coli and Shigella spp. exceeding 99%, and a similar protein expression pattern but are epidemiologically distinct. A bacterial collection of 45 E. coli, 48 Shigella flexneri, and 62 Shigella sonnei clinical isolates were submitted to lipid profiling in negative ion mode using the MALDI Biotyper Sirius® system after treatment with mild‐acid hydrolysis (acetic acid 1% v/v for 15 min at 98°C). Spectra were then analyzed using our in‐house machine learning algorithm and top‐ranked features used for the discrimination of the bacterial species. Here, as a proof‐of‐concept, we showed that lipid profiling might have the potential to differentiate E. coli from Shigella species using the analysis of the top five ranked features obtained by MALDI‐TOF MS in the negative ion mode of the MALDI Biotyper Sirius® system. Based on this new approach, MALDI‐TOF MS analysis of lipids might help pave the way toward these goals.
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Affiliation(s)
- Jade Pizzato
- Faculty of Natural Sciences, Department of Life Sciences, MRC Centre for Molecular Bacteriology & Infection, Imperial College London, England
| | - Wenhao Tang
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, England
| | - Sandrine Bernabeu
- CHU de Bicêtre, Laboratoire de Bactériologie-Hygiène, Assistance Publique des Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,INSERM UMR 1184, Team RESIST, Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Centre National de Référence de la Résistance aux Antibiotiques, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- INSERM UMR 1184, Team RESIST, Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Centre National de Référence de la Résistance aux Antibiotiques, Le Kremlin-Bicêtre, France
| | - Emmanuelle Bille
- Service de Microbiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, AP-HP Centre-Université de Paris, Paris, France
| | - Eric Farfour
- Service de Biologie Clinique, Hôpital Foch, Suresnes, France
| | - Thomas Guillard
- Université de Reims-Champagne-Ardenne, Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Laboratoire de Bactériologie-Virologie-Hygiène, Hospitalière-Parasitologie-Mycologie, Hôpital Robert Debré, CHU Reims, Reims, France
| | - Olivier Barraud
- CHU Limoges, Service de Bactériologie-Virologie-Hygiène, CIC1435, INSERM 1092, Université de Limoges, UMR, Limoges, France
| | - Vincent Cattoir
- Service de Bactériologie-Hygiène, CHU de Rennes, Rennes, France
| | - Chloe Plouzeau
- Service de Bactériologie et d'Hygiène hospitalière, Unité de microbiologie moléculaire et séquençage, CHU de Poitiers, Poitiers, France
| | - Stéphane Corvec
- Université de Nantes, CHU Nantes, Service de Bactériologie et des Contrôles Microbiologiques, INSERM, INCIT UMR 1302 F- 44000 Nantes, France
| | - Vahid Shahrezaei
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, England
| | - Laurent Dortet
- CHU de Bicêtre, Laboratoire de Bactériologie-Hygiène, Assistance Publique des Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,INSERM UMR 1184, Team RESIST, Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Centre National de Référence de la Résistance aux Antibiotiques, Le Kremlin-Bicêtre, France
| | - Gerald Larrouy-Maumus
- Faculty of Natural Sciences, Department of Life Sciences, MRC Centre for Molecular Bacteriology & Infection, Imperial College London, England
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3
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Solntceva V, Kostrzewa M, Larrouy-Maumus G. Detection of Species-Specific Lipids by Routine MALDI TOF Mass Spectrometry to Unlock the Challenges of Microbial Identification and Antimicrobial Susceptibility Testing. Front Cell Infect Microbiol 2021; 10:621452. [PMID: 33634037 PMCID: PMC7902069 DOI: 10.3389/fcimb.2020.621452] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
MALDI-TOF mass spectrometry has revolutionized clinical microbiology diagnostics by delivering accurate, fast, and reliable identification of microorganisms. It is conventionally based on the detection of intracellular molecules, mainly ribosomal proteins, for identification at the species-level and/or genus-level. Nevertheless, for some microorganisms (e.g., for mycobacteria) extensive protocols are necessary in order to extract intracellular proteins, and in some cases a protein-based approach cannot provide sufficient evidence to accurately identify the microorganisms within the same genus (e.g., Shigella sp. vs E. coli and the species of the M. tuberculosis complex). Consequently lipids, along with proteins are also molecules of interest. Lipids are ubiquitous, but their structural diversity delivers complementary information to the conventional protein-based clinical microbiology matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based approaches currently used. Lipid modifications, such as the ones found on lipid A related to polymyxin resistance in Gram-negative pathogens (e.g., phosphoethanolamine and aminoarabinose), not only play a role in the detection of microorganisms by routine MALDI-TOF mass spectrometry but can also be used as a read-out of drug susceptibility. In this review, we will demonstrate that in combination with proteins, lipids are a game-changer in both the rapid detection of pathogens and the determination of their drug susceptibility using routine MALDI-TOF mass spectrometry systems.
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Affiliation(s)
- Vera Solntceva
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | | | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
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4
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Zamyatina A, Heine H. Lipopolysaccharide Recognition in the Crossroads of TLR4 and Caspase-4/11 Mediated Inflammatory Pathways. Front Immunol 2020; 11:585146. [PMID: 33329561 PMCID: PMC7732686 DOI: 10.3389/fimmu.2020.585146] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
The innate immune response to lipopolysaccharide is essential for host defense against Gram-negative bacteria. In response to bacterial infection, the TLR4/MD-2 complex that is expressed on the surface of macrophages, monocytes, dendritic, and epithelial cells senses picomolar concentrations of endotoxic LPS and triggers the production of various pro-inflammatory mediators. In addition, LPS from extracellular bacteria which is either endocytosed or transfected into the cytosol of host cells or cytosolic LPS produced by intracellular bacteria is recognized by cytosolic proteases caspase-4/11 and hosts guanylate binding proteins that are involved in the assembly and activation of the NLRP3 inflammasome. All these events result in the initiation of pro-inflammatory signaling cascades directed at bacterial eradication. However, TLR4-mediated signaling and caspase-4/11-induced pyroptosis are largely involved in the pathogenesis of chronic and acute inflammation. Both extra- and intracellular LPS receptors—TLR4/MD-2 complex and caspase-4/11, respectively—are able to directly bind the lipid A motif of LPS. Whereas the structural basis of lipid A recognition by the TLR4 complex is profoundly studied and well understood, the atomic mechanism of LPS/lipid A interaction with caspase-4/11 is largely unknown. Here we describe the LPS-induced TLR4 and caspase-4/11 mediated signaling pathways and their cross-talk and scrutinize specific structural features of the lipid A motif of diverse LPS variants that have been reported to activate caspase-4/11 or to induce caspase-4/11 mediated activation of NLRP3 inflammasome (either upon transfection of LPS in vitro or upon infection of cell cultures with intracellular bacteria or by LPS as a component of the outer membrane vesicles). Generally, inflammatory caspases show rather similar structural requirements as the TLR4/MD-2 complex, so that a “basic” hexaacylated bisphosphorylated lipid A architecture is sufficient for activation. However, caspase-4/11 can sense and respond to much broader variety of lipid A variants compared to the very “narrow” specificity of TLR4/MD-2 complex as far as the number and the length of lipid chains attached at the diglucosamine backbone of lipid A is concerned. Besides, modification of the lipid A phosphate groups with positively charged appendages such as phosphoethanolamine or aminoarabinose could be essential for the interaction of lipid A/LPS with inflammatory caspases and related proteins.
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Affiliation(s)
- Alla Zamyatina
- Institute of Organic Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Holger Heine
- Research Group Innate Immunity, Research Center Borstel-Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Disease (DZL), Borstel, Germany
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5
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Froning M, Helmer PO, Hayen H. Identification and structural characterization of lipid A from Escherichia coli, Pseudomonas putida and Pseudomonas taiwanensis using liquid chromatography coupled to high-resolution tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8897. [PMID: 32673427 DOI: 10.1002/rcm.8897] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/06/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Lipid A is a part of the lipopolysaccharide layer, which is a main component of the outer membrane from Gram-negative bacteria. It can be sensed by mammalians to identify the presence of Gram-negative bacteria in their tissues and plays a key role in the pathogenesis of bacterial infections. Lipid A is also used as an adjuvant in human vaccines, emphasizing the importance of its structural analysis. METHODS In order to distinguish and characterize various lipid A species, a liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS) method was developed. Isolation of lipid A from different bacteria was carried out using a modified Bligh and Dyer extraction following a mild acid hydrolysis. Chromatography was performed using a bifunctional reversed-phase-based stationary phase. High-resolution MS using negative electrospray ionization was applied and MS/MS experiments utilizing high-energy collisional dissociation generated diagnostic product ions, which allowed the assignment of the side chains to distinct positions of the lipid A backbone. RESULTS The method was applied to lipid A isolations of Escherichia coli (E. coli), Pseudomonas putida (P. putida) and Pseudomonas taiwanensis (P. taiwanensis). Various lipid A species were identified by their accurate masses and their structures were characterized using MS/MS experiments. Previously described lipid A structures from E. coli were identified and their structures confirmed by MS/MS. For the biotechnologically relevant strains P. putida and P. taiwanensis, we confirmed species by MS/MS, which have previously only been analyzed using MS. In addition, several lipid A species were discovered that have not been previously described in the literature. CONCLUSIONS The combination of LC and MS/MS enabled the selective and sensitive identification and structural characterization of various lipid A species from Gram-negative bacteria. These species varied in their substituted side chains, speaking of fatty acids and phosphate groups. Characteristic product ions facilitated the assignment of side chains to distinct positions of the lipid A backbone.
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Affiliation(s)
- Matti Froning
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster, 48149, Germany
| | - Patrick O Helmer
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster, 48149, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster, 48149, Germany
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6
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Jabbar Siddiqui A, Le Sénéchal C, Vilain S, Buré C. Effect of matrices and additives on phosphorylated and ketodeoxyoctonic acid lipids A analysis by matrix-assisted laser desorption ionization-mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4600. [PMID: 32720737 DOI: 10.1002/jms.4600] [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: 03/10/2020] [Revised: 06/15/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
Lipid A is a major compound of the outer membrane of gram-negative bacteria and is a key factor of bacterial virulence. As lipid A's structure differs among bacterial species and varies between strains of the same species, knowing its modifications is essential to understand its implications in the infectious process. To analyze these lipids, matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) is a well-suited method that is fast and efficient. However, there are limitations with the matrix and additives used, such as the suppression of signal or prompt fragmentations that could give a false overview of lipid A composition in biological samples. For a comprehensive analysis of the entire lipid A species present in a sample, we tested 16 matrices and 11 additives on two commercial lipids A. The first commercial one contains single phosphorylation group, and the second contains two phosphorylation and two ketodeoxyoctonic acid (KDO) groups. The lipid A containing KDO groups was essentially detected by the 3-hydroxypicolinic acid (3-HPA) matrix, whereas the monophosphorylated lipid A could be detected by 13 matrices out of the 16. We also demonstrated that the signal of diphosphorylated lipid A can be enhanced with the use of additives in the matrix. Our study indicated that the best conditions to obtain a clear signal of both lipids A without prompt fragmentation was the use of 3-HPA with 10mM trifluoroacetic acid (TFA).
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Affiliation(s)
- Amna Jabbar Siddiqui
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bordeaux, F-33600, France
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Caroline Le Sénéchal
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bordeaux, F-33600, France
| | - Sébastien Vilain
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bordeaux, F-33600, France
| | - Corinne Buré
- CNRS, Bordeaux INP, CBMN, UMR 5248, University of Bordeaux, Bordeaux, F-33600, France
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7
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Anandan A, Vrielink A. Structure and function of lipid A-modifying enzymes. Ann N Y Acad Sci 2019; 1459:19-37. [PMID: 31553069 DOI: 10.1111/nyas.14244] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/26/2019] [Accepted: 09/05/2019] [Indexed: 12/30/2022]
Abstract
Lipopolysaccharides are complex molecules found in the cell envelop of many Gram-negative bacteria. The toxic activity of these molecules has led to the terminology of endotoxins. They provide bacteria with structural integrity and protection from external environmental conditions, and they interact with host signaling receptors to induce host immune responses. Bacteria have evolved enzymes that act to modify lipopolysaccharides, particularly the lipid A region of the molecule, to enable the circumvention of host immune system responses. These modifications include changes to lipopolysaccharide by the addition of positively charged sugars, such as N-Ara4N, and phosphoethanolamine (pEtN). Other modifications include hydroxylation, acylation, and deacylation of fatty acyl chains. We review the two-component regulatory mechanisms for enzymes that carry out these modifications and provide details of the structures of four enzymes (PagP, PagL, pEtN transferases, and ArnT) that modify the lipid A portion of lipopolysaccharides. We focus largely on the three-dimensional structures of these enzymes, which provide an understanding of how their substrate binding and catalytic activities are mediated. A structure-function-based understanding of these enzymes provides a platform for the development of novel therapeutics to treat antibiotic resistance.
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Affiliation(s)
- Anandhi Anandan
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia
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8
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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9
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Sándor V, Dörnyei Á, Makszin L, Kilár F, Péterfi Z, Kocsis B, Kilár A. Characterization of complex, heterogeneous lipid A samples using HPLC-MS/MS technique I. Overall analysis with respect to acylation, phosphorylation and isobaric distribution. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1043-1063. [PMID: 27506631 DOI: 10.1002/jms.3839] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/29/2016] [Accepted: 08/05/2016] [Indexed: 06/06/2023]
Abstract
We established a new reversed phase-high performance liquid chromatography method combined with electrospray ionization quadrupole time-of-flight tandem mass spectrometry for the simultaneous determination and structural characterization of different lipid A types in bacteria (Escherichia coli O111, Salmonella adelaide O35 and Proteus morganii O34) showing serological cross-reactivity. The complex lipid A mixtures (obtained by simple extraction and acid hydrolysis of the outer membrane lipopolysaccharides) were separated and detected without phosphate derivatization. Several previously unidentified ions were detected, which differed in the number and type of acyl chains and number of phosphate groups. In several cases, we observed the different retention of isobaric lipid A species, which had different secondary fatty acyl distribution at the C2' or the C3' sites. The fragmentation of the various, C4' monophosphorylated lipid A species in deprotonated forms provided structural assignment for each component. Fragmentation pathways of the tri-acylated, tetra-acylated, penta-acylated, hexa-acylated and hepta-acylated lipid A components and of the lipid A partial structures are suggested. As standards, the hexa-acylated ion at m/z 1716 with the E. coli-type acyl distribution and the hepta-acylated ion at m/z 1954 with the Salmonella-type acyl distribution were used. The results confirmed the presence of multiple forms of lipid A in all strains analyzed. In addition, the negative-ion mode MS permitted efficient detection for non-phosphorylated lipid A components, too. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Viktor Sándor
- Institute of Bioanalysis and Szentágothai Research Centre, University of Pécs, Szigeti út 12, 7624, Pécs, Hungary.
| | - Ágnes Dörnyei
- Department of Analytical and Environmental Chemistry, Faculty of Sciences, University of Pécs, Ifjúság útja 6, 7624, Pécs, Hungary
| | - Lilla Makszin
- Institute of Bioanalysis and Szentágothai Research Centre, University of Pécs, Szigeti út 12, 7624, Pécs, Hungary
| | - Ferenc Kilár
- Institute of Bioanalysis and Szentágothai Research Centre, University of Pécs, Szigeti út 12, 7624, Pécs, Hungary
- Department of Analytical and Environmental Chemistry, Faculty of Sciences, University of Pécs, Ifjúság útja 6, 7624, Pécs, Hungary
| | - Zoltán Péterfi
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Pécs, Szigeti út 12, 7624, Pécs, Hungary
| | - Béla Kocsis
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Pécs, Szigeti út 12, 7624, Pécs, Hungary
| | - Anikó Kilár
- MTA-PTE Molecular Interactions in Separation Science Research Group, Ifjúság útja 6, 7624, Pécs, Hungary
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10
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Morrison LJ, Parker WR, Holden DD, Henderson JC, Boll JM, Trent MS, Brodbelt JS. UVliPiD: A UVPD-Based Hierarchical Approach for De Novo Characterization of Lipid A Structures. Anal Chem 2016; 88:1812-20. [PMID: 26728944 DOI: 10.1021/acs.analchem.5b04098] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The lipid A domain of the endotoxic lipopolysaccharide layer of Gram-negative bacteria is comprised of a diglucosamine backbone to which a variable number of variable length fatty acyl chains are anchored. Traditional characterization of these tails and their linkages by nuclear magnetic resonance (NMR) or mass spectrometry is time-consuming and necessitates databases of pre-existing structures for structural assignment. Here, we introduce an automated de novo approach for characterization of lipid A structures that is completely database-independent. A hierarchical decision-tree MS(n) method is used in conjunction with a hybrid activation technique, UVPDCID, to acquire characteristic fragmentation patterns of lipid A variants from a number of Gram-negative bacteria. Structural assignments are derived from integration of key features from three to five spectra and automated interpretation is achieved in minutes without the need for pre-existing information or candidate structures. The utility of this strategy is demonstrated for a mixture of lipid A structures from an enzymatically modified E. coli lipid A variant. A total of 27 lipid A structures were discovered, many of which were isomeric, showcasing the need for a rapid de novo approach to lipid A characterization.
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Affiliation(s)
- Lindsay J Morrison
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - W Ryan Parker
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Dustin D Holden
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Jeremy C Henderson
- Department of Infectious Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - Joseph M Boll
- Department of Molecular Biosciences, University of Texas , Austin, Texas 78712, United States
| | - M Stephen Trent
- Department of Infectious Diseases, University of Georgia , Athens, Georgia 30602, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
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11
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O'Brien JP, Needham BD, Brown DB, Trent MS, Brodbelt JS. Top-Down Strategies for the Structural Elucidation of Intact Gram-negative Bacterial Endotoxins. Chem Sci 2014; 5:4291-4301. [PMID: 25386333 PMCID: PMC4224326 DOI: 10.1039/c4sc01034e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Re-modelling of lipopolysaccharides, which are the primary constituent of the outer cell membrane of Gram-negative bacteria, modulates pathogenesis and resistance to microbials. Reported herein is the characterization of intact Gram-negative bacterial lipooligosaccharides (LOS) via a new strategy utilizing online liquid chromatography (LC) coupled with ultraviolet photodissociation (UVPD) mass spectrometry. Compared to collision-based MS/MS methods, UVPD and UVPD/HCD promoted a greater array of cleavages within both the glycan and lipid moieties, including C-C, C-N, C-O cleavages in the acyl chains as well as glycosidic and cross-ring cleavages, thus providing the most far-reaching structural characterization of LOS. This LC-MS/MS strategy affords a robust analytical method to structurally characterize complex mixtures of bacterial endotoxins that maintains the integrity of the core oligosaccharide and lipid A domains of LOS, providing direct feedback about the cell envelope architectures and LOS modification strategies involved in resistance host innate immune defense.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
| | - Brittany D Needham
- The University of Texas at Austin, Department of Molecular Biosciences, 2506 Speedway A5000, Austin, TX, USA 78712
| | - Dusty B Brown
- The University of Texas at Austin, Department of Molecular Biosciences, 2506 Speedway A5000, Austin, TX, USA 78712
| | - M Stephen Trent
- The University of Texas at Austin, Department of Molecular Biosciences, 2506 Speedway A5000, Austin, TX, USA 78712
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, USA 78712
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12
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O'Brien JP, Needham BD, Henderson JC, Nowicki EM, Trent MS, Brodbelt JS. 193 nm ultraviolet photodissociation mass spectrometry for the structural elucidation of lipid A compounds in complex mixtures. Anal Chem 2014; 86:2138-45. [PMID: 24446701 PMCID: PMC3958132 DOI: 10.1021/ac403796n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
Here we implement ultraviolet photodissociation
(UVPD) in an online
liquid chromatographic tandem mass spectrometry (MS/MS) strategy to
support analysis of complex mixtures of lipid A combinatorially modified
during development of vaccine adjuvants. UVPD mass spectrometry at
193 nm was utilized to characterize the structures and fragment ion
types of lipid A from Escherichia coli, Vibrio
cholerae, and Pseudomonas aeruginosa using
an Orbitrap mass spectrometer. The fragment ions generated by UVPD
were compared to those from collision induced dissociation (CID) and
higher energy collision dissociation (HCD) with respect to the precursor
charge state. UVPD afforded the widest array of fragment ion types
including acyl chain C–O, C–N, and C–C bond cleavages
and glycosidic C–O and cross ring cleavages, thus providing
the most comprehensive structural analysis of the lipid A. UVPD exhibited
virtually no dependence on precursor ion charge state and was best
at determining lipid A structure including acyl chain length and composition,
giving it an advantage over collision based methods. UVPD was incorporated
into an LC–MS/MS methodology for the analysis of a number of
structural variants in a complex mixture of combinatorially engineered Escherichia coli lipid A.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry, The University of Texas at Austin , 1 University Station A5300, Austin, Texas 78712, United States
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13
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Bláhová L, Adamovský O, Kubala L, Švihálková Šindlerová L, Zounková R, Bláha L. The isolation and characterization of lipopolysaccharides from Microcystis aeruginosa, a prominent toxic water bloom forming cyanobacteria. Toxicon 2013; 76:187-96. [PMID: 24140921 DOI: 10.1016/j.toxicon.2013.10.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/30/2013] [Accepted: 10/08/2013] [Indexed: 02/05/2023]
Abstract
Massive toxic blooms of cyanobacteria represent a major threat to water supplies worldwide, yet serious gaps exist in understanding their complex toxic effects, including the role of lipopolysaccharides (LPS). The present comparative study focused on the levels and biological activities of LPS isolated from Microcystis aeruginosa, which is one of the most globally distributed toxic species. Using hot phenol extraction, LPS was isolated from 3 laboratory cultures and 11 natural water blooms. It formed 0.2-0.7% of the original dry biomass of the cyanobacteria, based on gravimetry. Additional analyses by commercial anti-LPS ELISA were correlated with gravimetry but showed concentrations that were about 7-times lower, which indicated either impurities in isolated LPS or the poor cross-reactivity of the antibodies used. LPS isolates from M. aeruginosa were potent pyrogens in the traditional Limulus amebocyte lysate (LAL)-test, but comparison with the PyroGene test demonstrated the limited selectivity of LAL with several interferences. The determined pyrogenicity (endotoxin units, EU) ranged from very low values in laboratory cultures (less than 0.003 up to 0.008-EU per 100 pg LPS) to higher values in complex bloom samples (0.01-0.078 EU per 100 pg of LPS), which suggested the role of bloom-associated bacteria in the overall effects. Potent pro-inflammatory effects of the studied LPS from both cultures and bloom samples were observed in a highly-relevant ex vivo human blood model by studying reactive oxygen species production in phagocytes as well as increased productions of interleukin 8, IL-8, and tumor necrosis factor α, TNF-α. LPS from M. aeruginosa seem to modulate several pathways involved in the regulation of both innate immunity and specific responses. In comparison to the standard pathogenic bacterial LPS (World Health Organization Escherichia coli O113:10 endotoxin; activity 1 EU per 100 pg), the studied cyanobacterial samples had pyrogenicity potencies that were at least 12-times lower. However, the health risks associated with LPS from M. aeruginosa should not be underestimated, especially with respect to diverse biological effects observed ex vivo and in the case of massive blooms in drinking water reservoirs, where the estimated pyrogenicity can reach up to 46,000 EU per mL of water.
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Affiliation(s)
- Lucie Bláhová
- Masaryk University, Faculty of Science, Research Centre for Toxic Compounds in the Environment (RECETOX), Kamenice 753/5, Building A29, CZ62500 Brno, Czech Republic
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14
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Needham BD, Trent MS. Fortifying the barrier: the impact of lipid A remodelling on bacterial pathogenesis. Nat Rev Microbiol 2013; 11:467-81. [PMID: 23748343 PMCID: PMC6913092 DOI: 10.1038/nrmicro3047] [Citation(s) in RCA: 392] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gram-negative bacteria decorate their outermost surface structure, lipopolysaccharide, with elaborate chemical moieties, which effectively disguises them from immune surveillance and protects them from the onslaught of host defences. Many of these changes occur on the lipid A moiety of lipopolysaccharide, a component that is crucial for host recognition of Gram-negative infection. In this Review, we describe the regulatory mechanisms controlling lipid A modification and discuss the impact of modifications on pathogenesis, bacterial physiology and bacterial interactions with the host immune system.
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Affiliation(s)
- Brittany D Needham
- The Institute of Cellular and Molecular Biology, The University of Texas at Austin, 78712, USA
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