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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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Pither MD, Andretta E, Rocca G, Balzarini F, Matamoros-Recio A, Colicchio R, Salvatore P, van Kooyk Y, Silipo A, Granucci F, Martin-Santamaria S, Chiodo F, Molinaro A, Di Lorenzo F. Deciphering the Chemical Language of the Immunomodulatory Properties of Veillonella parvula Lipopolysaccharide. Angew Chem Int Ed Engl 2024; 63:e202401541. [PMID: 38393988 DOI: 10.1002/anie.202401541] [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: 01/22/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 02/25/2024]
Abstract
Veillonella parvula, prototypical member of the oral and gut microbiota, is at times commensal yet also potentially pathogenic. The definition of the molecular basis tailoring this contrasting behavior is key for broadening our understanding of the microbiota-driven pathogenic and/or tolerogenic mechanisms that take place within our body. In this study, we focused on the chemistry of the main constituent of the outer membrane of V. parvula, the lipopolysaccharide (LPS). LPS molecules indeed elicit pro-inflammatory and immunomodulatory responses depending on their chemical structures. Herein we report the structural elucidation of the LPS from two strains of V. parvula and show important and unprecedented differences in both the lipid and carbohydrate moieties, including the identification of a novel galactofuranose and mannitol-containing O-antigen repeating unit for one of the two strains. Furthermore, by harnessing computational studies, in vitro human cell models, as well as lectin binding solid-phase assays, we discovered that the two chemically diverse LPS immunologically behave differently and have attempted to identify the molecular determinant(s) governing this phenomenon. Whereas pro-inflammatory potential has been evidenced for the lipid A moiety, by contrast a plausible "immune modulating" action has been proposed for the peculiar O-antigen portion.
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Affiliation(s)
- Molly Dorothy Pither
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia, 4, 80126, Naples, Italy
| | - Emanuela Andretta
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia, 4, 80126, Naples, Italy
| | - Giuseppe Rocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza dell'Ateneo Nuovo, 1, 20126, Milan, Italy
| | - Fabio Balzarini
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1007 MB, Amsterdam, The Netherlands
| | - Alejandra Matamoros-Recio
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas, CIB-CSIC, C/ Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Roberta Colicchio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini, 5, 80131, Naples, Italy
| | - Paola Salvatore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini, 5, 80131, Naples, Italy
| | - Yvette van Kooyk
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1007 MB, Amsterdam, The Netherlands
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia, 4, 80126, Naples, Italy
| | - Francesca Granucci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza dell'Ateneo Nuovo, 1, 20126, Milan, Italy
| | - Sonsoles Martin-Santamaria
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas, CIB-CSIC, C/ Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Fabrizio Chiodo
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1007 MB, Amsterdam, The Netherlands
- Institute of Biomolecular Chemistry, National Research Council (CNR), Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia, 4, 80126, Naples, Italy
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia, 4, 80126, Naples, Italy
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Di Lorenzo F, Paparo L, Pisapia L, Oglio F, Pither MD, Cirella R, Nocerino R, Carucci L, Silipo A, de Filippis F, Ercolini D, Molinaro A, Berni Canani R. The chemistry of gut microbiome-derived lipopolysaccharides impacts on the occurrence of food allergy in the pediatric age. Front Mol Biosci 2023; 10:1266293. [PMID: 37900913 PMCID: PMC10606559 DOI: 10.3389/fmolb.2023.1266293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction: Food allergy (FA) in children is a major health concern. A better definition of the pathogenesis of the disease could facilitate effective preventive and therapeutic measures. Gut microbiome alterations could modulate the occurrence of FA, although the mechanisms involved in this phenomenon are poorly characterized. Gut bacteria release signaling byproducts from their cell wall, such as lipopolysaccharides (LPSs), which can act locally and systemically, modulating the immune system function. Methods: In the current study gut microbiome-derived LPS isolated from fecal samples of FA and healthy children was chemically characterized providing insights into the carbohydrate and lipid composition as well as into the LPS macromolecular nature. In addition, by means of a chemical/MALDI-TOF MS and MS/MS approach we elucidated the gut microbiome-derived lipid A mass spectral profile directly on fecal samples. Finally, we evaluated the pro-allergic and pro-tolerogenic potential of these fecal LPS and lipid A by harnessing peripheral blood mononuclear cells from healthy donors. Results: By analyzing fecal samples, we have identified different gut microbiome-derived LPS chemical features comparing FA children and healthy controls. We also have provided evidence on a different immunoregulatory action elicited by LPS on peripheral blood mononuclear cells collected from healthy donors suggesting that LPS from healthy individuals could be able to protect against the occurrence of FA, while LPS from children affected by FA could promote the allergic response. Discussion: Altogether these data highlight the relevance of gut microbiome-derived LPSs as potential biomarkers for FA and as a target of intervention to limit the disease burden.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences, University Federico II, Naples, Italy
- Task Force on Microbiome Studies, University Federico II, Naples, Italy
| | - Lorella Paparo
- Department of Translational Medical Science, University Federico II, Naples, Italy
- ImmunoNutritionLab at CEINGE Biotechnologies Research Center, University Federico II, Naples, Italy
- European Laboratory for Investigation of Food Induced Diseases, University Federico II, Naples, Italy
| | - Laura Pisapia
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Franca Oglio
- Department of Translational Medical Science, University Federico II, Naples, Italy
- ImmunoNutritionLab at CEINGE Biotechnologies Research Center, University Federico II, Naples, Italy
| | | | - Roberta Cirella
- Department of Chemical Sciences, University Federico II, Naples, Italy
| | - Rita Nocerino
- Department of Translational Medical Science, University Federico II, Naples, Italy
- ImmunoNutritionLab at CEINGE Biotechnologies Research Center, University Federico II, Naples, Italy
| | - Laura Carucci
- Department of Translational Medical Science, University Federico II, Naples, Italy
- ImmunoNutritionLab at CEINGE Biotechnologies Research Center, University Federico II, Naples, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University Federico II, Naples, Italy
- Task Force on Microbiome Studies, University Federico II, Naples, Italy
| | - Francesca de Filippis
- Task Force on Microbiome Studies, University Federico II, Naples, Italy
- Department of Agriculture, University Federico II, Naples, Italy
| | - Danilo Ercolini
- Task Force on Microbiome Studies, University Federico II, Naples, Italy
- Department of Agriculture, University Federico II, Naples, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University Federico II, Naples, Italy
- Task Force on Microbiome Studies, University Federico II, Naples, Italy
- Department of Chemistry, School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Roberto Berni Canani
- Task Force on Microbiome Studies, University Federico II, Naples, Italy
- Department of Translational Medical Science, University Federico II, Naples, Italy
- ImmunoNutritionLab at CEINGE Biotechnologies Research Center, University Federico II, Naples, Italy
- European Laboratory for Investigation of Food Induced Diseases, University Federico II, Naples, Italy
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Zeiss DR, Molinaro A, Steenkamp PA, Silipo A, Piater LA, Di Lorenzo F, Dubery IA. Lipopolysaccharides from Ralstonia solanacearum induce a broad metabolomic response in Solanum lycopersicum. Front Mol Biosci 2023; 10:1232233. [PMID: 37635940 PMCID: PMC10450222 DOI: 10.3389/fmolb.2023.1232233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/06/2023] [Indexed: 08/29/2023] Open
Abstract
Ralstonia solanacearum, one of the most destructive crop pathogens worldwide, causes bacterial wilt disease in a wide range of host plants. The major component of the outer membrane of Gram-negative bacteria, lipopolysaccharides (LPS), has been shown to function as elicitors of plant defense leading to the activation of signaling and defense pathways in several plant species. LPS from a R. solanacearum strain virulent on tomato (LPSR. sol.), were purified, chemically characterized, and structurally elucidated. The lipid A moiety consisted of tetra- to hexa-acylated bis-phosphorylated disaccharide backbone, also decorated by aminoarabinose residues in minor species, while the O-polysaccharide chain consisted of either linear tetrasaccharide or branched pentasaccharide repeating units containing α-L-rhamnose, N-acetyl-β-D-glucosamine, and β-L-xylose. These properties might be associated with the evasion of host surveillance, aiding the establishment of the infection. Using untargeted metabolomics, the effect of LPSR. sol. elicitation on the metabolome of Solanum lycopersicum leaves was investigated across three incubation time intervals with the application of UHPLC-MS for metabolic profiling. The results revealed the production of oxylipins, e.g., trihydroxy octadecenoic acid and trihydroxy octadecadienoic acid, as well as several hydroxycinnamic acid amide derivatives, e.g., coumaroyl tyramine and feruloyl tyramine, as phytochemicals that exhibit a positive correlation to LPSR. sol. treatment. Although the chemical properties of these metabolite classes have been studied, the functional roles of these compounds have not been fully elucidated. Overall, the results suggest that the features of the LPSR. sol. chemotype aid in limiting or attenuating the full deployment of small molecular host defenses and contribute to the understanding of the perturbation and reprogramming of host metabolism during biotic immune responses.
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Affiliation(s)
- Dylan R. Zeiss
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Sant’Angelo, Naples, Italy
- Task Force on Microbiome Studies, University of Napoli Federico II, Complesso Universitario Monte Sant’Angelo, Naples, Italy
| | - Paul A. Steenkamp
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Alba Silipo
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Sant’Angelo, Naples, Italy
- Task Force on Microbiome Studies, University of Napoli Federico II, Complesso Universitario Monte Sant’Angelo, Naples, Italy
| | - Lizelle A. Piater
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Sant’Angelo, Naples, Italy
- Task Force on Microbiome Studies, University of Napoli Federico II, Complesso Universitario Monte Sant’Angelo, Naples, Italy
| | - Ian A. Dubery
- Research Centre for Plant Metabolomics, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
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Pither MD, Silipo A, Molinaro A, Di Lorenzo F. Extraction, Purification, and Chemical Degradation of LPS from Gut Microbiota Strains. Methods Mol Biol 2023; 2613:153-179. [PMID: 36587078 DOI: 10.1007/978-1-0716-2910-9_13] [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: 01/02/2023]
Abstract
It is estimated that more than 500 different bacterial species colonize the human gut, and they are collectively known as the gut microbiota. Such a massive bacterial presence is now considered an additional organ of the human body, thus becoming the object of an intense and daily growing research activity. Gram-negative bacteria represent a large percentage of the gut microbiota strains. The main constituent of the outer membrane of Gram-negatives is the lipopolysaccharide (LPS). Since its first discovery, LPS has been extensively studied for its structure-dependent capability to elicit a potent immune inflammatory reaction when perceived by specific immune receptors present in our body. Therefore, traditionally, LPS, due to its peculiar chemistry, has been associated with pathogenic bacteria, and it has been extensively studied for its dangerous effects on human health. However, LPS is also expressed on the cell surface of harmless and beneficial bacteria that colonize our intestines. This necessarily implies that the LPS from harmless gut microbes is "chemically different" from that owned by pathogenic ones, hence enabling successful colonization of the intestinal tract without creating a threat to the host immune system. Deciphering the structural features of LPS from these gut bacteria is essential to improve our still scarce knowledge of how the human host lives in a harmonious relationship with its own microbiota. To this end, LPS extraction and purification are essential steps in this field of research. Yet working with gut bacteria is extremely complex for a number of reasons, one being related to the fact that they produce an array of other glycans and glycoconjugates, such as capsular polysaccharides and/or exopolysaccharides, which render the isolation and characterization of the sole LPS not at all trivial. Here, we provide a protocol that might help when dealing with LPS from gut microbial species. We describe the preliminary manipulations and checks, extraction, and purification approaches, as well as the necessary chemical manipulations that should be performed to enable the characterization of the structure of an LPS by means of techniques like nuclear magnetic resonance spectroscopy and mass spectrometry.
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Affiliation(s)
- Molly Dorothy Pither
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples, Italy.
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