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Kokoulin MS, Dmitrenok PS, Romanenko LA. Structure of the Lipooligosaccharide from the Deep-Sea Marine Bacterium Idiomarina zobellii KMM 231 T, Isolated at a Depth of 4000 Meters. Mar Drugs 2022; 20:700. [PMID: 36355023 PMCID: PMC9695755 DOI: 10.3390/md20110700] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/06/2022] [Accepted: 11/06/2022] [Indexed: 05/31/2024] Open
Abstract
The structural characterization of lipopolysaccharides has critical implications for some biomedical applications, and marine bacteria are an inimitable source of new glyco-structures potentially usable in medicinal chemistry. On the other hand, lipopolysaccharides of marine Gram-negative bacteria present certain structural features that can help the understanding of the adaptation processes. The deep-sea marine Gram-negative bacterium Idiomarina zobellii KMM 231T, isolated from a seawater sample taken at a depth of 4000 m, represents an engaging microorganism to investigate in terms of its cell wall components. Here, we report the structural study of the R-type lipopolysaccharide isolated from I. zobellii KMM 231T that was achieved through a multidisciplinary approach comprising chemical analyses, NMR spectroscopy, and MALDI mass spectrometry. The lipooligosaccharide turned out to be characterized by a novel and unique pentasaccharide skeleton containing a very short mono-phosphorylated core region and comprising terminal neuraminic acid. The lipid A was revealed to be composed of a classical disaccharide backbone decorated by two phosphate groups and acylated by i13:0(3-OH) in amide linkage, i11:0 (3-OH) as primary ester-linked fatty acids, and i11:0 as a secondary acyl chain.
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Affiliation(s)
- Maxim S. Kokoulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159/2, Prospect 100 let Vladivostoku, Vladivostok 690022, Russia
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Di Lorenzo F, Duda KA, Lanzetta R, Silipo A, De Castro C, Molinaro A. A Journey from Structure to Function of Bacterial Lipopolysaccharides. Chem Rev 2021; 122:15767-15821. [PMID: 34286971 DOI: 10.1021/acs.chemrev.0c01321] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Lipopolysaccharide (LPS) is a crucial constituent of the outer membrane of most Gram-negative bacteria, playing a fundamental role in the protection of bacteria from environmental stress factors, in drug resistance, in pathogenesis, and in symbiosis. During the last decades, LPS has been thoroughly dissected, and massive information on this fascinating biomolecule is now available. In this Review, we will give the reader a third millennium update of the current knowledge of LPS with key information on the inherent peculiar carbohydrate chemistry due to often puzzling sugar residues that are uniquely found on it. Then, we will drive the reader through the complex and multifarious immunological outcomes that any given LPS can raise, which is strictly dependent on its chemical structure. Further, we will argue about issues that still remain unresolved and that would represent the immediate future of LPS research. It is critical to address these points to complete our notions on LPS chemistry, functions, and roles, in turn leading to innovative ways to manipulate the processes involving such a still controversial and intriguing biomolecule.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Katarzyna A Duda
- Research Center Borstel Leibniz Lung Center, Parkallee 4a, 23845 Borstel, Germany
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Cristina De Castro
- Task Force on Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.,Department of Agricultural Sciences, University of Naples Federico II, Via Università 96, 80055 Portici, Naples, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy.,Department of Chemistry, School of Science, Osaka University, 1-1 Osaka University Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Petit D, Teppa E, Cenci U, Ball S, Harduin-Lepers A. Reconstruction of the sialylation pathway in the ancestor of eukaryotes. Sci Rep 2018; 8:2946. [PMID: 29440651 PMCID: PMC5811610 DOI: 10.1038/s41598-018-20920-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/25/2018] [Indexed: 11/18/2022] Open
Abstract
The biosynthesis of sialylated molecules of crucial relevance for eukaryotic cell life is achieved by sialyltransferases (ST) of the CAZy family GT29. These enzymes are widespread in the Deuterostoma lineages and more rarely described in Protostoma, Viridiplantae and various protist lineages raising the question of their presence in the Last eukaryotes Common Ancestor (LECA). If so, it is expected that the main enzymes associated with sialic acids metabolism are also present in protists. We conducted phylogenomic and protein sequence analyses to gain insights into the origin and ancient evolution of ST and sialic acid pathway in eukaryotes, Bacteria and Archaea. Our study uncovered the unreported occurrence of bacterial GT29 ST and evidenced the existence of 2 ST groups in the LECA, likely originating from the endosymbiotic event that generated mitochondria. Furthermore, distribution of the major actors of the sialic acid pathway in the different eukaryotic phyla indicated that these were already present in the LECA, which could also access to this essential monosaccharide either endogenously or via a sialin/sialidase uptake mechanism involving vesicles. This pathway was lost in several basal eukaryotic lineages including Archaeplastida despite the presence of two different ST groups likely assigned to other functions.
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Affiliation(s)
- Daniel Petit
- Université de Limoges, Laboratoire Pereine 123, av. A. Thomas, 87060, Limoges Cedex, France
| | - Elin Teppa
- Bioinformatics Unit, Fundación Instituto Leloir -IIBBA CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Ugo Cenci
- University of Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F 59000, Lille, France
- UGSF, Bât. C9, Université de Lille - Sciences et Technologies, 59655, Villeneuve d'Ascq, France
| | - Steven Ball
- University of Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F 59000, Lille, France
- UGSF, Bât. C9, Université de Lille - Sciences et Technologies, 59655, Villeneuve d'Ascq, France
| | - Anne Harduin-Lepers
- University of Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F 59000, Lille, France.
- UGSF, Bât. C9, Université de Lille - Sciences et Technologies, 59655, Villeneuve d'Ascq, France.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010. MASS SPECTROMETRY REVIEWS 2015; 34:268-422. [PMID: 24863367 PMCID: PMC7168572 DOI: 10.1002/mas.21411] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 05/07/2023]
Abstract
This review is the sixth 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 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis.
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Affiliation(s)
- David J. Harvey
- Department of BiochemistryOxford Glycobiology InstituteUniversity of OxfordOxfordOX1 3QUUK
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Di Lorenzo F, De Castro C, Lanzetta R, Parrilli M, Silipo A, Molinaro A. Lipopolysaccharides as Microbe-associated Molecular Patterns: A Structural Perspective. CARBOHYDRATES IN DRUG DESIGN AND DISCOVERY 2015. [DOI: 10.1039/9781849739993-00038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The lipopolysaccharide (LPS) macromolecule is the major constituent of the external leaflet of the Gram-negative outer membrane, exerting a plethora of biological activities in animals and plants. Among all, it represents a defensive barrier which helps bacteria to resist antimicrobial compounds and external stress factors and is involved in most aspects of host–bacterium interactions such as recognition, adhesion and colonization. One of the most interesting and studied LPS features is its key role in the pathogenesis of Gram-negative infections potentially causing fever or circulatory shock. On the other hand, the LPS acts as a beneficial factor for the host since it is recognized by specific receptors of the host innate immune system; this recognition activates the host defenses culminating, in most cases, in destruction of the pathogen. Most of the biological roles of the LPS are strictly related to its primary structure; thus knowledge of the structural architecture of such a macromolecule, which is different even among bacterial strains belonging to the same species, is a first step but is essential in order to understand the molecular bases of the wide variety of biological activities exerted by LPSs.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Michelangelo Parrilli
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II Via Cinthia 4 80126 Naples Italy
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Kokoulin MS, Kalinovsky AI, Komandrova NA, Tovarchi VE, Tomshich SV, Nedashkovskaya OI, Vaskovsky VE. The structure of the O-specific polysaccharide from marine bacterium Litorimonas taeanensis G5T containing 2-acetamido-4-((3S,5S)-3,5-dihydroxyhexanamido)-2,4-dideoxy-d-quinovose and 2-acetamido-2,6-dideoxy-l-xylo-hexos-4-ulose. Carbohydr Res 2013; 375:105-11. [DOI: 10.1016/j.carres.2013.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
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Nazarenko EL, Crawford RJ, Ivanova EP. The structural diversity of carbohydrate antigens of selected gram-negative marine bacteria. Mar Drugs 2011; 9:1914-1954. [PMID: 22073003 PMCID: PMC3210612 DOI: 10.3390/md9101914] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/07/2011] [Accepted: 09/13/2011] [Indexed: 11/16/2022] Open
Abstract
Marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. Marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. Among these biologically active molecules, the carbohydrate antigens, lipopolysaccharides (LPSs, O-antigens) found in cell walls of gram-negative marine bacteria, show great potential as candidates in the development of drugs to prevent septic shock due to their low virulence. The structural diversity of LPSs is thought to be a reflection of the ability for these bacteria to adapt to an array of habitats, protecting the cell from being compromised by exposure to harsh environmental stress factors. Over the last few years, the variety of structures of core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been discovered. In this review, we discuss the most recently encountered structures that have been identified from bacteria belonging to the genera Aeromonas, Alteromonas, Idiomarina, Microbulbifer, Pseudoalteromonas, Plesiomonas and Shewanella of the Gammaproteobacteria phylum; Sulfitobacter and Loktanella of the Alphaproteobactera phylum and to the genera Arenibacter, Cellulophaga, Chryseobacterium, Flavobacterium, Flexibacter of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention is paid to the particular chemical features of the LPSs, such as the monosaccharide type, non-sugar substituents and phosphate groups, together with some of the typifying traits of LPSs obtained from marine bacteria. A possible correlation is then made between such features and the environmental adaptations undertaken by marine bacteria.
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Affiliation(s)
- Evgeny L. Nazarenko
- Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia; E-Mail:
| | - Russell J. Crawford
- Faculty of Life and Social Sciences, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia; E-Mail:
| | - Elena P. Ivanova
- Faculty of Life and Social Sciences, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia; E-Mail:
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Abstract
Bacterial lipopolysaccharides (LPSs) are the major component of the outer membrane of Gram-negative bacteria. They have a structural role since they contribute to the cellular rigidity by increasing the strength of cell wall and mediating contacts with the external environment that can induce structural changes to allow life in different conditions. Furthermore, the low permeability of the outer membrane acts as a barrier to protect bacteria from host-derived antimicrobial compounds. Lipopolysaccharides are amphiphilic macromolecules generally comprising three defined regions distinguished by their genetics, structures and function: the lipid A, the core oligosaccharide and a polysaccharide portion, the O-chain. In some Gram-negative bacteria LPS can terminate with the core portion to form rough type LPS (R-LPS, LOS). The core oligosaccharide is an often branched and phosphorylated heterooligosaccharide with less than fifteen sugars, more conserved in the inner region, proximal to the lipid A, and often carrying non-stoichiometric substitutions leading to variation and micro-heterogeneity. The core oligosaccharide contributes to the bacterial viability and stability of the outer membrane, can assure the serological specificity and possesses antigenic properties.
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