The structure of the core region of the lipopolysaccharide from Shewanella algae BrY, containing 8-amino-3,8-dideoxy-D-manno-oct-2-ulosonic acid

Structural Elucidation of a Novel Lipooligosaccharide from the Antarctic Bacterium OMVs Producer Shewanella sp. HM13

Shewanella sp. HM13 is a cold-adapted Gram-negative bacterium isolated from the intestine of a horse mackerel. It produces a large amount of outer membrane vesicles (OMVs), which are particles released in the medium where the bacterium is cultured. This strain biosynthesizes a single major cargo protein in the OMVs, a fact that makes Shewanella sp. HM13 a good candidate for the production of extracellular recombinant proteins. Therefore, the structural characterization of the components of the vesicles, such as lipopolysaccharides, takes on a fundamental role for understanding the mechanism of biogenesis of the OMVs and their applications. The aim of this study was to investigate the structure of the oligosaccharide (OS) isolated from Shewanella sp. HM13 cells as the first step for a comparison with that from the vesicles. The lipooligosaccharide (LOS) was isolated from dry cells, purified, and hydrolyzed by alkaline treatment. The obtained OS was analyzed completely, and the composition of fatty acids was obtained by chemical methods. In particular, the OS was investigated in detail by ¹H and 13C NMR spectroscopy and MALDI-TOF mass spectrometry. The oligosaccharide was characterized by the presence of a residue of 8-amino-3,8-dideoxy-manno-oct-2-ulosonic acid (Kdo8N) and of a d,d-heptose, with both residues being identified in other oligosaccharides from Shewanella species.

Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid

8-Amino-3,8-dideoxy-d-manno-octulosonic acid (Kdo8N) is a unique amino sugar that has thus far only been observed on the lipopolysaccharides of marine bacteria belonging to the genus Shewanella. Although its biological function is still unclear, it is thought that the sugar is important for the integrity of the bacterial cell outer membrane. A three-gene cluster required for the biosynthesis of Kdo8N was first identified in Shewanella oneidensis. Here we describe the three-dimensional structures of two of the enzymes required for Kdo8N biosynthesis in S. oneidensis, namely, KdnB and KdnA. The structure of KdnB was solved to 1.85-Å resolution, and its overall three-dimensional architecture places it into the Group III alcohol dehydrogenase superfamily. A previous study suggested that KdnB did not require NAD(P) for activity. Strikingly, although the protein was crystallized in the absence of any cofactors, the electron density map clearly revealed the presence of a tightly bound NAD(H). In addition, a bound metal was observed, which was shown via X-ray fluorescence to be a zinc ion. Unlike other members of the Group III alcohol dehydrogenases, the dinucleotide cofactor in KdnB is tightly bound and cannot be removed without leading to protein precipitation. With respect to KdnA, it is a pyridoxal 5'-phosphate or (PLP)-dependent aminotransferase. For this analysis, the structure of KdnA, trapped in the presence of the external aldimine with PLP and glutamate, was determined to 2.15-Å resolution. The model of KdnA represents the first structure of a sugar aminotransferase that functions on an 8-oxo sugar. Taken together the results reported herein provide new molecular insight into the biosynthesis of Kdo8N.

Gram-negative marine bacteria: structural features of lipopolysaccharides and their relevance for economically important diseases

Gram-negative marine bacteria can thrive in harsh oceanic conditions, partly because of the structural diversity of the cell wall and its components, particularly lipopolysaccharide (LPS). LPS is composed of three main parts, an O-antigen, lipid A, and a core region, all of which display immense structural variations among different bacterial species. These components not only provide cell integrity but also elicit an immune response in the host, which ranges from other marine organisms to humans. Toll-like receptor 4 and its homologs are the dedicated receptors that detect LPS and trigger the immune system to respond, often causing a wide variety of inflammatory diseases and even death. This review describes the structural organization of selected LPSes and their association with economically important diseases in marine organisms. In addition, the potential therapeutic use of LPS as an immune adjuvant in different diseases is highlighted.

The sugar 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) as a characteristic component of bacterial endotoxin — a review of its biosynthesis, function, and placement in the lipopolysaccharide core

The sugar 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) is a characteristic component of bacterial lipopolysaccharide (LPS, endotoxin). It connects the carbohydrate part of LPS with C6 of glucosamine or 2,3-diaminoglucose of lipid A by acid-labile α-ketosidic linkage. The number of Kdo units present in LPS, the way they are connected, and the occurrence of other substituents (P, PEtn, PPEtn, Gal, or β-l-Ara4N) account for structural diversity of the inner core region of endotoxin. In a majority of cases, Kdo is crucial to the viability and growth of bacterial cells. In this paper, the biosynthesis of Kdo and the mechanism of its incorporation into the LPS structure, as well as the location of this unique component in the endotoxin core structures, have been described.

The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the lipopolysaccharide of Shewanella oneidensis

Lipopolysaccharide (LPS; endotoxin) is an essential component of the outer monolayer of nearly all Gram-negative bacteria. LPS is composed of a hydrophobic anchor, known as lipid A, an inner core oligosaccharide, and a repeating O-antigen polysaccharide. In nearly all species, the first sugar bridging the hydrophobic lipid A and the polysaccharide domain is 3-deoxy-d-manno-octulosonic acid (Kdo), and thus it is critically important for LPS biosynthesis. Modifications to lipid A have been shown to be important for resistance to antimicrobial peptides as well as modulating recognition by the mammalian innate immune system. Therefore, lipid A derivatives have been used for development of vaccine strains and vaccine adjuvants. One derivative that has yet to be studied is 8-amino-3,8-dideoxy-d-manno-octulosonic acid (Kdo8N), which is found exclusively in marine bacteria of the genus Shewanella. Using bioinformatics, a candidate gene cluster for Kdo8N biosynthesis was identified in Shewanella oneidensis. Expression of these genes recombinantly in Escherichia coli resulted in lipid A containing Kdo8N, and in vitro assays confirmed their proposed enzymatic function. Both the in vivo and in vitro data were consistent with direct conversion of Kdo to Kdo8N prior to its incorporation into the Kdo8N-lipid A domain of LPS by a metal-dependent oxidase followed by a glutamate-dependent aminotransferase. To our knowledge, this oxidase is the first enzyme shown to oxidize an alcohol using a metal and molecular oxygen, not NAD(P)(+). Creation of an S. oneidensis in-frame deletion strain showed increased sensitivity to the cationic antimicrobial peptide polymyxin as well as bile salts, suggesting a role in outer membrane integrity.

The structural diversity of carbohydrate antigens of selected gram-negative marine bacteria

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.

Structural analysis of lipopolysaccharides from Gram-negative bacteria

This review covers data on composition and structure of lipid A, core, and O-polysaccharide of the known lipopolysaccharides from Gram-negative bacteria. The relationship between the structure and biological activity of lipid A is discussed. The data on roles of core and O-polysaccharide in biological activities of lipopolysaccharides are presented. The structural homology of some oligosaccharide sequences of lipopolysaccharides to gangliosides of human cell membranes is considered.

The structure of the carbohydrate backbone of the lipooligosaccharide from the halophilic bacterium Arcobacter halophilus

A novel oligosaccharide was isolated and identified from the lipooligosaccharide fraction of the halophilic marine bacterium Arcobacter halophilus. The complete structure was achieved by chemical analysis, 2D NMR spectroscopy, and MALDI mass spectrometry as the following: alpha-Glc-(1-->7)-alpha-Hep-(1-->5)-alpha-Kdo4P-(2-->6)-beta-GlcN4P-(1-->6)-alpha-GlcN1P.

The diversity of the core oligosaccharide in lipopolysaccharides

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.

The structure of the carbohydrate backbone of the LPS from Shewanella spp. MR-4

The rough type lipopolysaccharide isolated from Shewanella spp. strain MR-4 was analyzed using NMR, mass spectroscopy, and chemical methods. Two structural variants have been found, both contained 8-amino-3,8-dideoxy-d-manno-octulosonic acid and lacked L-glycero-D-manno-heptose. A minor variant of the LPS contained phosphoramide substituent.

The surface physicochemistry and adhesiveness of Shewanella are affected by their surface polysaccharides

Shewanella strains have previously been studied with regard to their cell surface ultrastructure and LPS composition. They have now been further characterized with respect to their surface physicochemistry and ability to adhere to haematite. The surfaces of the Shewanella strains were found to be electronegative and hydrophilic, and these properties could be correlated with LPS composition or the presence of capsular polysaccharides. Strains expressing rough LPS with no capsule were more hydrophobic and electronegative than those possessing smooth LPS or capsules. By combining different approaches, such as contact-angle measurement, hydrophilic/hydrophobic chromatography, microelectrophoresis, adhesion assays and calculation of interaction energies, it was shown that electrostatic interactions predominate over hydrophobic interactions at the cell-iron oxide interface. Bacterial adhesion to haematite was significantly reduced in strains expressing smooth LPS or a capsule. These findings remained true for Shewanella strains grown under either aerobic or anaerobic conditions, although the surfaces of anaerobic cells appeared to be less electronegative and more hydrophilic than those of aerobic cells.

Absolute configuration of 8-Amino-3,8-dideoxyoct-2-ulosonic acid, the chemical hallmark of lipopolysaccharides of the genus Shewanella

The novel monosaccharide 8-amino-3,8-dideoxyoct-2-ulosonic acid (Kdo8N) was isolated by methanolysis from the lipooligosaccharide of the marine Gram-negative bacterium Shewanella pacifica. After HPLC purification, the absolute configuration was determined by the Mosher ester method and proven to be 4 R,5 R,6 R,7 R. This established the d- manno- configuration of the monosaccharide.

Molecular structure of endotoxins from Gram-negative marine bacteria: an update

Marine bacteria are microrganisms that have adapted, through millions of years, to survival in environments often characterized by one or more extreme physical or chemical parameters, namely pressure, temperature and salinity. The main interest in the research on marine bacteria is due to their ability to produce several biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents. Nonetheless, lipopolysaccharides (LPSs), or their portions, from Gram-negative marine bacteria, have often shown low virulence, and represent potential candidates in the development of drugs to prevent septic shock. Besides, the molecular architecture of such molecules is related to the possibility of thriving in marine habitats, shielding the cell from the disrupting action of natural stress factors. Over the last few years, the depiction of a variety of structures of lipids A, core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been given. In particular, here we will examine the most recently encountered structures for bacteria belonging to the genera Shewanella, Pseudoalteromonas and Alteromonas, of the gamma-Proteobacteria phylum, and to the genera Flavobacterium, Cellulophaga, Arenibacter and Chryseobacterium, of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention will be paid to the chemical features expressed by these structures (characteristic monosaccharides, non-glycidic appendages, phosphate groups), to the typifying traits of LPSs from marine bacteria and to the possible correlation existing between such features and the adaptation, over years, of bacteria to marine environments.

Influence of Lipopolysaccharide on the Surface Proton-Binding Behavior of Shewanella spp

This study investigates the potentiometric properties of several strains of Shewanella spp. and determines whether these properties can be correlated with lipopolysaccharide (LPS) type. The LPS of eight Shewanella strains was characterized using silver-stained sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and their potentiometric properties determined using high-resolution acid-base titrations. Titrations showed that total ligand concentrations (L(T)) ranged from 0.903 +/- 0.007 micromol/mg (S. baltica 63) to 1.387 +/- 0.007 micromol/mg (S. amazonensis SB2B). Smooth strains (possessing O-side chains) exhibited higher mean L(T) values than rough strains (no O-side chain). A Tukey's honestly significantly different (HSD) test revealed, smooth strains exhibited significantly higher L(T) values than rough strains in 69% of comparisons. Comparison of individual pK(a) concentrations revealed that smooth LPS strains of Shewanella were relatively enriched in reactive groups at pK(a) 5, suggesting their LPS O-side chains contained detectable carboxyl groups. Combined pKa spectra from all eight Shewanella strains produced a common trend indicating that the way in which the surface proton-buffering capacity changes with pH is similar for the species studied here.

Lipopolysaccharides fromSerratia marcescens Possess One or Two 4-Amino-4-deoxy-L-arabinopyranose 1-Phosphate Residues in the Lipid A andD-glycero-D-talo-Oct-2-ulopyranosonic Acid in the Inner Core Region

The carbohydrate backbones of the core-lipid A region were characterized from the lipopolysaccharides (LPSs) of Serratia marcescens strains 111R (a rough mutant strain of serotype O29) and IFO 3735 (a smooth strain not serologically characterized but possessing the O-chain structure of serotype O19). The LPSs were degraded either by mild hydrazinolysis (de-O-acylation) and hot 4 M KOH (de-N-acylation), or by hydrolysis in 2 % aqueous acetic acid, or by deamination. Oligosaccharide phosphates were isolated by high-performance anion-exchange chromatography. Through the use of compositional analysis, electrospray ionization Fourier transform mass spectrometry, and 1H and 13C NMR spectroscopy applying various one- and two-dimensional experiments, we identified the structures of the carbohydrate backbones that contained D-glycero-D-talo-oct-2-ulopyranosonic acid and 4-amino-4-deoxy-L-arabinose 1-phosphate residues. We also identified some truncated structures for both strains. All sugars were D-configured pyranoses and alpha-linked, except where stated otherwise.

The structure of the capsular polysaccharide of Shewanella oneidensis strain MR-4

Capsular polysaccharides were extracted from Shewanella oneidensis strain MR-4, grown on two different culture media. The polysaccharides were analyzed using 1H and 13C NMR spectroscopy, and the following structure of the repeating unit was established: [structure: see text] where the residue of 4-amino-4,6-dideoxy-D-glucose (Qui4N) was substituted with different N-acyl groups depending on the growth media. All monosaccharides are present in the pyranose form. In the PS from cells grown on enriched medium (trypticase soy broth, TSB) aerobically it was N-acylated with 3-hydroxy-3-methylbutyrate (60%) or with 3-hydroxybutyrate (40%), whereas in the PS from cells grown on minimal medium (CDM) aerobically it was acylated mostly with 3-hydroxybutyrate (>90%).

Determination of endotoxin by the measurement of the acetylated methyl glycoside derivative of Kdo with gas–liquid chromatography-mass spectrometry

A gas-liquid chromatographic-mass spectrometric (GLC-MS) method was applied to the detection of 3-deoxy-d-manno-2-octulosonic acid (Kdo), a constituent of bacterial lipopolysaccharide (LPS, endotoxin). Samples containing LPS were dried, methanolyzed with 2 M HCl in methanol at 60 degrees C for 1 h and acetylated with acetic anhydride and pyridine (1:1, v/v) solution at 100 degrees C for 30 min, then the products were analyzed by GLC-MS or GLC-MSMS. Four acetylated methylglycoside methyl ester derivatives of Kdo are formed in these conditions, namely one with pyranose ring (Kdo1), two derivatives in the furanose form (Kdo2 and 3) and one derivative of anhydro Kdo (Kdo4), as results from their mass fragmentation patterns. Synthetic Kdo produced mainly Kdo4 derivative, whereas Kdo1 of pyranose ring shape was the predominating derivative formed from LPS. The ion fragment of m/z 375 was selected for the specific detection of this Kdo1 derivative, which might be applied for the endotoxin determination. That approach was used for the analysis of preparations of bacteria, bacteriophages and samples of animal sera. In order to ensure the removal of phosphate substitutions from Kdo, methanolyzed samples can be treated with alkaline phosphatase (2.6 U, pH 9.2, 37 degrees C, 15 min), what was elaborated on Vibrio LPS preparation.

Structural characterization of the carbohydrate backbone of the lipooligosaccharide of the marine bacterium Arenibacter certesii strain KMM 3941T

The structure of the carbohydrate backbone of the lipooligosaccharide (LOS) of the marine bacterium Arenibacter certesii strain KMM 3941(T) has been elucidated. The structure was obtained by means of compositional analysis, matrix-assisted laser desorption/ionization mass spectrometry and complete 1H and 13C and 31P NMR spectroscopy. It shows novel and interesting aspects and is the first description of Arenibacter lipopolysaccharides. Strong and mild alkaline treatments, to fully deacylate and only to O-deacylate the LOS were performed in order to determine the core structure. The core consists of a mixture of species differing by the presence of a non-stoichiometric alpha-d-rhamnose residue. The Kdo unit is substituted at O-5 by alpha-mannose and at O-4 by a alpha-galactosyluronic acid phosphate. The lipid A is constituted by a bis-phosphorylated disaccharide unit composed by a 2,3-diamino-2,3-dideoxy-beta-d-glucopyranose (DAG) residue as non-reducing end and a GlcN as reducing end.

The structure of the phosphorylated carbohydrate backbone of the lipopolysaccharide of the phytopathogen bacterium Pseudomonas tolaasii

A novel core-lipid A backbone oligosaccharide was isolated and identified from the lipopolysaccharide fraction of the mushrooms pathogen bacterium Pseudomonas tolaasii. The oligosaccharide was obtained by alkaline treatment of the lipopolysaccharide fraction. Since the repeating unit of the O-antigen contained one residue of -->4)-alpha-l-GulpNAcAN, the hydrolysis was accompanied by beta-elimination on this residue and following depolymerization, producing a mixture of oligosaccharides. The complete structural elucidation showed the presence of a single core glycoform and was achieved by chemical analysis and by (1)H, (31)P, and (13)C NMR spectroscopy applying various 1D and 2D experiments. [structure: see text]. All sugars are alpha-d-pyranoses, if not stated otherwise. Hep is l-glycero-d-manno-heptose, Kdo is 3-deoxy-d-manno-oct-2-ulosonic acid, P is phosphate. QuiN and DeltaGulNA are present in nonstoichiometric amount.