Found 122 structures.
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1. Compound ID: 175
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b-D-Galp-(1-2)-L-gro-a-D-manHepp-(1-3)-+ P-4)-+
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b-D-Quip3NAc-(1-3)-b-D-GalpNAc-(1-4)-b-D-Glcp-(1-4)-L-gro-a-D-manHepp-(1-5)-Kdop-(2--/lipid A/
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b-D-GlcpA-(1-2)-+ |
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Structure type: oligomer
Aglycon: lipid A
Compound class: LPS
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_130650,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_137777,IEDB_140087,IEDB_140088,IEDB_140090,IEDB_140630,IEDB_141794,IEDB_142488,IEDB_146664,IEDB_190606,IEDB_2189047,IEDB_423153,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 37
Caroff M, Karibian D "Structure of bacterial lipopolysaccharides" -
Carbohydrate Research 338(23) (2003) 2431-2447
Bacterial lipopolysaccharides are the major components of the outer surface of Gram-negative bacteria They are often of interest in medicine for their immunomodulatory properties. In small amounts they can be beneficial, but in larger amounts they may cause endotoxic shock. Although they share a common architecture, their structural details exert a strong influence on their activity. These molecules comprise: a lipid moiety, called lipid A, which is considered to be the endotoxic component, a glycosidic part consisting of a core of approximately 10 monosaccharides and, in 'smooth-type' lipopolysaccharides, a third region, named O-chain, consisting of repetitive subunits of one to eight monosaccharides responsible for much of the immunospecificity of the bacterial cell.
Lipopolysaccharide, structure, core, lipid A, endotoxin, O-chains
NCBI PubMed ID: 14670707Publication DOI: 10.1016/j.carres.2003.07.010Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: martine.carloff@bbmpc.u-psud.fr
Institutions: Equipe Endotoxines, UMR 8619 du Centre National de la Recherche Scientifique, IBBMC, Université de Paris-Sud, F-Orsay, France
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2. Compound ID: 405
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R-3HOBut-(1-6)-+ a-L-Fucp-(1-2)-+
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-3)-a-D-FucpNAc4N-(1-2)-a-D-Hepp-(1-3)-b-D-ManpNAc-(1-4)-b-D-Quip3NAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_136045,IEDB_142345,IEDB_142489,IEDB_144562,IEDB_152214,IEDB_174333,IEDB_885813,SB_86
The structure is contained in the following publication(s):
- Article ID: 135
Tzianabos A, Wang JY, Kasper DL "Biological chemistry of immunomodulation by zwitterionic polysaccharides" -
Carbohydrate Research 338(23) (2003) 2531-2538
Capsular polysaccharides isolated from pathogenic bacteria are comprised typically of many repeating units from one to eight or more monosaccharides in length. These polysaccharides stimulate the murine humoral immune system to elicit primarily IgM antibody responses. Studies conducted primarily in the mouse have characterized these polymers as T cell-independent antigens. These mouse studies and the relatively poor immunogenicity of polysaccharides in human hosts have led to the design of vaccines by coupling these polysaccharides to protein carriers to stimulate a T cell-dependent response. However, a newly described class of bacterial polysaccharides has been characterized that have the ability to modulate the cellular immune system. They are structurally diverse, but all share a zwitterionic charge motif that allows them to directly interact with T cells and antigen-presenting cells to initiate an immunomodulatory T cell response. These polymers, termed zwitterionic polysaccharides (ZPSs), elicit T cell-derived chemokines and cytokines that influence the immune response governing at least one classic host response to bacterial infection: abscess formation. This review will describe the biological and structural aspects of ZPSs that convey these activities.
T cell, polysaccharides, structure/function
NCBI PubMed ID: 14670714Publication DOI: 10.1016/j.carres.2003.06.005Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: atzianabos@channing.harvard.edu
Institutions: Department of Medicine, Channing Laboratory, 181 Longwood Ave., Brigham and Women's Hospital, Boston, MA 02115, USA
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3. Compound ID: 425
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Subst-(1-3)-b-D-Quip3N-(1-3)-a-L-Rhap4Me-(1-3)-a-L-Rhap-(1-3)-a-L-Rhap-(1-2)-a-L-6dTalp-(1--/p-trifluoroacetamidophenyl/
Subst = 3-hydroxy-2-methylbutanoic acid = SMILES CC(O)C(C){1}C(O)=O |
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Structure type: oligomer
Aglycon: p-trifluoroacetamidophenyl
Trivial name: pentasaccharide hapten
Contained glycoepitopes: IEDB_136098,IEDB_136105,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 155
Varga Z, Bajza I, Batta G, Lipták A "Synthesis of the pentasaccharide hapten from the glycopeptidolipid antigen of Mycobacterium avium serovar 17" -
Tetrahedron Letters 42(31) (2001) 5283-5286
Effective synthesis of the pentasaccharide hapten from the glycopeptidolipid antigen of Mycobacterium avium serovar 17 in a p-aminophenyl linker-containing form, using 3+2 block synthesis strategy, is described. A 2+3 block synthesis could not be achieved, although different glycosyl donors (1-Br, 1-SPh, 1-O-C(NH)CCl3) were used.
synthesis, antigen, oligosaccharide, Mycobacterium, block synthesis, glycopeptidolipid, hapten, linker, M.avium serovar 17, Mycobacteria, Mycobacterium avium, nilic acid, pentasaccharide
Journal NLM ID: 2984819RPublisher: Elsevier
Institutions: Department of Biochemistry, University of Debrecen, PO Box 55, Debrecen H- 4010, Hungary, Research Group for Carbohydrates of the Hungarian Academy of Sciences, PO Box 55, Debrecen H- 4010, Hungary, Research Group for Antibiotics of the Hungarian Academy of Sciences, PO Box 70, Debrecen H- 4010, Hungary
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4. Compound ID: 434
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S-3HOBut-(1-4)-+ S-3HOBut-(1-3)-+
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-2)-a-L-Rhap-(1-4)-a-D-GalpNAcA-(1-3)-a-D-QuipNAc4N-(1-2)-b-D-Quip3N-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136105,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 160
Veremeychenko SN, Zdorovenko GM "Peculiarity of the structure of the lipopolysaccharide of Pseudomonas fluorescens IMV 247 (biovar II)" -
Mikrobiologiia = Microbiology [Russian] 69(3) (2000) 362-369
The results of the study of the Pseudomonas fluorescens IMV 247 (biovar II) lipopolysaccharide (LPS) isolated from the dry bacterial mass by Westphal's method and purified by repeated ultracentrifugation are presented. The macromolecular organization of the LPS is characterized by the presence of S and R forms of LPS molecules in a 1:1 ratio. The structural components of the LPS molecule → lipid A, the core oligosaccharide, and the O-specific polysaccharide -- were isolated and characterized. 3-Hydroxydecanoic, 2-hydroxydodecanoic, 3-hydroxydodecanoic, and dodecanoic acids proved to be the main lipid A fatty acids. Glucosamine, phosphoethanolamine, and phosphorus were identified as the components of the lipid A hydrophilic portion. Glucose, galactose, arabinose, rhamnose, glucosamine, alanine, phosphoethanolamine, phosphorus, and 2-keto-3-deoxyoctulonate (KDO) were revealed in the heterogeneous fraction of the core oligosaccharide. The O-specific polysaccharide chain was composed of repeating tetrasaccharide units consisting of L-rhamnose (L-Rha), 3,6-dideoxy-3-[(S)-3-hydroxybutyramido]-D-glucose (D-Qui3NHb), 2-acetamido-2,4,6-trideoxy-4[(S)-3-hydroxybutyramido-D-glucose (D-QuiNAc4NHb), and 2-acetamido-2-deoxy-D-galacturonic acid (D-GalNAcA) residues. A peculiarity of the O-specific polysaccharide was that it released, upon partial acid hydrolysis, the nonreducing disaccharide GalNAcA → QuiNAc4NHb with a 3-hydroxybutyryl group glycosylated intramolecularly with a QuiN4N residue. Double immunodiffusion in agar and lipopolysaccharide precipitation reactions revealed no serological interrelationship between the strain studied and the P. fluorescens strains studied earlier.
Lipopolysaccharide, LPS, structure, strain, characterization, Pseudomonas, fatty acid, O-chain, biovar, Pseudomonas fluorescens
NCBI PubMed ID: 10920806Journal NLM ID: 0376652Publisher: Moskva: Izdatelstvo Nauka
Institutions: Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kiev, Ukraine.
Methods: NMR-2D, NMR
- Article ID: 4329
Knirel YA "Structure of O-antigens" -
Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.
Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis
Publication DOI: 10.1007/978-3-7091-0733-1_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 4335
Kondakova AN, Novototskaya-Vlasova KA, Shashkov AS, Drutskaya MS, Senchenkova SN, Shcherbakova VA, Gilichinsky DA, Nedospasov SA, Knirel YA "Structure of an acidic polysaccharide isolated from Psychrobacter maritimus 3pS containing a bacillosamine derivative" -
Carbohydrate Research 359 (2012) 7-10
An acidic polysaccharide was obtained from Psychrobacter maritimus 3pS isolated from a Siberian cryopeg sample (Kolyma lowland). The following structure of the tetrasaccharide repeating unit of the polysaccharide was established by sugar analysis along with (1)H and (13)C NMR spectroscopy: →2)-α-L-Rhap-(1→4)-α-D-GalpNAcA-(1→3)-α-D-QuipNAc4NHb-(1→3)-β-D-QuipNAc4NHb-(1→ where D-GalNAcA indicates 2-acetamido-2-deoxy-D-galacturonic acid and d-QuiNAc4NHb indicates 2-acetamido-2,4,6-trideoxy-4-[(S)-3-hydroxybutanoyl]amino-D-glucose.
acid, bacterial polysaccharide structure, 2, 4, 4-diamino-2, 2-acetamido-2-deoxy-D-galacturonic acid, Psychrobacter maritimus, 6-trideoxy-D-glucopyranose
NCBI PubMed ID: 22925757Publication DOI: 10.1016/j.carres.2012.07.007Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: annakond@gmail.com
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute for Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, 142290 Pushchino, Russia, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences,142290 Pushchino, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, ESI-MS, GLC, mild acid hydrolysis, DOC-PAGE, Smith degradation, GPC
- Article ID: 6301
Qin CJ, Ding MR, Tian GZ, Zou XP, Fu JJ, Hu J, Yin J "Chemical approaches towards installation of rare functional groups in bacterial surface glycans" -
Chinese Journal of Natural Medicines = Zhongguo Tianran Yaowu 20(6) (2022) 401-420
Bacterial surface glycans perform a diverse and important set of biological roles, and have been widely used in the treatment of bacterial infectious diseases. The majority of bacterial surface glycans are decorated with diverse rare functional groups, including amido, acetamidino, carboxamido and pyruvate groups. These functional groups are thought to be important constituents for the biological activities of glycans. Chemical synthesis of glycans bearing these functional groups or their variants is essential for the investigation of structure-activity relationships by a medicinal chemistry approach. To date, a broad choice of synthetic methods is available for targeting the different rare functional groups in bacterial surface glycans. This article reviews the structures of naturally occurring rare functional groups in bacterial surface glycans, and the chemical methods used for installation of these groups.
chemical synthesis, acetamidino group, amido group, bacterial surface glycan, carboxamido group, pyruvyl ketal
NCBI PubMed ID: 35750381Publication DOI: 10.1016/S1875-5364(22)60177-8Journal NLM ID: 101504416Publisher: Beijing: Science Press; Elsevier
Correspondence: J. Yin
Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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5. Compound ID: 1338
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R-3HOBut-(1-6)-+ a-L-Fucp-(1-2)-+
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-2)-D-gro-a-D-manHepp-(1-3)-b-D-ManpNAc-(1-4)-b-D-Quip3NAc-(1-3)-a-D-FucpNAc4N-(1- |
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Structure type: polymer chemical repeating unit
Trivial name: PS A2
Compound class: CPS
Contained glycoepitopes: IEDB_136045,IEDB_142345,IEDB_142489,IEDB_144562,IEDB_152214,IEDB_174333,IEDB_2189046,IEDB_885813,SB_86
The structure is contained in the following publication(s):
- Article ID: 419
Wang Y, Kalka-Moll WM, Roehrl MH, Kasper DL "Structural basis of the abscess-modulating polysaccharide A2 from Bacteroides fragilis" -
Proceedings of the National Academy of Sciences of the USA 97 (2000) 13478-13483
Zwitterionic capsular polysaccharides from pathogenic bacteria have peculiar immunological properties. They are capable of eliciting T-cell proliferation and modulating the course of abscess formation. To understand the molecular basis of this characteristic immune response, we are conducting detailed structure-function studies on these polysaccharides. We have identified, purified, and characterized an abscess-modulating polysaccharide, PS A2, from the clinical strain Bacteroides fragilis 638R. Here, we report the elucidation of both the chemical and three-dimensional structures of PS A2 by NMR spectroscopy, chemical methods, gas chromatography-mass spectrometry, and restrained molecular dynamics calculations. PS A2 consists of a pentasaccharide repeating unit containing mannoheptose, N-acetylmannosamine, 3-acetamido-3,6-dideoxyglucose, 2-amino-4-acetamido-2,4,6-trideoxygalactose, fucose, and 3-hydroxybutanoic acid. PS A2 is zwitterionic and carries one cationic free amine and one anionic carboxylate in each repeating unit. It forms an extended right-handed helix with two repeating units per turn and a pitch of 20 A. Positive and negative charges are exposed on the outer surface of the polymer in a regularly spaced pattern, which renders them easily accessible to other molecules. The helix is characterized by repeated large grooves whose lateral boundaries are occupied by the charges. The three-dimensional structure of PS A2 explicitly suggests mechanisms of interaction between zwitterionic polysaccharides and proteins
polysaccharide, Bacteroides, Bacteroides fragilis
NCBI PubMed ID: 11106392Publication DOI: 10.1073/pnas.97.25.13478Journal NLM ID: 7505876Publisher: National Academy of Sciences
Correspondence: ywang@channing.harvard.edu
Institutions: Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Graduate Program in the Biological and Biomedical Sciences, Division of Medical Sciences, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
Methods: 13C NMR, 1H NMR, GLC-MS, NMR-2D, MD simulations
- Article ID: 5791
Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" -
Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.
polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component
Publication DOI: 10.1016/B978-0-12-819475-1.00005-5Publisher: Elsevier
Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
Editors: Barchi J, Kamerling H
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
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6. Compound ID: 1411
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L-Ala2Ac-(1-3)-+
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-3)-a-D-GalpNAcA-(1-3)-b-D-QuipNAc-(1-4)-b-D-Quip3N-(1- |
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Structure type: polymer chemical repeating unit
Compound class: CPS
The structure is contained in the following publication(s):
- Article ID: 441
Wang Z, Larocque S, Vinogradov E, Brisson JR, Dacanay A, Greenwell M, Brown LL, Li J, Altman E "Structural studies of the capsular polysaccharide and lipopolysaccharide O-antigen of Aeromonas salmonicida strain 80204-1 produced under in vitro and in vivo growth conditions" -
European Journal of Biochemistry 271(22) (2004) 4507-4516
Aeromonas salmonicida is a pathogenic aquatic bacterium and the causal agent of furunculosis in salmon. In the course of this study, it was found that when grown in vitro on tryptic soy agar, A. salmonicida strain 80204-1 produced a capsular polysaccharide with the identical structure to that of the lipopolysaccharide O-chain polysaccharide. A combination of 1D and 2D NMR methods, including a series of 1D analogues of 3D experiments, together with capillary electrophoresis-electrospray MS (CE-ES-MS), compositional and methylation analyses and specific modifications was used to determine the structure of these polysaccharides. Both polymers were shown to be composed of linear trisaccharide repeating units consisting of 2-acetamido-2-deoxy-d-galacturonic acid (GalNAcA), 3-[(N-acetyl-L-alanyl)amido]-3,6-dideoxy-d-glucose{3-[(N-acetyl-l-alanyl)a mido]-3-deoxy-d-quinovose, Qui3NAlaNAc} and 2-acetamido-2,6-dideoxy-d-glucose (2-acetamido-2-deoxy-d-quinovose, QuiNAc) and having the following structure: [→3)-α-D-GalpNAcA-(1→3)-β-D-QuipNAc-(1→4)-β-D-Quip3NAlaNAc -(1-](n), where GalNAcA is partly presented as an amide and AlaNAc represents N-acetyl-l-alanyl group. CE-ES-MS analysis of CPS and O-chain polysaccharide confirmed that 40% of GalNAcA was present in the amide form. Direct CE-ES-MS/MS analysis of in vivo cultured cells confirmed the formation of a novel polysaccharide, a structure also formed in vitro, which was previously undetectable in bacterial cells grown within implants in fish, and in which GalNAcA was fully amidated
Lipopolysaccharide, NMR, capsular polysaccharide, Aeromonas salmonicida
NCBI PubMed ID: 15560791Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: eleonora.altman@nrc-cnrc.gc.ca
Institutions: Institute for Biological Sciences, National Research Council of Canada, Ottawa, Canada, Institute for Marine Biosciences, National Research Council of Canada, Halifax, Canada
Methods: methylation, NMR-2D, NMR, carboxyl reduction, CE-ESI-MS
- Article ID: 4359
Nazarenko EL, Crawford RJ, Ivanova EP "The structural diversity of carbohydrate antigens of selected Gram-negative marine bacteria" -
Marine Drugs 9(10) (2011) 1914-1954
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 Alphaproteobacteria 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.
O-specific polysaccharides, carbohydrate antigens, marine microorganisms
NCBI PubMed ID: 22073003Publication DOI: 10.3390/md9101914Journal NLM ID: 101213729Publisher: Basel, Switzerland: Molecular Diversity Preservation International
Correspondence: elnaz@piboc.dvo.ru
Institutions: Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia, Faculty of Life and Social Sciences, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
Methods: 13C NMR, 1H NMR, methylation, periodate oxidation, NMR-2D, FAB-MS, partial acid hydrolysis, NMR, HF solvolysis, sugar analysis, 31P NMR, ESI-MS, acid hydrolysis, mild acid hydrolysis, HPAEC, ESI-ICR-MS, Smith degradation, chemical methods, MALDI-TOF MS, MS, de-O-acetylation, NMR-1D, GPC, alkaline hydrolysis, CE-ESI-MS, CE-MS, hydrazinolysis
- Article ID: 5791
Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" -
Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.
polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component
Publication DOI: 10.1016/B978-0-12-819475-1.00005-5Publisher: Elsevier
Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
Editors: Barchi J, Kamerling H
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
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7. Compound ID: 1427
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-3)-a-L-FucpNAc-(1-3)-a-D-QuipNAc-(1-3)-a-L-FucpNAc-(1-2)-b-D-Quip3NAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
The structure is contained in the following publication(s):
- Article ID: 449
De Castro C, Molinaro A, Nunziata R, Lanzetta R, Parrilli M, Holst O "Structural determination of the O-specific chain of the lipopolysaccharide from Pseudomonas cichorii" -
European Journal of Organic Chemistry (11) (2002) 1770-1775
The complete structure of the O-specific polysaccharide isolated from the phytopathogenic bacterium Pseudomonas cichorii strain 5707 has been determined by spectroscopic, computational, and chemical techniques. It consists of a linear tetrasaccharide repeating unit as represented in the formula 3)-a-L-Fucp2NAc-(1-3)-a-D-Quip2NAc-(1-3)-a-LFucp2NAc-(1-2)-b-D-Quip3NAc-(1-
NMR spectroscopy, structure elucidation, O-chain, Molecular mechanics, natural products
Publication DOI: 10.1002/1099-0690(200206)Journal NLM ID: 9805750Publisher: Wiley-VCH
Correspondence: decastro@unina.it
Institutions: Instituto de Qumica Organica, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain, Dipartimento di Chimica Organica e Biochimica, Universita Napoli ''Federico II'', Complesso Universitario Monte Angelo, Via Cintia 4, 80126 Napoli, Italy, Dipartimento di Scienze Chimico-Agrarie, Universita' di Napoli ''Federico II'', 80055 Portici, Napoli, Italy, Dipartimento di Biotecnologie Agrarie, Universita' di Firenze, 50144 Firenze, Italy
Methods: methylation, NMR-2D, NMR
- Article ID: 3744
Molinaro A, Newman M, Lanzetta R, Parrilli M "The structures of lipopolysaccharides from plant-associated Gram-negative bacteria" -
European Journal of Organic Chemistry 2009(34) (2009) 5887-5896
Gram-negative bacterial lipopolysaccharides (LPSs) have multiple roles in plant-microbe interactions. LPSs contribute to the low permeabilities of bacterial outer membranes, which act as barriers to protect bacteria from plant-derived antimicrobial substances. Conversely, perception of LPSs by plant cells can lead to the triggering of defence responses or to the priming of the plant to respond more rapidly and/or to a greater degree to subsequent pathogen challenge. LPSs are thus key molecules in the interactions between bacteria and plants, either in symbiosis or pathogenesis. Since LPSs are glycoconjugates genetically and chemically consisting of three different molecular regions, their detailed structure elucidation is a very topical and major scientific task for chemists, and is achieved by a combination of state-of-art chemical and spectroscopic techniques. Knowledge of LPSs' chemical structures is an important prerequisite for any further understanding of the biological processes in plant-microbe interactions. Moreover, the LPSs from Gram-negative bacteria - especially those originating from plant-associated bacteria - are a great source of novel monosaccharides with unusual and occasionally astounding chemical structures, never found in the eukaryotic world. This review presents the structures of LPSs from plant-associated bacteria isolated and identified from 2001 onwards.
lipopolysaccharides, structure elucidation, glycolipids, innate immunity, immunochemistry, plant-associated bacteria
Publication DOI: 10.1002/ejoc.200900682Journal NLM ID: 9805750Publisher: Wiley-VCH
Correspondence: molinaro@unina.it
Institutions: Dipartimento di Chimica Organica e Biochimica, Università degli Studi di Napoli “Federico II”, via Cinthia 4, 80126 Napoli, Italy, Fax: +39-081-674393, Faculty of Life Sciences, Department of Plant Biology & Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark
- Article ID: 4329
Knirel YA "Structure of O-antigens" -
Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.
Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis
Publication DOI: 10.1007/978-3-7091-0733-1_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
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8. Compound ID: 1449
|
-4)-b-D-Quip3NAc-(1-6)-a-D-GlcpNAc-(1-4)-b-D-GlcpA-(1-3)-a-D-GalpNAc-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_137340,IEDB_137473,IEDB_1391961,IEDB_140630,IEDB_141584,IEDB_141807,IEDB_151531,IEDB_423153,IEDB_885822
The structure is contained in the following publication(s):
- Article ID: 460
Torzewska A, Kocharova NA, Zatonsky GV, Blaszczyk A, Bystrova OV, Shashkov AS, Knirel YA, Rozalski A "Structure of the O-polysaccharide and serological cross-reactivity of the Providencia stuartii O33 lipopolysaccharide containing 4-(N-acetyl-D-aspart-4-yl)amino-4,6-dideoxy-D-glucose" -
FEMS Immunology and Medical Microbiology 41(2) (2004) 133-139
The O-polysaccharide of Providencia stuartii O33 was obtained by mild acid degradation of the lipopolysaccharide and the following structure of the tetrasaccharide repeating unit was established: →6)-α-D-GlcpNAc-(1→4)-α-D-GalpA-(1→3)-α-D-GlcpNAc-(1→3)-β-D-Quip4N(Ac-D-Asp)-(1→, where d-Qui4N(Ac-D-Asp) is 4-(N-acetyl-D-aspart-4-yl)amino-4,6-dideoxy-D-glucose. Structural studies were performed using sugar and methylation analyses and NMR spectroscopy, including conventional 2D 1H, 1H COSY, TOCSY, NOESY and 1H, 13C HSQC experiments as well as COSY and NOESY experiments in an H2O-D2O mixture to reveal correlations for NH protons. The O-polysaccharide of P. stuartii O33 shares an α-D-GlcpNAc-(1→3)-β-D-Quip4N(Ac-D-Asp) epitope with that of Proteus mirabilis O38, which seems to be responsible for a marked serological cross-reactivity of anti-P. stuartii O33 serum with the lipopolysaccharide of the latter bacterium. P. stuartii O33 is serologically related also to P. stuartii O4, whose O-polysaccharide contains a lateral β-D-Qui4N(Ac-L-Asp) residue.
Lipopolysaccharide, O-antigen, bacterial polysaccharide structure, serological relationship, Providencia stuartii
NCBI PubMed ID: 15145457Journal NLM ID: 9315554Publisher: Elsevier
Correspondence: rozala@biol.uni.lodz.pl
Institutions: Department of Immunobiology of Bacteria, Institute of Microbiology and Immunology, University of Lodz, Banacha 12/16,90-237 Lodz, Poland
Methods: methylation, NMR-2D, NMR
- Article ID: 542
Kocharova NA, Blaszczyk A, Zatonsky GV, Torzewska A, Bystrova OV, Shashkov AS, Knirel YA, Rozalski A "Structure and cross-reactivity of the O-antigen of Providencia stuartii O18 containing 3-acetamido-3,6-dideoxy-D-glucose" -
Carbohydrate Research 339(2) (2004) 409-413
The O-polysaccharide (O-antigen) of Providencia stuartii O18 was obtained by mild acid degradation of the lipopolysaccharide and studied by chemical methods and NMR spectroscopy, including 2D 1H,1H COSY, TOCSY, NOESY and 1H,13C HSQC experiments. The following structure of the tetrasaccharide repeating unit of the polysaccharide was established: [structure: see text] where Qui3NAc is 3-acetamido-3,6-dideoxyglucose. Anti-P. stuartii O18 serum cross-reacted with the O-antigen of Proteus genomospecies 4, which could be accounted for the marked structural similarities of the main chain.
Lipopolysaccharide, O-polysaccharide, bacterial polysaccharide structure, Providencia stuartii, Providencia O-serogroup
NCBI PubMed ID: 14698900Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: rozala@biol.uni.lodz.pl
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Departement of Immunobiology of Bacteria, Institute of Microbiology and Immunology, University of Lodz, PL 90-237, Lodz, Poland
Methods: methylation, NMR-2D, NMR, sugar analysis
- Article ID: 1589
Zych K, Perepelov AV, Siwinska M, Knirel YA, Sidorczyk Z "Structures of the O-polysaccharides and Classification of Proteus Genomospecies 4, 5 and 6 Into Respective Proteus Serogroups" -
FEBS Journal 272(21) (2005) 5536-5543
An acidic branched O-polysaccharide was isolated by mild acid degradation of the lipopolysaccharide (LPS) of Proteus genomospecies 4 and studied by sugar and methylation analyses along with 1H and 13C NMR spectroscopy, including 2D COSY, TOCSY, ROESY and H-detected 1H,13C HSQC experiments. The following structure of the pentasaccharide repeating unit of the O-polysaccharide was established, which is unique among Proteus polysaccharide structures: [see formula in text] where Qui3NAc stands for 3-acetamido-3,6-dideoxyglucose. Based on the O-polysaccharide structure and serological data, we propose classifying Proteus genomospecies 4 into a new, separate Proteus serogroup, O56. A weak cross-reactivity of Proteus genomospecies 4 antiserum with LPS of Providencia stuartii O18 and Proteus vulgaris OX2 was observed and is discussed in view of a similarity of the O-polysaccharide structures. Structural and serological investigations showed that Proteus genomospecies 5 and 6 should be classified into the existing Proteus serogroups O8 and O69, respectively.
O-antigen, Proteus, Proteus mirabilis, serological classification, 3-Acetamido-3, 6-dideoxy-d-glucose, O-serogroup
NCBI PubMed ID: 16262693Publication DOI: 10.1111/j.1742-4658.2005.04958.xJournal NLM ID: 101229646Publisher: Blackwell Publishing
Correspondence: zsidor@biol.uni.lodz.pl
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of General Microbiology, Institute of Microbiology and Immunology, University of Łódź, Poland
Methods: methylation, NMR, sugar analysis
- Article ID: 4329
Knirel YA "Structure of O-antigens" -
Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.
Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis
Publication DOI: 10.1007/978-3-7091-0733-1_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 4363
Ovchinnikova OG, Liu B, Guo D, Kocharova NA, Bialczak-Kokot M, Shashkov AS, Feng L, Rozalski A, Wang L, Knirel YA "Structural, serological, and genetic characterization of the O-antigen of Providencia alcalifaciens O40" -
FEMS Immunology and Medical Microbiology 66(3) (2012) 382-392
The O-polysaccharide chain of the lipopolysaccharide (O-antigen) on the bacterial cell surface is one of the most structurally variable cell components and serves as a basis for serotyping of Gram-negative bacteria, including human opportunistic pathogens of the genus Providencia. In this work, the O-antigen of Providencia alcalifaciens O40 was obtained by mild acid degradation of the isolated lipopolysaccharide and studied by chemical methods and high-resolution NMR spectroscopy. The following structure of the O-polysaccharide was established: -4)-b-D-Quip3NFo-(1-3)-a-D-Galp-(1-3)-b-D-GlcpA-(1-3)-b-D-GalpNAc-(1- where GlcA stands for glucuronic acid and Qui3NFo for 3,6-dideoxy-3-formamidoglucose. The O40-antigen was found to be structurally and serologically related to the O-antigens of P. alcalifaciens O5 and Providencia stuartii O18. The O40-antigen gene cluster between cpxA and yibK was sequenced, and the gene functions were predicted in silico. In agreement with the O-polysaccharide structure established, the genes for the synthesis of dTDP-D-Qui3NFo, UDP-D-Gal, UDP-D-GlcA, and UDP-D-GalNAc as well as those encoding three glycosyltransferases, flippase (Wzx), and O-antigen polymerase (Wzy) were recognized. In addition, homologues of wza, wzb, and wzc genes, which are required for the surface expression of capsular polysaccharides, were found within the gene cluster, suggesting that the O-polysaccharide studied is a part of the capsule-related form of the lipopolysaccharide called K(LPS).
Lipopolysaccharide, Providencia, Providencia alcalifaciens, 3, O-antigen gene cluster, O-Polysaccharide structure, 6-dideoxy-3-formamidoglucose
NCBI PubMed ID: 23163869Publication DOI: 10.1111/1574-695X.12002Journal NLM ID: 9315554Publisher: Elsevier
Correspondence: olga.ovchinnikova@gmail.com
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
Methods: 13C NMR, 1H NMR, NMR-2D, DNA sequencing, sugar analysis, ESI-MS, mild acid hydrolysis, serological methods
- Article ID: 4589
Ovchinnikova OG, Rozalski A, Liu B, Knirel YA "O-Antigens of bacteria of the genus Providencia: structure, serology, genetics, and biosynthesis" -
Biochemistry (Moscow) 78(7) (2013) 798-817
The genus Providencia consists of eight species of opportunistic pathogenic enterobacteria that can cause enteric diseases and urinary tract infections. The existing combined serological classification scheme of three species, P. alcalifaciens, P. stuartii, and P. rustigianii, is based on the specificity of O-antigens (O-polysaccharides) and comprises 63 O-serogroups. Differences between serogroups are related to polymorphism at a specific genome locus, the O-antigen gene cluster, responsible for O-antigen biosynthesis. This review presents data on structures of 36 O-antigens of Providencia, many of which contain unusual monosaccharides and non-carbohydrate components. The structural data correlate with the immunospecificity of the O-antigens and enable substantiation on a molecular level of serological relationships within the genus Providencia and between strains of Providencia and bacteria of the genera Proteus, Escherichia, and Salmonella. Peculiar features of the O-antigen gene cluster organization in 10 Providencia serogroups and biosynthetic pathways of nucleotide precursors of specific monosaccharide components of the O-antigens also are discussed.
Lipopolysaccharide, biosynthesis, O-antigen, gene cluster, Providencia, serological specificity
NCBI PubMed ID: 24010842Publication DOI: 10.1134/S0006297913070110Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Correspondence: olga.ovchinnikova@gmail.com
Institutions: ND Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of Lodz, PL 90-237 Lodz, Poland, TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, 300457 Tianjin, P. R. China
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9. Compound ID: 1475
|
b-D-Quip3NAc-(1-6)-b-D-Galf-(1-4)-a-L-Rhap-(1-3)-+
|
-4)-a-D-Manp-(1-4)-b-D-Galp-(1-4)-b-D-Glcp-(1- |
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Structure type: polymer chemical repeating unit
; n = 17
Compound class: S-layer glycoprotein
Contained glycoepitopes: IEDB_130701,IEDB_136044,IEDB_136095,IEDB_136105,IEDB_137472,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_144983,IEDB_146664,IEDB_152206,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_44,SB_6,SB_67,SB_7,SB_72,SB_88
The structure is contained in the following publication(s):
- Article ID: 468
Schäffer C, Messner P "Surface-layer glycoproteins: an example for the diversity of bacterial glycosylation with promising impacts on nanobiotechnology" -
Glycobiology 14(8) (2004) 31R-42R
Bacterial cell surface layers, referred to simply as S-layers, have been described for all major phylogenetic groups of bacteria, which may indicate their pivotal role for a bacterium in its natural habitat. They have the unique ability to assemble into two-dimensional crystalline arrays that completely cover the bacterial cells. Glycosylation represents the most frequent modification of S-layer proteins. S-layer glycoproteins constitute a class of glycoconjugates first isolated in the mid-1970s, but S-layer glycoprotein research is still being regarded as an 'exotic field of glycobiology,' possibly because of its 'noneukaryotic' character. Extensive work over the past 30 years provided evidence of an enormous diversity of S-layer glycoproteins that have been created in nature over 3 billion years of prokaryotic evolution. These glycoconjugates are substantially different from eukaryotic glycoproteins, with regard to both composition and structure; nevertheless, some general structural concepts may be deduced. The awareness of the high application potential of S-layer glycoproteins, especially in combination with their intrinsic cell surface display feature, in the field of modern nanobiotechnology as a base for glycoengineering has recently led to the investigation of the S-layer protein glycosylation process at the molecular level, which has lagged behind the structural studies due to the lack of suitable molecular tools. From that work an even more interesting picture of this class of glycoconjugates is emerging. The availability of purified enzymes from S-layer glycan biosynthesis pathways exhibiting increased stabilities and/or rare sugar specificities in conjunction with preliminary genomic data on S-layer glycan biosynthesis clusters will pave the way for the rational design of S-layer neoglycoproteins.
LPS, bacterial glycosylation, genomic glycosylation loci, glycan diversity, glycoengineering, S-layer nanoglycobiology
NCBI PubMed ID: 15044388Publication DOI: 10.1093/glycob/cwh064Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: paul.messner@boka.ac.at
Institutions: Center for NanoBiotechnology, University of Applied Life Sciences and Natural Resources, Gregor-Mendel-Strasse 33, A-1180 Wien, Austria
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10. Compound ID: 1490
|
b-D-Quip3NAc-(1-6)-b-D-Galf-(1-4)-a-L-Rhap-(1-3)-+
|
-3)-b-D-Manp-(1-4)-b-D-Galp-(1-4)-a-D-Glcp-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
; n=17
Aglycon: core -> Tyr of S-layer protein
Trivial name: S-layer glycoprotein
Contained glycoepitopes: IEDB_136044,IEDB_136095,IEDB_136105,IEDB_137472,IEDB_137485,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_152206,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_44,SB_6,SB_7,SB_72,SB_88
The structure is contained in the following publication(s):
- Article ID: 471
Novotny R, Pfoestl A, Messner P, Schäffer C "Genetic organization of chromosomal S-layer glycan biosynthesis loci of Bacillaceae" -
Glycoconjugate Journal 20(7-8) (2004) 435-447
S-layer glycoproteins are cell surface glycoconjugates that have been identified in archaea and in bacteria. Usually, S-layer glycoproteins assemble into regular, crystalline arrays covering the entire bacterium. Our research focuses on thermophilic Bacillaceae, which are considered a suitable model system for studying bacterial glycosylation. During the past decade, investigations of S-layer glycoproteins dealt with the elucidation of the highly variable glycan structures by a combination of chemical degradation methods and nuclear magnetic resonance spectroscopy. It was only recently that the molecular characterization of the genes governing the formation of the S-layer glycoprotein glycan chains has been initiated. The S-layer glycosylation (slg) gene clusters of four of the 11 known S-layer glycan structures from members of the Bacillaceae have now been studied. The clusters are approximately 16 to approximately 25 kb in size and transcribed as polycistronic units. They include nucleotide sugar pathway genes that are arranged as operons, sugar transferase genes, glycan processing genes, and transporter genes. So far, the biochemical functions only of the genes required for nucleotide sugar biosynthesis have been demonstrated experimentally. The presence of insertion sequences and the decrease of the G + C content at the slg locus suggest that the investigated organisms have acquired their specific S-layer glycosylation potential by lateral gene transfer. In addition, S-layer protein glycosylation requires the participation of housekeeping genes that map outside the cluster. The gene encoding the respective S-layer target protein is transcribed monocistronically and independently of the slg cluster genes. Its chromosomal location is not necessarily in close vicinity to the slg gene cluster.
bacterial glycosylation, S-layer, glycosylation gene cluster, sugar nucleotides, S-layer gene, glycan biosynthesis
NCBI PubMed ID: 15316277Publication DOI: 10.1023/B:GLYC.0000038290.74944.65Journal NLM ID: 8603310Publisher: Kluwer Academic Publishers
Institutions: University of Applied Life Sciences and Natural Resources, Center for NanoBiotechnology, Gregor-Mendel Strasse 33, A-1180 Wien, Austria
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11. Compound ID: 1754
|
a-D-Glcp-(1-2)-+
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-4)-b-D-GalpA-(1-3)-a-D-GalpNAc-(1-4)-b-D-Qui3NAc-(1-6)-b-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_135813,IEDB_137340,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_885822,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 542
Kocharova NA, Blaszczyk A, Zatonsky GV, Torzewska A, Bystrova OV, Shashkov AS, Knirel YA, Rozalski A "Structure and cross-reactivity of the O-antigen of Providencia stuartii O18 containing 3-acetamido-3,6-dideoxy-D-glucose" -
Carbohydrate Research 339(2) (2004) 409-413
The O-polysaccharide (O-antigen) of Providencia stuartii O18 was obtained by mild acid degradation of the lipopolysaccharide and studied by chemical methods and NMR spectroscopy, including 2D 1H,1H COSY, TOCSY, NOESY and 1H,13C HSQC experiments. The following structure of the tetrasaccharide repeating unit of the polysaccharide was established: [structure: see text] where Qui3NAc is 3-acetamido-3,6-dideoxyglucose. Anti-P. stuartii O18 serum cross-reacted with the O-antigen of Proteus genomospecies 4, which could be accounted for the marked structural similarities of the main chain.
Lipopolysaccharide, O-polysaccharide, bacterial polysaccharide structure, Providencia stuartii, Providencia O-serogroup
NCBI PubMed ID: 14698900Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: rozala@biol.uni.lodz.pl
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Departement of Immunobiology of Bacteria, Institute of Microbiology and Immunology, University of Lodz, PL 90-237, Lodz, Poland
Methods: methylation, NMR-2D, NMR, sugar analysis
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12. Compound ID: 1816
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L-Ser2Ac-(1-3)-+
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-4)-b-D-Quip3N-(1-3)-b-D-Ribf-(1-4)-b-D-Galp-(1-3)-a-D-GlcpNAc-(1- |
Show graphically |
Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136044,IEDB_137340,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_149136,IEDB_150899,IEDB_150900,IEDB_151531,IEDB_190606,SB_137,SB_165,SB_166,SB_187,SB_195,SB_29,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 571
Feng L, Wang W, Tao J, Guo H, Krause G, Beutin L, Wang L "Identification of Escherichia coli O114 O-antigen gene cluster and development of an O114 serogroup-specific PCR assay" -
Journal of Clinical Microbiology 42(8) (2004) 3799-3804
Screening for the Escherichia coli O serotype is the traditional test for identification of E. coli clones. The O-antigen gene cluster of the E. coli O114 type strain was sequenced, and 12 open reading frames were assigned functions on the basis of homology. By screening against all 186 E. coli and Shigella O serotypes, five genes specific to E. coli O114 were identified. A PCR assay based on the O-antigen-specific genes was developed and tested on 41 clinical isolates of E. coli O114. The PCR assay was shown to be highly specific and sensitive. When tested with pork and water samples, as few as 0.12 CFU of E. coli O114 g(-1) were detected. Thus, the PCR assays established in this study can be used to reliably identify E. coli O114 strains and may also be used to detect E. coli O114 strains in food, water, and other environmental samples.
PCR, Escherichia coli, gene cluster, Shigella, Serotypes, O-serotype, O-antigen-specific
NCBI PubMed ID: 15297533Journal NLM ID: 7505564Publisher: American Society for Microbiology
Correspondence: wanglei@nankai.edu.cn
Institutions: TEDA School of Biological Sciences and Biotechnology, TEDA College, Nankai University, TEDA, Tianjin 300457, People's Republic of China
Methods: PCR, DNA sequencing
- Article ID: 1778
Knirel YA, Kochetkov NK "The structure of lipopolysaccharides of gram-negative bacteria. III. The structure of O-antigens: A review" -
Biochemistry (Moscow) 59(12) (1994) 1325-1383
This review summarizes data on the composition and structure of the O-antigens, the polysaccharide chains of the outer-membrane lipopolysaccharides (LPS) of Gram-negative bacteria defining the immunospecificity of these microbial cells. Special reference is given to some structural features of the O-antigens, such as the presence of unique monosaccharides and noncarbohydrate components, masked regularity, and the occurrence in one microorganism of LPS with structurally different polysaccharide chains. Antigenic relationships between microorganisms belonging to different taxonomic groups are discussed.
structure, O-antigen, chemical composition, bacterial lipopolysaccharides, Salmonella livingstone C1
NCBI PubMed ID: 7533007Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 2373
Dmitriev BA, L'vov V, Tokhtamysheva NV, Shashkov AS, Kochetkov NK, Jann B, Jann K "Cell wall lipopolysaccharide of Escherichia coli O114:H2. Structure of the polysaccharide chain" -
European Journal of Biochemistry 134 (1983) 517-521
The O-specific polysaccharide of the 0114 antigen (lipopolysaccharide) of Escherichia coli 0114 and oligosaccharides obtained from it by Smith degradation and hydrogen fluoride solvolysis were analyzed, using proton and 13C nuclear magnetic resonance spectroscopy and methylation. The results indicated that the 0114 polysaccharide has the tetrasaccharide repeating unit α-N-acetylglucosamine(1→4)β-3,6-dideoxy-3-(N-acetyl-L-seryl)aminoglucose(1→3)β-ribofuranose(1→4)galactose. In the polysaccharide the repeating units are joined through β1→3-galactosyl linkages. This structure is compared with that of the serologically cross-reacting Shigella boydii 08 antigen and the serological similarity is discussed.
NCBI PubMed ID: 6309515Publication DOI: 10.1111/j.1432-1033.1983.tb07597.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Institutions: Institut Organicheskoj Khimii imeni N. D. Zelinskogo, Akademiya Nauk S.S.S.R., Leninskij prospekt 47, Moskva, USSR, Max-Planck-Institut für Immunbiologie, Stübeweg 51, D-7800 Freiburg-Zähringen, Federal Republic of Germany
Methods: 13C NMR, 1H NMR, GC-MS
- Article ID: 2684
Knirel YA, Vinogradov EV, Shashkov AS, Sidorczyk Z, Rozalski A, Radziejewska-Lebrecht I, Kaca W "Structural study of O-specific polysaccharides of Proteus" -
Journal of Carbohydrate Chemistry 12 (1993) 379-414
Proteus bacteria are important human opportunistic pathogens which frequently cause urinary tract infections. According to Bergey's Manual of Systematic Bacteriology,1 this genus includes three species: P. mirabilis, P. vulgaris, and P. myxofaciens. A novel species of P. penneri has been recently proposed2,3 for strains formerly called P. vulgaris biogroup I. Proteus is an antigenically heterogeneous group of bacteria, and this is mainly associated with diverse composition and structures of O-specific polysaccharide chains of outer-membrane lipopolysaccharides (O-antigens). The Kauffman-Perch serological classification4 of P. mirabilis and P. vulgaris includes 49 O-serogroups. However, a number of S-strains remain unclassified,5 including strains of P. penneri.
Publication DOI: 10.1080/07328309308019396Journal NLM ID: 8218151Publisher: Marcel Dekker
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky pr. 47, Moscow, B-334, Russia
Methods: 13C NMR, NMR
- Article ID: 3197
Stenutz R, Weintraub A, Widmalm G "The structures of Escherichia coli O-polysaccharide antigens" -
FEMS Microbiology Reviews 30(3) (2006) 382-403
Escherichia coli is usually a non-pathogenic member of the human colonic flora. However, certain strains have acquired virulence factors and may cause a variety of infections in humans and in animals. There are three clinical syndromes caused by E. coli: (i) sepsis/meningitis; (ii) urinary tract infection and (iii) diarrhoea. Furthermore the E. coli causing diarrhoea is divided into different 'pathotypes' depending on the type of disease, i.e. (i) enterotoxigenic; (ii) enteropathogenic; (iii) enteroinvasive; (iv) enterohaemorrhagic; (v) enteroaggregative and (vi) diffusely adherent. The serotyping of E. coli based on the somatic (O), flagellar (H) and capsular polysaccharide antigens (K) is used in epidemiology. The different antigens may be unique for a particular serogroup or antigenic determinants may be shared, resulting in cross-reactions with other serogroups of E. coli or even with other members of the family Enterobacteriacea. To establish the uniqueness of a particular serogroup or to identify the presence of common epitopes, a database of the structures of O-antigenic polysaccharides has been created. The E. coli database (ECODAB) contains structures, nuclear magnetic resonance chemical shifts and to some extent cross-reactivity relationships. All fields are searchable. A ranking is produced based on similarity, which facilitates rapid identification of strains that are difficult to serotype (if known) based on classical agglutinating methods. In addition, results pertinent to the biosynthesis of the repeating units of O-antigens are discussed. The ECODAB is accessible to the scientific community at http://www.casper.organ.su.se/ECODAB/
NMR, structure, serotype, O-antigen, Enterobacteriacea, database
NCBI PubMed ID: 16594963Publication DOI: 10.1111/j.1574-6976.2006.00016.xJournal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: andrej.weintraub@ki.se
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- Article ID: 3274
Sidorczyk Z, Swierzko A, Vinogradov EV, Knirel YA, Shashkov AS "Structural and immunochemical studies of the O-specific polysaccharide of Proteus penneri strain 14" -
Archivum Immunologiae et Therapiae Experimentalis 42(3) (1994) 209-215
The complete structure of the O-antigen of Proteus penneri strain 14, containing D-alanine and L-alanine was established using methylation, solvolysis with anhydrous hydrogen fluoride, partial acid hydrolysis, 1H- and 13C-NMR spectroscopy. The role of partial structures of the pentasaccharide repeating unit in manifesting serological specificity and cross-reactivity of this strain with some other bacteria is discussed.
Lipopolysaccharide, structure, role, strain, structural, polysaccharide, O-antigen, repeating unit, O antigen, hydrogen, acid, immunology, O-polysaccharide, bacteria, O-specific, O-specific polysaccharide, Proteus, serological, specificity, Proteus penneri, methylation, spectroscopy, immunochemical, partial structure, pentasaccharide, cross-reactivity, crossreactivity, PDF, solvolysis, hydrogen fluoride, D-alanine, lysis
NCBI PubMed ID: 7487355Journal NLM ID: 0114365Publisher: Basel, Boston: Birkhaüser
Correspondence: zsidor@biol.uni.lodz.pl
Institutions: Institute of Microbiology and Immunology, University of Lodz, Poland.
Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, chemical analysis, mild acid hydrolysis, NMR-1D, serological methods
- Article ID: 3832
Clark CG, Grant CC, Trout-Yakel KM, Tabor H, Ng LK, Rahn K, Franklin K, Kropinski AM "The O28 Antigen Gene Clusters of Salmonella enterica subsp. enterica Serovar Dakar and Serovar Pomona Are Different" -
International Journal of Microbiology 2010 (2010) 209291
A 10 kb O-antigen gene cluster was sequenced from a Salmonella enterica subsp. enterica Dakar O28 reference strain and from two S. Pomona serogroup O28 isolates. The two S. Pomona O antigen gene clusters showed only moderate identity with the S. Dakar O28 gene cluster, suggesting that the O antigen oligosaccharides may contain one or more sugars conferring the O28 epitope but may otherwise be different. These novel findings are absolutely critical for the correct interpretation of molecular serotyping assays targeting genes within the O antigen gene clusters of these Salmonella serotypes and suggest the possibility that the O antigen gene clusters of other Salmonella serovars may also be heterogenous.
O-antigen, gene cluster, serogroup, Salmonella enterica
NCBI PubMed ID: 20652070Journal NLM ID: 101516125Publisher: Hindawi Publishing Corporation
Correspondence: kropinsk@queensu.ca
Institutions: Enteric Diseases Program, Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada R3E 3R2
Methods: genetic methods
- Article ID: 4292
Dziadziuszko H, Kumirska J, Muza S, Czerwicka M, Lubecka EA, Stepnowski P, Kunikowska D "Immunochemical studies of Salmonella Dakar and Salmonella Telaviv O-antigens (serogroup O:28)" -
FEMS Microbiology Letters 326(1) (2012) 55-61
Salmonella Dakar and Salmonella Telaviv bacteria belong to serogroup O:28, which represents 107 serovars and possesses only the epitope O28. Salmonella Telaviv has the subfactors O28(1) and O28(2) , whereas S. Dakar has O28(1) and O28(3) . So far, only limited serological and immunological information for this serogroup is available in the literature. Knowledge of the structures of their O-polysaccharides and the immunochemical investigations performed in this work allowed to reveal the nature of subfactor O28(1) as attributed to the presence of 3-linked (or 3,4-disubstituted) α-D-GalpNAc in the main chains of S. Dakar and S. Telaviv O-polysaccharides. An explanation for the cross-reactions between Salmonella enterica O28 O-antigens and other Salmonella O-polysaccharides and their structural similarity to Escherichia coli O-serogroups is also given.
monoclonal antibody, Serogroup O:28, Salmonella bacterial strains, immunochemical study, O-antigen (OPS), epitope O28
NCBI PubMed ID: 22092663Publication DOI: 10.1111/j.1574-6968.2011.02431.xJournal NLM ID: 7705721Publisher: Blackwell Publishing
Correspondence: kumirska@ chem.univ.gda.pl
Institutions: Department of Molecular Microbiology and Serology, National Salmonella Centre, Medical University of Gdansk, Gdansk, Poland
Methods: periodate oxidation, SDS-PAGE, ELISA, serological methods
- Article ID: 4646
Zhou D, Utkina N, Li D, Dong C, Druzhinina T, Veselovsky V, Liu B "Biochemical characterization of a new b-1,3-galactosyltransferase WbuP from Escherichia coli O114 that catalyzes the second step in O-antigen repeating-unit" -
Carbohydrate Research 381 (2013) 43-50
In this study, synthetic acceptor substrate GlcNAc α-PO3-PO3-(CH2)11-O-phenyl (GlcNAc-PP-PhU) was employed in glycosyl transferase assays to characterize the WbuP galactosyltransferase activity. This activity was time- and enzyme concentration-dependent. The optimal enzyme activity was observed at pH 6.5 and 25°C. The enzyme requires Mn(2+) ions for maximal activity and detergents in the assay did not increase glycosyltransfer activity. The enzyme was shown to be specific for the UDP-Gal donor substrate. Kinetic parameters were determined for UDP-Gal, and GlcNAc-PP-PhU. The enzyme product was determined to have a ?-1,3-linkage using strategies based on exoglycosidase digestion combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) as well as collision-induced dissociation electrospray ionization ion trap multiple tandem MS (CID-ESI-IT-MS(n)). Our results conclusively demonstrate that the wbuP gene of Escherichia coli O114 encodes a UDP-Gal: GlcNAc ?-pyrophosphate-lipid ?-1,3-Gal-transferase that transfers the second sugar moiety in the assembly of the O114 repeating unit.
Escherichia coli, mass spectrometry, glycosyl transferase, Functional characterization, Escherichia coli O-antigen
NCBI PubMed ID: 24056013Publication DOI: 10.1016/j.carres.2013.08.021Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: daweizhou@nankai.edu.cn
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 HongDa Street, TEDA, Tianjin, China
Methods: PCR, GC-MS, SDS-PAGE, glycosyltransferase assays, kinetics assays, ESI-MS, MALDI-TOF MS, CID-MS/MS, biochemical methods
- Article ID: 5472
Liu B, Furevi A, Perepelov AV, Guo X, Cao H, Wang Q, Reeves PR, Knirel YA, Wang L, Widmalm G "Structure and genetics of Escherichia coli O antigens" -
FEMS Microbiology Reviews 44(6) (2020) 655-683
Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and four (O14, O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.
structure, O antigen, Escherichia coli, gene cluster, serogroup, diversity
NCBI PubMed ID: 31778182Publication DOI: 10.1093/femsre/fuz028Journal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: G. Widmalm
; Lei Wang
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China, School of Molecular and Microbial Bioscience (G08), University of Sydney, Sydney, Australia, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Article ID: 6301
Qin CJ, Ding MR, Tian GZ, Zou XP, Fu JJ, Hu J, Yin J "Chemical approaches towards installation of rare functional groups in bacterial surface glycans" -
Chinese Journal of Natural Medicines = Zhongguo Tianran Yaowu 20(6) (2022) 401-420
Bacterial surface glycans perform a diverse and important set of biological roles, and have been widely used in the treatment of bacterial infectious diseases. The majority of bacterial surface glycans are decorated with diverse rare functional groups, including amido, acetamidino, carboxamido and pyruvate groups. These functional groups are thought to be important constituents for the biological activities of glycans. Chemical synthesis of glycans bearing these functional groups or their variants is essential for the investigation of structure-activity relationships by a medicinal chemistry approach. To date, a broad choice of synthetic methods is available for targeting the different rare functional groups in bacterial surface glycans. This article reviews the structures of naturally occurring rare functional groups in bacterial surface glycans, and the chemical methods used for installation of these groups.
chemical synthesis, acetamidino group, amido group, bacterial surface glycan, carboxamido group, pyruvyl ketal
NCBI PubMed ID: 35750381Publication DOI: 10.1016/S1875-5364(22)60177-8Journal NLM ID: 101504416Publisher: Beijing: Science Press; Elsevier
Correspondence: J. Yin
Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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13. Compound ID: 1831
|
3HO2,3MePro-5-oxo-(1-3)-+
|
-2)-b-D-Quip3N-(1-3)-a-L-Rhap-(1-3)-a-D-FucpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136105,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 578
Veremeichenko SN, Zdorovenko GM "Structure and properties of the lipopolysaccharide of Pseudomonas fluorescens IMV 2366 (biovar III)" -
Mikrobiologiia = Microbiology [Russian] 73(3) (2004) 260-266
The lipopolysaccharide (LPS) preparation isolated from the bacterial mass of Pseudomonas fluorescens IMV 2366 (biovar III) by Westphal's method and purified by repeated ultracentrifugation was characterized by the presence of the S- and R-forms of molecules. The following structural portions of the LPS molecule were obtained in the individual state and characterized: lipid A, core oligosaccharide, and O-specific polysaccharide. The main components of the lipid A hydrophobic moiety were 3-hydoxydecanoic, 2-hydroxydodecanoic, 3-hydroxydodecanoic, dodecanoic, and hexadecanoic fatty acids. Glucosamine, phosphoethanolamine, and phosphorus were identified as the components of the lipid A hydrophilic moiety. Rhamnose, glucose, galactose, glucosamine, galactosamine, alanine, phosphoethanolamine, phosphorus, 2-keto-3-desoxyoctulosonic acid (KDO), as well as 2-amino-2,6-didesoxygalactose (FucN) and 3-amino-3,6-didesoxyglucose (Qui3N), were revealed in the composition of the core oligosaccharide fractions. O-specific polysaccharide chains were established to be composed of repeating trisaccharide units consisting of residues of L-rhamnose (L-Rha), 2-acetamido-2,6-didesoxy-D-galactose (D-FucNAc), and 3-acylamido-3,6-didesoxy-D-glucose (D-Qui3NAcyl), where Acyl = 3-hydroxy-2,3-dimethyl-5-hydroxyprolyl. Neither double immunodiffusion in agar not the immunoenzyme assay revealed serological relations between the strain studied and the P. fluorescens strains studied earlier.
Lipopolysaccharide, LPS, structure, lipid A, core oligosaccharide, O-specific polysaccharide, Pseudomonas fluorescens
NCBI PubMed ID: 15315223Journal NLM ID: 0376652Publisher: Moskva: Izdatelstvo Nauka
Institutions: NPK (Research and Production Company) Diaprof-Med, ul. Svetlitskogo 35, Kiev, 04123 Ukraine, Zabolotnyi Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, ul. Zabolotnogo 154, Kiev, 03143 Ukraine
Methods: 13C NMR, 1H NMR, ion-exchange chromatography
- Article ID: 1310
Zatonsky GV, Kocharova NA, Veremeychenko SN, Zdorovenko EL, Shapovalova VY, Shashkov AS, Zdorovenko GM, Knirel YA "Somatic antigens of pseudomonads: structure of the O-specific polysaccharide of Pseudomonas fluorescens IMV 2366 from (biovar C)" -
Carbohydrate Research 337(21-23) (2002) 2365-2370
The O-specific polysaccharide of P. fluorescens IMV 2366 was studied by sugar and methylation analyses along with 1H and 13C NMR spectroscopy, including 2D gsCOSY, TOCSY, gsNOESY, H-detected 1H,(13)C gsHSQC, HMQC-TOCSY, and gsHMBC experiments. The polysaccharide contains L-rhamnose, 2-acetamido-2,6-dideoxy-D-galactose (D-FucNAc) and 3-acylamido-3,6-dideoxy-D-glucose (D-Qui3NAcyl, where Acyl is 3-hydroxy-2,3-dimethyl-5-oxoprolyl). The structure 1 of the polysaccharide was found to be similar to the structure 2 of a 6-deoxy-L-talose (L6dTal)-containing O-specific polysaccharide of a non-classified P. fluorescens strain, 361, studied earlier [Khomenko, V. A.; Naberezhnykh, G. A.; Isakov, V. V.; Solov'eva, T. F.; Ovodov, Y. S.; Knirel, Y. A.; Vinogradov, E. V. Bioorg. Khim. 1986, 12, 1641-1648; Naberezhnykh, G. A.; Khomenko, V. A.; Isakov, V. V., El'kin, Y. N.; Solov'eva, T. F.; Ovodov, Y. S. Bioorg. Khim. 1987, 13, 1428-1429]. [for structures see text]
O-antigen, Bacterial polysaccharide, 3-Acetamido-3, 6-dideoxy-d-glucose, Pseudomonas fluorescens, 3-Hydroxy-2, structurel lipopolysaccharide, 3-dimethyl-5-oxoprolyl
NCBI PubMed ID: 12433503Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: knirel@ioc.ac.ru
Institutions: ND Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation, Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, 03143 Kiev, Ukraine
Methods: methylation, NMR-2D, NMR
- Article ID: 4329
Knirel YA "Structure of O-antigens" -
Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.
Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis
Publication DOI: 10.1007/978-3-7091-0733-1_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 6301
Qin CJ, Ding MR, Tian GZ, Zou XP, Fu JJ, Hu J, Yin J "Chemical approaches towards installation of rare functional groups in bacterial surface glycans" -
Chinese Journal of Natural Medicines = Zhongguo Tianran Yaowu 20(6) (2022) 401-420
Bacterial surface glycans perform a diverse and important set of biological roles, and have been widely used in the treatment of bacterial infectious diseases. The majority of bacterial surface glycans are decorated with diverse rare functional groups, including amido, acetamidino, carboxamido and pyruvate groups. These functional groups are thought to be important constituents for the biological activities of glycans. Chemical synthesis of glycans bearing these functional groups or their variants is essential for the investigation of structure-activity relationships by a medicinal chemistry approach. To date, a broad choice of synthetic methods is available for targeting the different rare functional groups in bacterial surface glycans. This article reviews the structures of naturally occurring rare functional groups in bacterial surface glycans, and the chemical methods used for installation of these groups.
chemical synthesis, acetamidino group, amido group, bacterial surface glycan, carboxamido group, pyruvyl ketal
NCBI PubMed ID: 35750381Publication DOI: 10.1016/S1875-5364(22)60177-8Journal NLM ID: 101504416Publisher: Beijing: Science Press; Elsevier
Correspondence: J. Yin
Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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14. Compound ID: 1859
|
b-D-Quip3NAc-(1-6)-b-D-Galf-(1-4)-a-L-Rhap-(1-3)-+
|
-4)-a-D-Manp-(1-4)-b-D-Galp-(1-4)-b-D-Glcp-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
; n=17
Contained glycoepitopes: IEDB_130701,IEDB_136044,IEDB_136095,IEDB_136105,IEDB_137472,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_144983,IEDB_146664,IEDB_152206,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_44,SB_6,SB_67,SB_7,SB_72,SB_88
The structure is contained in the following publication(s):
- Article ID: 597
Altman E, Schäffer C, Brisson J, Messner P "Characterization of the glycan structure of a major glycopeptide from the surface layer glycoprotein of Clostridium thermosaccharolyticum E207-71" -
European Journal of Biochemistry 229 (1995) 308-315
The squarely arranged surface layer (S-layer) glycoprotein of Clostridium thermosaccharolyticum E207-71 was isolated from bacterial cells which were grown under defined culture conditions. By sodium dodecyl sulfate polyacrylamide gel electrophoresis, the S-layer showed a series of distinct bands with apparent molecular masses in the range 83-210 kDa. Upon deglycosylation by trifluoromethanesulfonic acid, only the single band at 83 kDa remained unchanged. After pronase digestion of the intact S-layer glycoprotein, the degradation products were isolated by gel-permeation chromatography, cation-exchange chromatography and isoelectric focusing. Three main fractions and an amino sugar containing minor fraction were obtained. The main fractions, which showed identical carbohydrate compositions, were further purified by reverse-phase chromatography and characterized by monosaccharide analysis, Smith degradation, methylation analysis, and one-dimensional and two-dimensional nuclear magnetic resonance spectroscopy. The combined chemical and spectroscopical evidence suggest the following glycan structure for the main fractions: [Sequence: See text].
bacteria, Clostridium, glycoprotein, Eubacteria, surface layer, crystalline bacterial cell surface layer
NCBI PubMed ID: 7744045Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Institutions: Institute for Biological Sciences, National Research Council, Ottawa, Canada
Methods: periodate oxidation, NMR-2D, SDS-PAGE, Smith degradation, HPLC, electron microscopy, enzymatic digestion, colorimetry
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15. Compound ID: 1874
|
b-D-GlcpNAc-(1-2)-+
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a-D-GalpNAc-(1-4)-+ | b-D-Glcp-(1-4)-+
| | |
b-D-Quip3NAc-(1-3)-b-D-GalpNAc-(1-3)-a-D-Galp-(1-3)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-5)-Kdo
|
P-7)-+ |
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Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130648,IEDB_130650,IEDB_135813,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_140087,IEDB_140088,IEDB_140090,IEDB_141584,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_885822,IEDB_983931,SB_192,SB_21,SB_7
The structure is contained in the following publication(s):
- Article ID: 610
Aspinall GO, Lynch CM, Pang H, Shaver RT, Moran AP "Chemical structures of the core region of Campylobacter jejuni O:3 lipopolysaccharide and an associated polysaccharide" -
European Journal of Biochemistry 231 (1995) 570-578
The complete structure for the core oligosaccharide region of the water-insoluble low-Mr, lipopolysaccharide of Campylobacter jejuni serotype 0:3 from phenol/water extraction of bacterial cells was assigned through studies on derivatives of the liberated oligosaccharide. Structure determinations were performed using 1H-NMR and 31P-NMR spectroscopies, methylation analysis supported by fast-atom-bombardment mass spectrometry, and Smith degradation experiments. It was concluded that the complete chains in the core oligosaccharide had the following structure in which a proportion of the terminal residues were phosphorylated: . From a similar series of experiments, it was concluded that an associated polysaccharide, which was isolated from the water phase of the phenoVwater extracts, had the following repeating unit in which a proportion of the previously unknown L-glycero-D-ido-heptose (L-a-D-ido-Hep) residues were present as 3-hydroxypropanoyl esters, and were not covalently linked to the lipopolysaccharide: -[→3)-L-a-D-Ido-Hep-(l→4)-a-D-Gal-(l-]n-.
Lipopolysaccharide, LPS, structure, core, polysaccharide, O-antigen, Campylobacter, Campylobacter jejuni, core region, region
NCBI PubMed ID: 7544281Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Institutions: Department of Microbiology, University College, Galway, Ireland, Department of Chemistry, York University, Toronto, Ontario, Canada, Carbohydrate Research Centre, Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada
Methods: deacetylation, NMR-2D, FAB-MS, GC-MS, dephosphorylation, GC, Smith degradation
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