Show legend Show as text

Structure type: oligomer
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_983931,SB_192,SB_7

• Article ID: 19
  Borrelli S, Hegedus O, Shaw DH, Jansson P, Lindberg AA "The tetrasaccharide L-a-D-heptose1->2-L-a-D-heptose1->3-L-a-D-heptose1->(3-deoxy-D-manno-octulosonic acid) and phosphate in lipid A define the conserved epitope in Haemophilus lipopolysaccharides recognized by a monoclonal antibody" - Infection and Immunity 63 (1995) 3683-3692
  

  A murine monoclonal antibody, MAHI 3 (immunoglobulin G2b), that is broadly reactive with Haemophilus influenzae lipopolysaccharides (LPSs) but nonreactive with all enterobacterial LPSs tested was generated by fusing mouse myeloma cells with spleen cells of BALB/c mice immunized with azide-killed H. influenzae RM.7004. MAHI 3 bound to all H. influenzae, all other human Haemophilus spp., all Bordetella pertussis and Bordetella parapertussis, and all Aeromonas spp. tested but not to any Neisseria or Moraxella catarrhalis strains, as determined by enzyme immunoassay, colony dot immunoblotting, and immunoblotting. In an inhibition enzyme immunoassay, MAHI 3 reacted with all 45 H. influenzae LPSs tested but not with the LPS from the rough mutant I69 Rd-/b+, which has only 3-deoxy-D-manno-octulosonic acid (P) [Kdop(P)] and lipid A. The antibody was not inhibited by H. influenzae lipid A or lipid-free polysaccharide isolated after mild acid hydrolysis. Only native LPSs show positive inhibitory activity, indicating that part of lipid A is involved in the binding of MAHI 3. From the results, it is indicated that the structural element recognized by MAHI 3 is Hep α1→2 Hep α1→3 Hep α1→ Kdo together with part of lipid A, including the phosphate

  Lipopolysaccharide, Haemophilus, L-glycero-D-manno-heptose, lipopolysaccharides, LPS, core, tetrasaccharide, acid, Kdo, antibodies, antibody, conserved, epitope, lipid, lipid A, monoclonal, monoclonal antibodies, monoclonal antibody, phosphate, recognition

  NCBI PubMed ID: 7543887
  Journal NLM ID: 0246127
  Publisher: American Society for Microbiology
  Correspondence: Pererk.Jansson@kfc.m13.hs.sll.se
  Institutions: Department of Immunology, Microbiology, Pathology and Infectious Diseases, Karolinska Institute, Huddinge, Sweden
  Methods: de-O-acylation, SDS-PAGE, alkaline de-O-N-acylation, dephosphorylation, chemical analysis, EIA, inhibition studies, dot immunoblotting
  
   
  
  Aeromonas sobria SJ-25
  CSDB ID 1773 (all data & tools)

Show legend Show as text

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

• 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: 14670707
  Publication DOI: 10.1016/j.carres.2003.07.010
  Journal NLM ID: 0043535
  Publisher: 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
  
   
  
  Vibrio parahaemolyticus O12
  CSDB ID 31482 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_151527,IEDB_151531,IEDB_225177,IEDB_423153,IEDB_885823

• Article ID: 113
  Toukach FV, Bartodziejska B, Senchenkova SN, Wykrota M, Shashkov AS, Rozalski A, Knirel YA "Structure of a new acidic O-antigen of Proteus vulgaris O22 containing O-acetylated 3-acetamido-3,6-dideoxy-D-glucose" - Carbohydrate Research 318(1-4) (1999) 146-153
  

  The acidic O-specific polysaccharide of Proteus vulgaris O22 was studied using 1H and 13C NMR spectroscopy, including 2D COSY, TOCSY, NOESY, and H-detected 1H, 13C heteronuclear multiple-quantum coherence (HMQC) experiments, and the following structure for the branched pentasaccharide repeating unit was established: [sequence: see text] where Qui3NAc is 3-acetamido-3,6-dideoxyglucose, O-acetylation of QuiNAc at position 4 is stoichiometric and at position 2 nonstoichiometric. Serological relationships of P. vulgaris O22 with some other Proteus strains were substantiated on the level of the O-antigen structures.

  Lipopolysaccharide, O-antigen, O-specific polysaccharide, O-acetylation, Proteus vulgaris, 3-Acetamido-3, 6-dideoxy-d-glucose

  NCBI PubMed ID: 10515053
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, R-117913 Moscow, Russian Federation, Institute of Microbiology and Immunology, University of Lodz, Banacha 12/16, PL-90-237 Lodz, Poland.
  Methods: 13C NMR, 1H NMR, methylation, NMR-2D, NMR, serological methods
  
   
  
  Proteus vulgaris O22
  CSDB ID 5224 (all data & tools)
• Article ID: 1467
  Knirel YA, Kaca W, Rozalski A, Sidorczyk Z "Structure of the O-antigenic polysaccharides of Proteus bacteria" - Polish Journal of Chemistry 73 (1999) 895-907
  

  Data on the composition and structure of the O-specific polysaccharides (O-antigens) of the lipopolysaccharides of the genus Proteus are summarized and discussed as the molecular basis for serotyping of these medically important bacteria.

  structure, O-antigen, Proteus, Bacterial polysaccharide, epitope specificity

  Journal NLM ID: 7901356
  WWW link: http://www.ichf.edu.pl/pjch/pj-1999/pj0699.htm#0895
  Publisher: Państwowe Wydawnictwo Naukowe
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences,Leninsky Prospekt 47, Moscow, Russia, Institute of Microbiology and Immunology, University of ŁódźŸ, Banacha 12/16, 90-237 ŁódŸź, Poland, Center of Microbiology and Virology, Polish Academy of Sciences, Lodowa 106, 93-232 ŁódźŸ, Poland
  
   
  
  Proteus vulgaris O22
  CSDB ID 31850 (all data & tools)

Show legend Show as text

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

• 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: 14670714
  Publication DOI: 10.1016/j.carres.2003.06.005
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: atzianabos@channing.harvard.edu
  Institutions: Department of Medicine, Channing Laboratory, 181 Longwood Ave., Brigham and Women's Hospital, Boston, MA 02115, USA
  
   
  
  Bacteroides fragilis 638
  CSDB ID 31498 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: p-trifluoroacetamidophenyl
Trivial name: pentasaccharide hapten
Contained glycoepitopes: IEDB_136098,IEDB_136105,IEDB_225177,IEDB_885823

• 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: 2984819R
  Publisher: 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
  
   
  
  Mycobacterium avium 17
  CSDB ID 5281 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136105,IEDB_225177,IEDB_885823

• 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: 10920806
  Journal NLM ID: 0376652
  Publisher: Moskva: Izdatelstvo Nauka
  Institutions: Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kiev, Ukraine.
  Methods: NMR-2D, NMR
  
   
  
  Pseudomonas fluorescens IMV 247
  CSDB ID 5289 (all data & tools)
• 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_3
  Publisher: Springer
  Correspondence: knirel@ioc.ac.ru
  Editors: Knirel YA, Valvano MA
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Pseudomonas fluorescens bv. B IMV 247
  CSDB ID 27729 (all data & tools)
• 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: 22925757
  Publication DOI: 10.1016/j.carres.2012.07.007
  Journal NLM ID: 0043535
  Publisher: 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
  
   
  
  Pseudomonas fluorescens IMV 247
  CSDB ID 28431 (all data & tools)
• 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: 35750381
  Publication DOI: 10.1016/S1875-5364(22)60177-8
  Journal NLM ID: 101504416
  Publisher: 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
  
   
  
  Pseudomonas fluorescens IMV 247
  CSDB ID 21153 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_151527,IEDB_151531,IEDB_225177,IEDB_423153,IEDB_885823

• Article ID: 113
  Toukach FV, Bartodziejska B, Senchenkova SN, Wykrota M, Shashkov AS, Rozalski A, Knirel YA "Structure of a new acidic O-antigen of Proteus vulgaris O22 containing O-acetylated 3-acetamido-3,6-dideoxy-D-glucose" - Carbohydrate Research 318(1-4) (1999) 146-153
  

  The acidic O-specific polysaccharide of Proteus vulgaris O22 was studied using 1H and 13C NMR spectroscopy, including 2D COSY, TOCSY, NOESY, and H-detected 1H, 13C heteronuclear multiple-quantum coherence (HMQC) experiments, and the following structure for the branched pentasaccharide repeating unit was established: [sequence: see text] where Qui3NAc is 3-acetamido-3,6-dideoxyglucose, O-acetylation of QuiNAc at position 4 is stoichiometric and at position 2 nonstoichiometric. Serological relationships of P. vulgaris O22 with some other Proteus strains were substantiated on the level of the O-antigen structures.

  Lipopolysaccharide, O-antigen, O-specific polysaccharide, O-acetylation, Proteus vulgaris, 3-Acetamido-3, 6-dideoxy-d-glucose

  NCBI PubMed ID: 10515053
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, R-117913 Moscow, Russian Federation, Institute of Microbiology and Immunology, University of Lodz, Banacha 12/16, PL-90-237 Lodz, Poland.
  Methods: 13C NMR, 1H NMR, methylation, NMR-2D, NMR, serological methods
  
   
  
  Proteus vulgaris O22
  CSDB ID 5305 (all data & tools)

Show legend Show as text

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

• 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: 11106392
  Publication DOI: 10.1073/pnas.97.25.13478
  Journal NLM ID: 7505876
  Publisher: 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
  
   
  
  Bacteroides fragilis 638R
  CSDB ID 8637 (all data & tools)
• 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/B978-0-12-819475-1.00005-5
  Publisher: 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
  
   
  
  Bacteroides fragilis 638R
  CSDB ID 7021 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS

• 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: 15560791
  Journal NLM ID: 0107600
  Publisher: 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
  
   
  
  Aeromonas salmonicida 80204-1
  CSDB ID 8906 (all data & tools)
• 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: 22073003
  Publication DOI: 10.3390/md9101914
  Journal NLM ID: 101213729
  Publisher: 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
  
   
  
  Aeromonas salmonicida 80204-1
  CSDB ID 28495 (all data & tools)
• 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/B978-0-12-819475-1.00005-5
  Publisher: 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
  
   
  
  Aeromonas salmonicida 80204-1
  CSDB ID 6763 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide

• 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: 9805750
  Publisher: 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
  
   
  
  Pseudomonas cichorii
  CSDB ID 8916 (all data & tools)
• 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.200900682
  Journal NLM ID: 9805750
  Publisher: 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
  
   
  
  Pseudomonas cichorii 5707
  CSDB ID 24112 (all data & tools)
• 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_3
  Publisher: Springer
  Correspondence: knirel@ioc.ac.ru
  Editors: Knirel YA, Valvano MA
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Pseudomonas cichorii
  CSDB ID 27735 (all data & tools)

Show legend Show as text

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

• 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: 15145457
  Journal NLM ID: 9315554
  Publisher: 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
  
   
  
  Providencia stuartii O18
  CSDB ID 9072 (all data & tools)
• 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: 14698900
  Journal NLM ID: 0043535
  Publisher: 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
  
   
  
  Providencia stuartii O18
  CSDB ID 9275 (all data & tools)
• 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: 16262693
  Publication DOI: 10.1111/j.1742-4658.2005.04958.x
  Journal NLM ID: 101229646
  Publisher: 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
  
   
  
  Providencia stuartii O18
  CSDB ID 10467 (all data & tools)
• 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_3
  Publisher: Springer
  Correspondence: knirel@ioc.ac.ru
  Editors: Knirel YA, Valvano MA
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Providencia stuartii O18
  CSDB ID 27589 (all data & tools)
• 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: 23163869
  Publication DOI: 10.1111/1574-695X.12002
  Journal NLM ID: 9315554
  Publisher: 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
  
   
  
  Providencia stuartii O18
  CSDB ID 28541 (all data & tools)
• 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: 24010842
  Publication DOI: 10.1134/S0006297913070110
  Journal NLM ID: 0376536
  Publisher: 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
  
   
  
  Providencia stuartii O18:H14 (H89)
  CSDB ID 29679 (all data & tools)

Show legend Show as text

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

• 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: 15044388
  Publication DOI: 10.1093/glycob/cwh064
  Journal NLM ID: 9104124
  Publisher: 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
  
   
  
  Thermoanaerobacterium thermosaccharolyticum E207-71
  CSDB ID 31626 (all data & tools)

Show legend Show as text

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

• 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: 15316277
  Publication DOI: 10.1023/B:GLYC.0000038290.74944.65
  Journal NLM ID: 8603310
  Publisher: Kluwer Academic Publishers
  Institutions: University of Applied Life Sciences and Natural Resources, Center for NanoBiotechnology, Gregor-Mendel Strasse 33, A-1180 Wien, Austria
  
   
  
  Thermoanaerobacterium thermosaccharolyticum E207-71
  CSDB ID 9033 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_130646,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_140108,IEDB_140122,IEDB_140630,IEDB_141794,IEDB_141807,IEDB_151527,IEDB_151531,IEDB_190606,IEDB_423153,SB_165,SB_166,SB_187,SB_195,SB_30,SB_7,SB_88

• Article ID: 504
  Lycknert K, Widmalm G "Dynamics of the Escherichia coli O91 O-antigen polysaccharide in solution as studied by carbon-13 NMR relaxation" - Biomacromolecules 5(3) (2004) 1015-1020
  

  The dynamics of the O-antigen part of the lipopolysaccharide from the enterohemorrhagic Escherichia coli O91 has been determined in solution using (13)C NMR relaxation measurements at two magnetic field strengths,9.4 and 14.1 T, thereby facilitating the testing of several dynamical models. The biological repeating unit, consisting of five sugar residues and substituents, could be determined by spectral analysis of different (1)H,(13)C correlations and corroborated by the relaxation data. The site specifically (13)C-labeled material was shown to have approximately 10 repeating units with a narrow distribution. A model-free analysis of the relaxation data revealed a complex dynamical behavior where the sugar residues could be described by a global correlation time (tau(m) = 5.4 ns), generalized order parameters (S(2) approximately 0.63), and different correlation times for internal motions related to their position in the repeating unit along the polymer (tau(e) approximately 360-520 ps). One of the sugar residues showed, in addition, a chemical exchange contribution. Furthermore, a substituent on another sugar residue was described by two order parameters (S(f)(2) = 0.51 and S(s)(2) = 0.21). The solution dynamics of the polysaccharide are thus described by highly intricate motions, both in amplitude and time scales. These results are of significance in the general description of polysaccharides surrounding bacterial cell surfaces and in the presentation of antigenic epitopes to the immune system of an invaded host.

  Lipopolysaccharide, NMR, chemistry, correlation, Bacterial, host, significance, polysaccharide, O-antigen, repeating unit, analysis, O antigen, cell, polymer, Escherichia, Escherichia coli, epitope, complex, epitopes, dynamics, biological, chemical, sugar, polysaccharides, position, surface, antigenic, time, site, measurement, solution, relaxation, distribution, exchange, organic, antigenic epitopes, behavior, biological repeating unit, chemical exchange, enterohemorrhagic, immune, immune system, internal motion, model, models, motion, order, presentation

  NCBI PubMed ID: 15132695
  Journal NLM ID: 100892849
  Publisher: Washington, DC: American Chemical Society
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  Methods: NMR, MD simulations
  
   
  
  Escherichia coli O91
  CSDB ID 9226 (all data & tools)
• Article ID: 751
  Kjellberg A, Weintraub A, Widmalm G "Structural determination and biosynthetic studies of the O-antigenic polysaccharide from the enterohemorrhagic Escherichia coli O91 using 13C-enrichment and NMR spectroscopy" - Biochemistry 38(38) (1999) 12205-12211
  

  The structure of the O-antigenic polysaccharide from the enterohemorrhagic Escherichia coli O91 has been determined using primarily NMR spectroscopy on the (13)C-enriched polysaccharide. The O-antigen is composed of pentasaccharide repeating units with the following structure: →4)-β-D-Galp-(1→4)-β-D-GlcpNAc-(1→4)-β-D-GlcpA-6-N-Gly-(1→3)-β-D-GlcpNAc-(1→4)-α-D-Quip-3-N-[(R)-3-hydroxy butyra mido]-(1→. The bacterium was grown with D-[UL-(13)C]glucose in the medium which resulted in an overall degree of labeling of approximately 65% in the sugar residues and approximately 50% in the N-acyl substituents, indicating some metabolic dilution in the latter. The (13)C-enrichment of the polysaccharide proved valuable since NMR assignments could be made on the basis of (13)C, (13)C-connectivity in uniformly labeled residues. The biosynthesis of the (R)-3-hydroxybutyramido substituent via C(2) fragments was identified by NMR spectroscopy. The (R)-configuration at C3 is in accord with fatty acid biosynthesis. Additional cultures with specifically labeled D-[1-(13)C]glucose or D-[6-(13)C]glucose corroborated the direct incorporation of glucose as the building block for the hexose skeletons in the polysaccharide and the biosynthesis of acyl substituents occurring via the triose pool followed by decarboxylation to give acetyl building blocks labeled with (13)C at the methyl group.

  NMR, biosynthetic, structural, polysaccharide, Escherichia, Escherichia coli, determination, O-antigenic, O-antigenic polysaccharide, structural determination, NMR spectroscopy, spectroscopy, antigenic, enterohemorrhagic

  NCBI PubMed ID: 10493787
  Journal NLM ID: 0370623
  Publisher: American Chemical Society
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  Methods: NMR
  
   
  
  Escherichia coli O91
  CSDB ID 895 (all data & tools)
• 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: 16594963
  Publication DOI: 10.1111/j.1574-6976.2006.00016.x
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: andrej.weintraub@ki.se
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  
   
  
  Escherichia coli O91
  CSDB ID 20701 (all data & tools)
• Article ID: 4675
  Fontana C, Kovacs H, Widmalm G "NMR structure analysis of uniformly C-labeled carbohydrates" - Journal of Biomolecular NMR 56(2) (2014) 95-110
  

  In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of 13C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly 13C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-13C)-sucrose, 342 Da] and one compound of medium molecular weight (13C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The 13C resonances are traced using 13C-13C correlations from homonuclear experiments, such as (H)CC-CT-COSY, (H)CC-NOESY, CC-CT-TOCSY and/or virtually decoupled (H)CC-TOCSY. Based on the assignment of the 13C resonances, the 1H chemical shifts are derived in a straightforward manner using one-bond 1H-13C correlations from heteronuclear experiments (HC-CT-HSQC). In order to avoid the 1 J CC splitting of the 13C resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either 13C or 1H detected experiments, namely CC-CT-COSY, band-selective (H)CC-TOCSY, HC-CT-HSQC-NOESY or long-range HC-CT-HSQC. However, due to the short T2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the 1H-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the 13C-enriched polysaccharide were assigned by using HC-H2BC spectra. The assignment of the N-acetyl groups with 15N at natural abundance was completed by using HN-SOFAST-HMQC, HNCA, HNCO and 13C-detected (H)CACO spectra.

  NMR, carbohydrates, structure, Escherichia coli, Structure determination, 13C-uniform labeling

  NCBI PubMed ID: 24771296
  Publication DOI: 10.1007/s10858-014-9830-6
  Journal NLM ID: 9110829
  Publisher: ESCOM Science Publishers
  Correspondence: G. Widmalm
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  Methods: 13C NMR, 1H NMR, NMR-2D, 13C-enriched polysaccharide
  
   
  
  Escherichia coli O91
  CSDB ID 30235 (all data & tools)
• 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: 31778182
  Publication DOI: 10.1093/femsre/fuz028
  Journal NLM ID: 8902526
  Publisher: 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
  
   
  
  Escherichia coli O91
  CSDB ID 1597 (all data & tools)

Show legend Show as text

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

• 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: 14698900
  Journal NLM ID: 0043535
  Publisher: 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
  
   
  
  Proteus genomospecies 4
  CSDB ID 9431 (all data & tools)