Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_1394181,IEDB_145010

• Article ID: 381
  Skurnik M, Zhang L "Molecular genetics and biochemistry of Yersinia lipopolysaccharide" - APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica 104(12) (1996) 849-872
  

  Studies on the molecular genetics of bacterial LPS serve at least two main purposes: (i) to help develop an understanding of the biology, biochemistry and genetics of this bacterial surface macromolecule, and (ii) to provide a basis for both vaccine development and virulence experiments. Both of these goals have been the driving force in studies of Yersinia LPS carried out during the last decade. Here we will review the progress made in the molecular genetics and biochemistry of Yersinia LPS. A deep understanding has been achieved with respect to Y. enterocolitica serotype O:3, reaching as far as a detailed analysis of the gene clusters directing the biosynthesis of the outer core oligosaccharide and of the O-ag. The O-ag gene clusters of Y. enterocolitica serotype O:8 and Y. pseudotuberculosis serotypes O:2a and O:5a have also been cloned and partially characterized LPS biosynthesis of these Yersinia species includes examples of the two major variations recognized in the biosynthesis of this macromolecule: (i) homopolymeric or O-antigen polymerase-independent biosynthesis, and (ii) heteropolymeric or O-antigen polymerase-dependent biosynthesis.

  Lipopolysaccharide, genetic, gene, genetics, O-antigen, biochemistry, Yersinia, molecular genetics

  NCBI PubMed ID: 9048864
  Publication DOI: 10.1111/j.1699-0463.1996.tb04951.x
  Journal NLM ID: 8803400
  Publisher: Copenhagen: Munksgaard
  Institutions: Turku Centre for Biotechnology, University of Turku, Finland, department of Medical Microbiology, University of Turku, Turku, Finland
  
   
  
  Yersinia bercovieri O10
  CSDB ID 31516 (all data & tools)
• Article ID: 2915
  Gorshkova RP, Isakov V V, Zubkov VA, Ovodov YS "Structure of O-specific polysaccharide of lipopolysaccharide from Yersinia bercovieri O:10" - Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 20(11) (1994) 1231-1235
  

  O-specific polysaccharide composed of D-rhamnose and 3,6-dideoxy-4-C-(L- glycero-1-hydroxyethyl)-D-xylo-hexopyranose (yersiniose A) residues was obtained on mild acid degradation of the Yersinia bercovieri lipopolysaccharide. On the basis of 1H- and 13C-NMR data, methylation studies and Smith degradation, the following structure was suggested for the polysaccharide repeating unit: [formula: see text]

  NCBI PubMed ID: 7533492
  Journal NLM ID: 7804941
  Publisher: Moskva: Nauka
  Institutions: Pacific Institute of Bioorganic Chemistry, Far East Science Centre, Academy of Sciences of the U.S.S.R., Vladivostok
  Methods: 13C NMR
  
   
  
  Yersinia bercovieri O10
  CSDB ID 110897 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_1394181,IEDB_144831,IEDB_145005,IEDB_145006,IEDB_145010

• Article ID: 469
  Mattos KA, Todeschini AR, Heise N, Jones C, Previato JO, Mendonça-Previato L "Nitrogen-fixing bacterium Burkholderia brasiliensis produces a novel yersiniose A-containing O-polysaccharide" - Glycobiology 15(3) (2005) 313-321
  

  Burkholderia brasiliensis, a Gram-negative diazotrophic endophytic bacterium, was first isolated from roots, stems and leaves of rice plant in Brazil. The polysaccharide moiety was released by ammonolysis from the B. brasiliensis lipopolysaccharide (LPS), allowing the unambiguous characterization of a 3,6-dideoxy-4-C-(1-hydroxyethyl)-D-xylo-hexose (Yersiniose A), an uncommon feature for Burkholderia LPS. The complete structure of the yersiniose A-containing O-antigen was identified by sugar and methylation analyses and nuclear magnetic resonance spectroscopy. Our results show that the repeating oligosaccharide motif of LPS O-chain consists of a branched tetrasaccharide with the following structure: →2-α-D-Rhap-(1→3)-[α-YerAp-(1→2)]-α-D-Rhap-(1→3)-α-D-Rhap-(1→

  Lipopolysaccharide, LPS, oligosaccharide, structure, branched, tetrasaccharide, characterization, polysaccharide, Burkholderia, O-antigen, O antigen, O-polysaccharide, O polysaccharide, bacteria, sugar, motif, methylation, Magnetic Resonance Spectroscopy, nuclear, nuclear magnetic resonance, nuclear magnetic resonance spectroscopy, resonance, spectroscopy, Gram-negative, O-chain, plant, leaf, nitrogen fixing, root, yersiniose

  NCBI PubMed ID: 15509723
  Publication DOI: 10.1093/glycob/cwi009
  Journal NLM ID: 9104124
  Publisher: IRL Press at Oxford University Press
  Correspondence: luciamp@biof.ufrj.br
  Institutions: Instituto de Biofisica Carlos Chagas Filho, Centro de Ciencias da Saude, Bloco G, Universidade Federal do Rio de Janeiro, 21944-970, Cidade Universitaria, Ilha do Fundao, Rio de Janeiro, RJ, Brasil
  Methods: methylation, NMR-2D, NMR, sugar analysis
  
   
  
  Burkholderia brasilensis M130
  CSDB ID 8948 (all data & tools)
• Article ID: 3821
  Banoub JH, El Aneed A, Cohen AM, Joly N "Structural investigation of bacterial lipopolysaccharides by mass spectrometry and tandem mass spectrometry" - Mass Spectrometry Reviews 29(4) (2010) 606-650
  

  Mass spectrometric studies are now playing a leading role in the elucidation of lipopolysaccharide (LPS) structures through the characterization of antigenic polysaccharides, core oligosaccharides and lipid A components including LPS genetic modifications. The conventional MS and MS/MS analyses together with CID fragmentation provide additional structural information complementary to the previous analytical experiments, and thus contribute to an integrated strategy for the simultaneous characterization and correct sequencing of the carbohydrate moiety.

  LPS, O-antigen, lipid A, core oligosaccharide, MS and MS/MS analyses

  NCBI PubMed ID: 20589944
  Publication DOI: 10.1002/mas.20258
  Journal NLM ID: 8219702
  Publisher: Wiley
  Correspondence: joe.banoub@dfo-mpo.gc.ca
  Institutions: Fisheries and Oceans Canada, Science Branch, Special Projects, P.O. Box 5667, St. John's, Newfoundland, Canada A1C 5X1, Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada A1B 3V6, College of Pharmacy and Nutrition, University of Saskatchewan, Thorvaldson Building, 110 Science Place, Saskatoon, Saskatchewan, Canada S7N 5C9, Unité de Catalyse et de Chimie du Solide, Site de l'Artois—UMR CNRS 8181, I.U.T. de Béthune, Département Chimie, 1230 rue de l'Université, BP819, 62408 Béthune Cedex, France, Institute for Marine Biosciences Room 219A, (NRC-IMB), National Research Council of Canada, Government of Canada, 1411 Oxford Street, Halifax, NS, Canada B3H 3Z1
  Methods: MS/MS, MS
  
   
  
  Burkholderia brasilensis
  CSDB ID 25184 (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
  
   
  
  Burkholderia brasilensis
  CSDB ID 27891 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_136045,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144998,IEDB_145669,IEDB_146664,IEDB_150092,IEDB_151531,IEDB_152214,IEDB_174333,IEDB_225177,IEDB_885823,IEDB_983931,SB_192,SB_86

• Article ID: 1087
  Pavliak V, Uhrin D, Brisson J, Tzianabos AO, Kasper DL, Jennings HJ "Structural elucidation of the capsular polysaccharide of Bacteroides fragilis strain 23745M1" - Carbohydrate Research 275(2) (1995) 333-341
  

  The capsule of Bacteroides fragilis (ATCC23745) consists of two distinct polysaccharides, the separation of which could not be accomplished. The mouse-passaged strain (23745M1), however, yielded a preponderant polysaccharide which was isolated and purified. Using mainly high resolution NMR spectroscopy, the structure of the polysaccharide was elucidated and it is composed of the following repeating unit: [formula see text]

  strain, structural, capsular, polysaccharide, capsular polysaccharide, elucidation, Bacteroides, Bacteroides fragilis

  NCBI PubMed ID: 8529227
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, K1A OR6, Canada, Channing Laboratory, Brigham and Women's Hospital, Boston, MA, USA, Beth IsraelHospital, HarvardMedicalSchool, Boston, MA, USA
  Methods: NMR-2D, NMR
  
   
  
  Bacteroides fragilis 23745M1
  CSDB ID 4024 (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 23745M1
  CSDB ID 7022 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141582,IEDB_141584,IEDB_153207,IEDB_2218588,IEDB_885822

• 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: 7533007
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Yersinia intermedia O4,33
  CSDB ID 108426 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141582,IEDB_141584,IEDB_153207,IEDB_2218588,IEDB_885822

• 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: 7533007
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Yersinia enterocolitica O4,32
  CSDB ID 108427 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141582,IEDB_141584,IEDB_153207,IEDB_2218588,IEDB_885822

• Article ID: 3072
  Zubkov VA, Gorshkova RP, Ovodov YS "Structural studies of the O-specific polysaccharide chain of the Yersinia intermedia O:4,33 lipopolysaccharide" - Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 14 (1988) 65-68
  
  Journal NLM ID: 7804941
  Publisher: Moskva: Nauka
  Institutions: Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok
  Methods: 13C NMR
  
   
  
  Yersinia intermedia 4,33
  CSDB ID 110616 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_1394181,IEDB_144831,IEDB_145005,IEDB_145006,IEDB_145010

• Article ID: 3459
  de Lederkremer RM, Marino C "Deoxy sugars: Occurrence and synthesis" - Advances in Carbohydrate Chemistry and Biochemistry 61 (2008) 143-216
  

  No abstract available

  synthesis, deoxy sugars

  NCBI PubMed ID: 17931551
  Publication DOI: 10.1016/S0065-2318(07)61004-X
  Journal NLM ID: 0240537
  Institutions: CIHIDECAR, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Ciudad Universitaria, 1428 Buenos Aires, Argentina
  Methods: 13C NMR, 1H NMR, NMR-2D, MS, composition analysis, NMR-1D
  
   
  
  Burkholderia brasilensis
  CSDB ID 22910 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_1394181,IEDB_144831,IEDB_145005,IEDB_145006,IEDB_145010

• Article ID: 3459
  de Lederkremer RM, Marino C "Deoxy sugars: Occurrence and synthesis" - Advances in Carbohydrate Chemistry and Biochemistry 61 (2008) 143-216
  

  No abstract available

  synthesis, deoxy sugars

  NCBI PubMed ID: 17931551
  Publication DOI: 10.1016/S0065-2318(07)61004-X
  Journal NLM ID: 0240537
  Institutions: CIHIDECAR, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Ciudad Universitaria, 1428 Buenos Aires, Argentina
  Methods: 13C NMR, 1H NMR, NMR-2D, MS, composition analysis, NMR-1D
  
   
  
  Burkholderia brasilensis
  CSDB ID 22910 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_1394181,IEDB_145010

• 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
  
   
  
  Yersinia bercovieri O10
  CSDB ID 27650 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: core
Compound class: O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_885822

• Article ID: 4375
  Post DM, Yu L, Krasity BC, Choudhury B, Mandel MJ, Brennan CA, Ruby EG, McFall-Ngai MJ, Gibson BW, Apicella MA "The O-antigen and core carbohydrate of Vibrio fischeri lipopolysaccharide: Composition and analysis of their role in Euprymna scolopes light organ colonization" - Journal of Biological Chemistry 287(11) (2012) 8515-8530
  

  Vibrio fischeri exists in a symbiotic relationship with the Hawaiian bobtail squid, Euprymna scolopes, where the squid provides a home for the bacteria and the bacteria in turn provide camouflage that helps protect the squid from nighttime predators. Like other Gram-negative organisms, V. fischeri expresses lipopolysaccharide (LPS) on its cell surface. The structure of the O-antigen and the core components of the LPS and their possible role in colonization of the squid have not previously been determined. In these studies an O-antigen ligase mutant, waaL, was utilized to determine the structures of these LPS components and their roles in colonization of the squid. WaaL ligates the O-antigen to the core of the LPS; thus, LPS from waaL mutants lack O-antigen. Our results show that the V. fischeri waaL mutant has a motility defect, is significantly delayed in colonization, and is unable to compete with the wild-type strain in co-colonization assays. Comparative analyses of the LPS from the wild-type and waaL strains showed that the V. fischeri LPS has a single O-antigen repeat composed of yersiniose, 8-epi-legionaminic acid and N-acetylfucosamine. In addition, the LPS from the waaL strain showed that the core structure consists of L-glycero-D-manno-heptose, D-glycero-D-manno-heptose, glucose, 3-deoxy-D-manno-octulosonic acid (Kdo), N-acetylgalactosamine, 8-epi-legionaminic acid, phosphate and phosphoethanolamine. These studies indicate that the unusual V. fischeri O-antigen sugars play a role in the early phases of bacterial colonization of the squid.

  Lipopolysaccharide, Bacterial, O-antigen, yersiniose, colonization, Vibrio fischeri

  NCBI PubMed ID: 22247546
  Publication DOI: 10.1074/jbc.M111.324012
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: michael-apicella@uiowa.edu
  Institutions: Buck Institute for Research on Aging, Novato, California 94945, USA
  Methods: 13C NMR, 1H NMR, NMR-2D, PCR, GC-MS, SDS-PAGE, 31P NMR, MALDI-MS, biological assays, composition analysis, NMR-1D
  
   
  
  Vibrio fischeri ES114
  CSDB ID 27286 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_151528,IEDB_190606,IEDB_225177,IEDB_885823,SB_7

• Article ID: 4423
  Zdorovenko EL, Valueva OA, Varbanets LD, Shashkov AS, Knirel YA "Structure of the O-antigen of Budvicia aquatica 20186, a new bacterial polysaccharide that contains 3,6-dideoxy-4-C-[(S)-1-hydroxyethyl]-D-xylo-hexose (yersiniose A)" - Carbohydrate Research 352 (2012) 219-222
  

  The following structure of the O-specific polysaccharide (O-antigen) of Budvicia aquatica 20186 was elucidated by sugar analysis along with 1D and 2D (1)H and (13)C NMR spectroscopy: →4)-α-L-Rhap-(1→3)-α-D-Galp-(1→2)-α-Yerp-(1→3)-β-D-GalpNAc-(1→ where Yer stands for 3,6-dideoxy-4-C-[(S)-1-hydroxyethyl]-D-xylo-hexose (yersiniose A).

  O-antigen, bacterial polysaccharide structure, lipolysaccharide, Budvicia aquatica, Yersiniose A

  NCBI PubMed ID: 22429774
  Publication DOI: 10.1016/j.carres.2012.02.017
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: zdorovenkoe@mail.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, GLC, NMR-1D, GPC
  
   
  
  Budvicia aquatica 20186
  CSDB ID 27367 (all data & tools)

Show legend Show as text

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

• Article ID: 4556
  Kondakova AN, Drutskaya MS, Shashkov AS, Nedospasov SA, Akimov VN, Arbatsky NP, Galchenko VF, Knirel YA "Structure of the O-polysaccharide of Pseudomonas mandelii CYar1 containing 3,6-dideoxy-4-C-[(S)-1-hydroxyethyl]-D-xylo-hexose (yersiniose A)" - Carbohydrate Research 381 (2013) 128-131
  

  The O-polysaccharide isolated by mild acid hydrolysis of the lipopolysaccharide of Pseudomonas mandelii CYar1 was studied by sugar analysis and 1D and 2D (1)H and (13)C NMR spectroscopies. The following structure of the O-polysaccharide was established:

  Lipopolysaccharide, O-antigen, bacterial polysaccharide structure, yersiniose, Pseudomonas mandelii

  NCBI PubMed ID: 24096274
  Publication DOI: 10.1016/j.carres.2013.08.016
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: A.N. Kondakova
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: 13C NMR, 1H NMR, methylation, NMR-2D, sugar analysis, acid hydrolysis, GLC, NMR-1D, GPC
  
   
  
  Pseudomonas mandelii CYar
  CSDB ID 29242 (all data & tools)

Show legend Show as text

Structure type: monomer
Compound class: O-polysaccharide, O-antigen

• Article ID: 5502
  Sizova OV, Shashkov AS, Dmitrenok AS, Toukach PV, Knirel YA, Shaikhutdinova RZ, Ivanov SA, Kislichkina AA, Bogun AG, Dentovskaya SV "Structure and gene cluster of the O-polysaccharide of Yersinia rohdei H274-36/78" - International Journal of Biological Macromolecules 122 (2019) 555-561
  

  A branched O-polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Yersinia rohdei H274-36/78 and found to contain d-rhamnose, d-mannose, and 3,6-dideoxy-4-C-[(S)-1-hydroxyethyl]-d-xylo-hexose called yersiniose A (Yer). Partial acid hydrolysis of the O-polysaccharide eliminated Yer residues to give a modified linear polysaccharide. Studies by sugar analysis and (1)H and (13)C NMR spectroscopy, including computational NMR analysis, enabled structure elucidation of a hexasaccharide repeating unit of the O-polysaccharide having two Yer residues attached as monosaccharide side chains. The O-antigen gene cluster of Y. rohdei H274-36/78 located between JUMPStart and galF genes contained putative genes for synthesis of precursors of two O-antigen constituents, GDP-d-Man and GDP-d-Rha, whereas genes responsible for synthesis of CDP-Yer were within the chromosome outside the O-antigen gene cluster. Glycosyltransferase genes and ABC 2 transporter genes were present in the O-antigen gene cluster, and hence the structure established is consistent with the polysaccharide synthesis gene content of the genome.

  Lipopolysaccharide, O-specific polysaccharide, bacterial polysaccharide structure, yersiniose, O-antigen gene cluster, NMR simulation, Yersinia rohdei

  NCBI PubMed ID: 30385338
  Publication DOI: 10.1016/j.ijbiomac.2018.10.189
  Journal NLM ID: 7909578
  Publisher: Butterworth-Heinemann
  Correspondence: netbox@toukach.ru
  Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russian Federation
  Methods: 13C NMR, 1H NMR, GLC-MS, NMR-2D, de-O-acylation, sugar analysis, GLC, Smith degradation, HPLC, GPC, bioinformatic analysis, mild acid degradation, genome sequencing, 13C NMR analysis by GODDESS and GRASS
  
   
  
  Yersinia rohdei H274-36/78 (SCRAMB-O-B-7599)
  CSDB ID 2309 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130701,IEDB_1394181,IEDB_144983,IEDB_145010,IEDB_152206,IEDB_983930,SB_44,SB_67,SB_72

• Article ID: 5502
  Sizova OV, Shashkov AS, Dmitrenok AS, Toukach PV, Knirel YA, Shaikhutdinova RZ, Ivanov SA, Kislichkina AA, Bogun AG, Dentovskaya SV "Structure and gene cluster of the O-polysaccharide of Yersinia rohdei H274-36/78" - International Journal of Biological Macromolecules 122 (2019) 555-561
  

  A branched O-polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Yersinia rohdei H274-36/78 and found to contain d-rhamnose, d-mannose, and 3,6-dideoxy-4-C-[(S)-1-hydroxyethyl]-d-xylo-hexose called yersiniose A (Yer). Partial acid hydrolysis of the O-polysaccharide eliminated Yer residues to give a modified linear polysaccharide. Studies by sugar analysis and (1)H and (13)C NMR spectroscopy, including computational NMR analysis, enabled structure elucidation of a hexasaccharide repeating unit of the O-polysaccharide having two Yer residues attached as monosaccharide side chains. The O-antigen gene cluster of Y. rohdei H274-36/78 located between JUMPStart and galF genes contained putative genes for synthesis of precursors of two O-antigen constituents, GDP-d-Man and GDP-d-Rha, whereas genes responsible for synthesis of CDP-Yer were within the chromosome outside the O-antigen gene cluster. Glycosyltransferase genes and ABC 2 transporter genes were present in the O-antigen gene cluster, and hence the structure established is consistent with the polysaccharide synthesis gene content of the genome.

  Lipopolysaccharide, O-specific polysaccharide, bacterial polysaccharide structure, yersiniose, O-antigen gene cluster, NMR simulation, Yersinia rohdei

  NCBI PubMed ID: 30385338
  Publication DOI: 10.1016/j.ijbiomac.2018.10.189
  Journal NLM ID: 7909578
  Publisher: Butterworth-Heinemann
  Correspondence: netbox@toukach.ru
  Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russian Federation
  Methods: 13C NMR, 1H NMR, GLC-MS, NMR-2D, de-O-acylation, sugar analysis, GLC, Smith degradation, HPLC, GPC, bioinformatic analysis, mild acid degradation, genome sequencing, 13C NMR analysis by GODDESS and GRASS
  
   
  
  Yersinia rohdei H274-36/78 (SCRAMB-O-B-7599)
  CSDB ID 2315 (all data & tools)